Changes between Initial Version and Version 1 of Ticket #4176, comment 1


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Timestamp:
Jan 27, 2021, 9:47:39 AM (5 years ago)
Author:
pett

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  • Ticket #4176, comment 1

    initial v1  
    1 {{{
    21Sorry about the massive log. Should have left it out - it's irrelevant to the actual issue.
    3 ________________________________
    4 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
    5 Sent: 27 January 2021 15:24
    6 To: Tristan Croll <tic20@cam.ac.uk>
    7 Subject: [ChimeraX] #4176: ChimeraX bug report submission
    8 
    9 #4176: ChimeraX bug report submission
    10 ---------------------------+-----------------------------
    11  Reporter:  Tristan Croll  |                Type:  defect
    12    Status:  new            |            Priority:  normal
    13 Component:  Unassigned     |          Blocked By:
    14  Blocking:                 |  Notify when closed:
    15 ---------------------------+-----------------------------
    16  {{{
    17  The following bug report has been submitted:
    18  Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-
    19  centos-7.8.2003-Core
    20  ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
    21  Description
    22  I have an ISOLDE session containing a very large, complex model.
    23  Everything in the session itself is well-behaved, but when I save to mmCIF
    24  and reopen five residues are duplicated. One of these is a protein residue
    25  (somehow ended up appearing twice in its `Chain` object, no idea how -
    26  easy enough to fix). The other four are two pairs of sugars, each internal
    27  to an O-linked glycan (like in the attached image). Much less sure how to
    28  fix that, other than to delete the duplicate residues in the reopened
    29  mmCIF. Any clues?
    30 
    31  Log:
    32  UCSF ChimeraX version: 1.1 (2020-09-09)
    33  © 2016-2020 Regents of the University of California. All rights reserved.
    34 
    35  > open working.cxs
    36 
    37  restore_snapshot for "RotamerRestraintMgr" returned None
    38 
    39  Log from Mon Jan 25 22:36:36 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    40  © 2016-2020 Regents of the University of California. All rights reserved.
    41 
    42  > open working.cxs
    43 
    44  restore_snapshot for "RotamerRestraintMgr" returned None
    45 
    46  Log from Sat Jan 23 15:29:45 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    47  © 2016-2020 Regents of the University of California. All rights reserved.
    48 
    49  > open working.cxs
    50 
    51  restore_snapshot for "RotamerRestraintMgr" returned None
    52 
    53  Log from Wed Jan 20 20:19:45 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    54  © 2016-2020 Regents of the University of California. All rights reserved.
    55 
    56  > open working.cxs
    57 
    58  restore_snapshot for "RotamerRestraintMgr" returned None
    59 
    60  Log from Wed Jan 20 18:04:18 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    61  © 2016-2020 Regents of the University of California. All rights reserved.
    62 
    63  > open working_fme.cxs
    64 
    65  restore_snapshot for "RotamerRestraintMgr" returned None
    66 
    67  Failed to restore chiral restraints. This is usually not a problem - they
    68  will
    69  be automatically regenerated on first simulation.
    70 
    71  Log from Tue Jan 19 20:41:55 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    72  © 2016-2020 Regents of the University of California. All rights reserved.
    73 
    74  > open working_fme.cxs
    75 
    76  restore_snapshot for "RotamerRestraintMgr" returned None
    77 
    78  Failed to restore chiral restraints. This is usually not a problem - they
    79  will
    80  be automatically regenerated on first simulation.
    81 
    82  Log from Tue Jan 19 19:42:56 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    83  © 2016-2020 Regents of the University of California. All rights reserved.
    84 
    85  > open working.cxs
    86 
    87  restore_snapshot for "RotamerRestraintMgr" returned None
    88 
    89  Log from Tue Jan 19 15:18:30 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    90  © 2016-2020 Regents of the University of California. All rights reserved.
    91 
    92  > open working.cxs
    93 
    94  restore_snapshot for "RotamerRestraintMgr" returned None
    95 
    96  Log from Mon Jan 18 21:58:27 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    97  © 2016-2020 Regents of the University of California. All rights reserved.
    98 
    99  > open working.cxs
    100 
    101  restore_snapshot for "RotamerRestraintMgr" returned None
    102 
    103  Log from Thu Jan 14 20:29:04 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    104  © 2016-2020 Regents of the University of California. All rights reserved.
    105 
    106  > open working.cxs
    107 
    108  restore_snapshot for "RotamerRestraintMgr" returned None
    109 
    110  Log from Thu Jan 14 18:05:53 2021UCSF ChimeraX version: 1.1 (2020-09-09)
    111  © 2016-2020 Regents of the University of California. All rights reserved.
    112 
    113  > open model1a_2020_11_04.cxs
    114 
    115  restore_snapshot for "RotamerRestraintMgr" returned None
    116 
    117  Log from Wed Nov 4 20:47:05 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    118  © 2016-2020 Regents of the University of California. All rights reserved.
    119 
    120  > open model1a_2020_11_02.cxs
    121 
    122  restore_snapshot for "RotamerRestraintMgr" returned None
    123 
    124  Log from Mon Nov 2 17:41:56 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    125  © 2016-2020 Regents of the University of California. All rights reserved.
    126 
    127  > open working.cxs
    128 
    129  restore_snapshot for "RotamerRestraintMgr" returned None
    130 
    131  Log from Sat Oct 31 21:36:29 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    132  © 2016-2020 Regents of the University of California. All rights reserved.
    133 
    134  > open
    135  >
    136  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/reassigning_ligands.cxs
    137  > format session
    138 
    139  restore_snapshot for "RotamerRestraintMgr" returned None
    140 
    141  Log from Fri Oct 30 09:34:25 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    142  © 2016-2020 Regents of the University of California. All rights reserved.
    143 
    144  > open
    145  >
    146  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/reassigning_ligands.cxs
    147  > format session
    148 
    149  restore_snapshot for "RotamerRestraintMgr" returned None
    150 
    151  Log from Fri Oct 30 09:16:38 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    152  © 2016-2020 Regents of the University of California. All rights reserved.
    153 
    154  > open working.cxs
    155 
    156  restore_snapshot for "RotamerRestraintMgr" returned None
    157 
    158  Log from Thu Oct 29 16:35:33 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    159  © 2016-2020 Regents of the University of California. All rights reserved.
    160 
    161  > open working.cxs
    162 
    163  restore_snapshot for "RotamerRestraintMgr" returned None
    164 
    165  restore_snapshot for "RotamerRestraintMgr" returned None
    166 
    167  Log from Wed Oct 28 21:12:33 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    168  © 2016-2020 Regents of the University of California. All rights reserved.
    169 
    170  > open working.cxs
    171 
    172  restore_snapshot for "RotamerRestraintMgr" returned None
    173 
    174  restore_snapshot for "RotamerRestraintMgr" returned None
    175 
    176  Log from Tue Oct 27 22:03:57 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    177  © 2016-2020 Regents of the University of California. All rights reserved.
    178 
    179  > open working.cxs
    180 
    181  restore_snapshot for "RotamerRestraintMgr" returned None
    182 
    183  Log from Fri Oct 23 21:33:44 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    184  © 2016-2020 Regents of the University of California. All rights reserved.
    185 
    186  > open working.cxs
    187 
    188  restore_snapshot for "RotamerRestraintMgr" returned None
    189 
    190  Log from Fri Oct 23 12:38:35 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    191  © 2016-2020 Regents of the University of California. All rights reserved.
    192 
    193  > open working.cxs
    194 
    195  restore_snapshot for "RotamerRestraintMgr" returned None
    196 
    197  restore_snapshot for "RotamerRestraintMgr" returned None
    198 
    199  Log from Thu Oct 22 21:38:47 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    200  © 2016-2020 Regents of the University of California. All rights reserved.
    201 
    202  > open working_3.cxs
    203 
    204  restore_snapshot for "RotamerRestraintMgr" returned None
    205 
    206  restore_snapshot for "RotamerRestraintMgr" returned None
    207 
    208  Log from Thu Oct 22 17:00:13 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    209  © 2016-2020 Regents of the University of California. All rights reserved.
    210 
    211  > open
    212  >
    213  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/reopened.cxs
    214 
    215  restore_snapshot for "RotamerRestraintMgr" returned None
    216 
    217  Log from Thu Oct 22 16:23:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    218  © 2016-2020 Regents of the University of California. All rights reserved.
    219 
    220  > open working_2.cxs
    221 
    222  restore_snapshot for "RotamerRestraintMgr" returned None
    223 
    224  Log from Thu Oct 22 16:02:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    225  © 2016-2020 Regents of the University of California. All rights reserved.
    226 
    227  > open
    228  >
    229  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cxs
    230 
    231  restore_snapshot for "RotamerRestraintMgr" returned None
    232 
    233  Log from Thu Oct 22 13:56:05 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    234  © 2016-2020 Regents of the University of California. All rights reserved.
    235 
    236  > open ../old_model_in_map_1b.cxs
    237 
    238  Log from Thu Oct 22 06:57:21 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    239  © 2016-2020 Regents of the University of California. All rights reserved.
    240 
    241  > open model1b_working.cxs
    242 
    243  restore_snapshot for "RotamerRestraintMgr" returned None
    244 
    245  Log from Wed Oct 21 20:17:18 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    246  © 2016-2020 Regents of the University of California. All rights reserved.
    247 
    248  > open model1b_working.cxs
    249 
    250  restore_snapshot for "RotamerRestraintMgr" returned None
    251 
    252  Log from Wed Oct 21 20:13:59 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    253  © 2016-2020 Regents of the University of California. All rights reserved.
    254 
    255  > open
    256  >
    257  /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/model1b_working.cxs
    258 
    259  restore_snapshot for "RotamerRestraintMgr" returned None
    260 
    261  Log from Wed Oct 21 19:55:36 2020UCSF ChimeraX version: 1.1 (2020-09-09)
    262  © 2016-2020 Regents of the University of California. All rights reserved.
    263  How to cite UCSF ChimeraX
    264 
    265  > open
    266  /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/rc-
    267  > dlh1-model1b_rearranged.pdb format pdb
    268 
    269  Chain information for rc-dlh1-model1b_rearranged.pdb #1
    270  ---
    271  Chain | Description
    272  AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX |
    273  No
    274  description available
    275  Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available
    276  Ag | No description available
    277  B | No description available
    278  BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX Ba
    279  Bb
    280  Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available
    281  C | No description available
    282  C1 | No description available
    283  H1 | No description available
    284  H2 | No description available
    285  L | No description available
    286  M | No description available
    287 
    288 
    289  > open
    290  >
    291  /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/class1b_26A.mrc
    292 
    293  Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    294  0.0224, step 2, values float32
    295 
    296  > clipper associate #2 toModel #1
    297 
    298  Chain information for rc-dlh1-model1b_rearranged.pdb
    299  ---
    300  Chain | Description
    301  1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AF 1.2/AG 1.2/AH 1.2/AI 1.2/AJ
    302  1.2/AK
    303  1.2/AL 1.2/AM 1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU
    304  1.2/AV
    305  1.2/AW 1.2/AX | No description available
    306  1.2/Aa 1.2/Ab 1.2/Ac 1.2/Ad 1.2/Ae 1.2/Af 1.2/Ah 1.2/Ai 1.2/Aj 1.2/Ak
    307  1.2/Al
    308  1.2/Am 1.2/An 1.2/Ao 1.2/Ap | No description available
    309  1.2/Ag | No description available
    310  1.2/B | No description available
    311  1.2/BA 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BF 1.2/BG 1.2/BH 1.2/BI 1.2/BJ
    312  1.2/BK
    313  1.2/BL 1.2/BM 1.2/BN 1.2/BO 1.2/BP 1.2/BQ 1.2/BR 1.2/BS 1.2/BT 1.2/BU
    314  1.2/BV
    315  1.2/BW 1.2/BX 1.2/Ba 1.2/Bb 1.2/Bc 1.2/Bd 1.2/Be 1.2/Bf 1.2/Bg 1.2/Bh
    316  1.2/Bi
    317  1.2/Bj 1.2/Bk 1.2/Bl 1.2/Bm 1.2/Bn 1.2/Bo 1.2/Bp | No description
    318  available
    319  1.2/C | No description available
    320  1.2/C1 | No description available
    321  1.2/H1 | No description available
    322  1.2/H2 | No description available
    323  1.2/L | No description available
    324  1.2/M | No description available
    325 
    326 
    327  > delete :GPC@HO45
    328 
    329  > ui tool show Shell
    330 
    331  /opt/UCSF/ChimeraX/lib/python3.7/site-
    332  packages/IPython/core/history.py:226:
    333  UserWarning: IPython History requires SQLite, your history will not be
    334  saved
    335  warn("IPython History requires SQLite, your history will not be saved")
    336 
    337  > select ~protein
    338 
    339  10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 8 models selected
    340 
    341  > ui tool show ISOLDE
    342 
    343  > set selectionWidth 4
    344 
    345  Done loading forcefield
    346 
    347  > select ~protein
    348 
    349  10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 13 models
    350  selected
    351 
    352  > addh
    353 
    354  Summary of feedback from adding hydrogens to rc-
    355  dlh1-model1b_rearranged.pdb
    356  #1.2
    357  ---
    358  warning | Skipped 8 atom(s) with bad connectivities; see log for details
    359  notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2)
    360  chain AA; guessing termini instead
    361  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain
    362  AB;
    363  guessing termini instead
    364  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain
    365  AC;
    366  guessing termini instead
    367  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain
    368  AD;
    369  guessing termini instead
    370  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain
    371  AE;
    372  guessing termini instead
    373  82 messages similar to the above omitted
    374  Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2,
    375  /AC
    376  HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2,
    377  /AJ
    378  HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2,
    379  /AQ
    380  HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2,
    381  /AX
    382  HIS 2, /Aa MET 1, /Ab MET 1, /Ac MET 1, /Ad MET 1, /Ae MET 1, /Af MET 1,
    383  /Ag
    384  MET 1, /Ah MET 1, /Ai MET 1, /Aj MET 1, /Ak MET 1, /Al MET 1, /Am MET 1,
    385  /An
    386  MET 1, /Ao MET 1, /Ap MET 1, /B PRO 25, /BA MET 1, /BB MET 1, /BC MET 1,
    387  /BD
    388  MET 1, /BE MET 1, /BF MET 1, /BG MET 1, /BH MET 1, /BI MET 1, /BJ MET 1,
    389  /BK
    390  MET 1, /BL MET 1, /BM MET 1, /BN MET 1, /BO MET 1, /BP MET 1, /BQ MET 1,
    391  /BR
    392  MET 1, /BS MET 1, /BT MET 1, /BU MET 1, /BV MET 1, /BW MET 1, /BX MET 1,
    393  /Ba
    394  MET 1, /Bb MET 1, /Bc MET 1, /Bd MET 1, /Be MET 1, /Bf MET 1, /Bg MET 1,
    395  /Bh
    396  MET 1, /Bi MET 1, /Bj MET 1, /Bk MET 1, /Bl MET 1, /Bm MET 1, /Bn MET 1,
    397  /Bo
    398  MET 1, /Bp MET 1, /C ALA 15, /H1 MET 1, /H2 SER 1, /L ALA 1, /M MET 1
    399  Chain-initial residues that are not actual N termini: /C1 GLN 1, /H2 ARG
    400  38
    401  Chain-final residues that are actual C termini: /BA PHE 38, /BB PHE 38,
    402  /BC
    403  PHE 38, /BD PHE 38, /BE PHE 38, /BF PHE 38, /BG PHE 38, /BH PHE 38, /BI
    404  PHE
    405  38, /BJ PHE 38, /BK PHE 38, /BL PHE 38, /BM PHE 38, /BN PHE 38, /BO PHE
    406  38,
    407  /BP PHE 38, /BQ PHE 38, /BR PHE 38, /BS PHE 38, /BT PHE 38, /BU PHE 38,
    408  /BV
    409  PHE 38, /BW PHE 38, /BX PHE 38, /Ba PHE 38, /Bb PHE 38, /Bc PHE 38, /Bd
    410  PHE
    411  38, /Be PHE 38, /Bf PHE 38, /Bg PHE 38, /Bh PHE 38, /Bi PHE 38, /Bj PHE
    412  38,
    413  /Bk PHE 38, /Bl PHE 38, /Bm PHE 38, /Bn PHE 38, /Bo PHE 38, /Bp PHE 38
    414  Chain-final residues that are not actual C termini: /AA PRO 48, /AB PRO
    415  48,
    416  /AC PRO 48, /AD PRO 48, /AE PRO 48, /AF PRO 48, /AG PRO 48, /AH PRO 48,
    417  /AI
    418  PRO 48, /AJ PRO 48, /AK PRO 48, /AL PRO 48, /AM PRO 48, /AN PRO 48, /AO
    419  PRO
    420  48, /AP PRO 48, /AQ PRO 48, /AR PRO 48, /AS PRO 48, /AT PRO 48, /AU PRO
    421  48,
    422  /AV PRO 48, /AW PRO 48, /AX PRO 48, /Aa ALA 60, /Ab ALA 60, /Ac ALA 60,
    423  /Ad
    424  ALA 60, /Ae ALA 60, /Af ALA 60, /Ag LEU 67, /Ah ALA 60, /Ai ALA 60, /Aj
    425  ALA
    426  60, /Ak ALA 60, /Al ALA 60, /Am ALA 60, /An ALA 60, /Ao ALA 60, /Ap ALA
    427  60, /B
    428  ILE 123, /C ILE 313, /C1 LEU 92, /H1 HIS 67, /H2 ILE 181, /H2 ARG 36, /L
    429  TRP
    430  272, /M TYR 324
    431  Skipping possible acceptor with bad geometry: /C ARG 302 O
    432  Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O
    433 
    434  Skipping possible acceptor with bad geometry: /C ARG 302 OXT
    435  Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT
    436 
    437  Skipping possible acceptor with bad geometry: /C ARG 302 OXT
    438  Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT
    439 
    440  Skipping possible acceptor with bad geometry: /C ARG 302 O
    441  Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O
    442 
    443  Skipping possible acceptor with bad geometry: /C ARG 302 O
    444  Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O
    445 
    446  3 messages similar to the above omitted
    447  4746 hydrogen bonds
    448  Adding 'H' to /H2 ARG 38
    449  /AA PRO 48 is not terminus, removing H atom from 'C'
    450  /AB PRO 48 is not terminus, removing H atom from 'C'
    451  /AC PRO 48 is not terminus, removing H atom from 'C'
    452  /AD PRO 48 is not terminus, removing H atom from 'C'
    453  /AE PRO 48 is not terminus, removing H atom from 'C'
    454  42 messages similar to the above omitted
    455  44090 hydrogens added
    456 
    457 
    458  > save model1b_working.cxs
    459 
    460  opened ChimeraX session
    461 
    462  > select up
    463 
    464  101 atoms, 100 bonds, 1 residue, 1 model selected
    465 
    466  > show sel
    467 
    468  > select clear
    469 
    470  > style sel ball
    471 
    472  Changed 100 atom styles
    473 
    474  > select :GPC
    475 
    476  4013 atoms, 3973 bonds, 40 residues, 1 model selected
    477 
    478  > show sel
    479 
    480  > select :GPC@HC19
    481 
    482  40 atoms, 40 residues, 1 model selected
    483 
    484  > select :GPC
    485 
    486  4013 atoms, 3973 bonds, 40 residues, 1 model selected
    487 
    488  > delete sel
    489 
    490  MD template USER_BCL for residue BCL L604 contains extra atoms that are
    491  not in
    492  a coordinate template, and are not directly connected to existing atoms.
    493  Since
    494  MD templates do not explicitly provide geometry,these atoms will not be
    495  built.
    496 
    497  > select sel&@CBD
    498 
    499  1 atom, 1 residue, 1 model selected
    500 
    501  > style sel sphere
    502 
    503  Changed 1 atom style
    504 
    505  > style sel stick
    506 
    507  Changed 1 atom style
    508 
    509  > select up
    510 
    511  139 atoms, 147 bonds, 1 residue, 1 model selected
    512  Deleted the following atoms from residue BCL L604: HHC1, HHD1
    513  Deleted the following atoms from residue BCL L602: HHD2, HHC2, HHD1, HHC1
    514  Deleted the following atoms from residue BPH L606: H12, H92, HHD1, H41,
    515  H93,
    516  H91, H52, H11, HHD2, H43, H61, H51, H62, H42, H71, H72
    517 
    518  > save model1b_working.cxs
    519 
    520  opened ChimeraX session
    521  Deleted the following atoms from residue MQ8 M405: H272, H9, H502, H122,
    522  C49,
    523  C46, H172, H503, C50, H461, H471, H222, H11, H422, H492, H6, H472, C48,
    524  H462,
    525  H7, H501, C47, H8, H491, H372, H322
    526  Deleted the following atoms from residue BCL M601: HHD2, HHD1
    527  Deleted the following atoms from residue BCL M603: HHD1, HHD2, HHC1, HHC2
    528  Deleted the following atoms from residue BPH M605: H11, H62, H72, H42,
    529  H12,
    530  H91, H52, H71, HHD2, H93, H51, H92, HHD1, H61, H43, H41
    531  Residue RCC M701 has only 0 connected atoms in common with template GPC.
    532  At
    533  least 3 matching atoms are needed.
    534 
    535  > save model1b_working.cxs
    536 
    537  > delete sel
    538 
    539  > save model1b_working.cxs
    540 
    541  opened ChimeraX session
    542 
    543  > open
    544  >
    545  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb
    546 
    547  Summary of feedback from opening
    548  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb
    549  ---
    550  warnings | Ignored bad PDB record found on line 317
    551  LINK NE2 HIS AA 29 MG BCL AA 57
    552 
    553  Ignored bad PDB record found on line 318
    554  LINK NE2 HIS AB 29 MG BCL AB 57
    555 
    556  Ignored bad PDB record found on line 319
    557  LINK NE2 HIS AC 29 MG BCL AC 57
    558 
    559  Ignored bad PDB record found on line 320
    560  LINK NE2 HIS AD 29 MG BCL AD 57
    561 
    562  Ignored bad PDB record found on line 321
    563  LINK NE2 HIS AE 29 MG BCL AE 57
    564 
    565  75 messages similar to the above omitted
    566  Start residue of secondary structure not found: HELIX 1 1 PROAA 10 PHEAA
    567  36 1
    568  26
    569  Start residue of secondary structure not found: HELIX 2 2 ALAAA 40 LYSAA
    570  45 1
    571  5
    572  Start residue of secondary structure not found: HELIX 3 3 ARGAB 3 TRPAB 5
    573  1 2
    574  Start residue of secondary structure not found: HELIX 4 4 PROAB 10 GLNAB
    575  35 1
    576  25
    577  Start residue of secondary structure not found: HELIX 5 5 ALAAB 40 LEUAB
    578  42 1
    579  2
    580  207 messages similar to the above omitted
    581 
    582  Chain information for working_noh_real_space_refined.pdb #2
    583  ---
    584  Chain | Description
    585  AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX |
    586  No
    587  description available
    588  BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg
    589  bh
    590  bi bj bk bl bm bo bp | No description available
    591  BB BD BE BI BV BW bn | No description available
    592  C | No description available
    593  H1 | No description available
    594  H2 | No description available
    595  L | No description available
    596  M | No description available
    597  UA | No description available
    598  UB | No description available
    599  UC | No description available
    600  aa | No description available
    601  ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available
    602 
    603 
    604  > matchmaker #2 to #1
    605 
    606  Parameters
    607  ---
    608  Chain pairing | bb
    609  Alignment algorithm | Needleman-Wunsch
    610  Similarity matrix | BLOSUM-62
    611  SS fraction | 0.3
    612  Gap open (HH/SS/other) | 18/18/6
    613  Gap extend | 1
    614  SS matrix |  |  | H | S | O
    615  ---|---|---|---
    616  H | 6 | -9 | -6
    617  S |  | 6 | -6
    618  O |  |  | 4
    619  Iteration cutoff | 2
    620 
    621  Matchmaker rc-dlh1-model1b_rearranged.pdb, chain M (#1.2) with
    622  working_noh_real_space_refined.pdb, chain M (#2), sequence alignment score
    623  =
    624  1582
    625  RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 324
    626  pairs:
    627  1.723)
    628 
    629 
    630  > delete #2/UA,UB,UC
    631 
    632  > open
    633  >
    634  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    635 
    636  Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    637  0.0224, step 2, values float32
    638 
    639  > clipper associate #3 toModel #2
    640 
    641  Chain information for working_noh_real_space_refined.pdb
    642  ---
    643  Chain | Description
    644  2.2/AA 2.2/AB 2.2/AC 2.2/AD 2.2/AE 2.2/AF 2.2/AG 2.2/AH 2.2/AI 2.2/AJ
    645  2.2/AK
    646  2.2/AL 2.2/AM 2.2/AN 2.2/AO 2.2/AP 2.2/AQ 2.2/AR 2.2/AS 2.2/AT 2.2/AU
    647  2.2/AV
    648  2.2/AW 2.2/AX | No description available
    649  2.2/BA 2.2/BC 2.2/BF 2.2/BG 2.2/BH 2.2/BJ 2.2/BK 2.2/BL 2.2/BM 2.2/BN
    650  2.2/BO
    651  2.2/BP 2.2/BQ 2.2/BR 2.2/BS 2.2/BT 2.2/BU 2.2/BX 2.2/ba 2.2/bb 2.2/bc
    652  2.2/bd
    653  2.2/be 2.2/bf 2.2/bg 2.2/bh 2.2/bi 2.2/bj 2.2/bk 2.2/bl 2.2/bm 2.2/bo
    654  2.2/bp |
    655  No description available
    656  2.2/BB 2.2/BD 2.2/BE 2.2/BI 2.2/BV 2.2/BW 2.2/bn | No description
    657  available
    658  2.2/C | No description available
    659  2.2/H1 | No description available
    660  2.2/H2 | No description available
    661  2.2/L | No description available
    662  2.2/M | No description available
    663  2.2/aa | No description available
    664  2.2/ab 2.2/ac 2.2/ad 2.2/ae 2.2/af 2.2/ag 2.2/ah 2.2/ai 2.2/aj 2.2/ak
    665  2.2/al
    666  2.2/am 2.2/an 2.2/ao 2.2/ap | No description available
    667 
    668 
    669  > select #2:GPC
    670 
    671  1800 atoms, 1760 bonds, 40 residues, 1 model selected
    672 
    673  > select #2:RCC
    674 
    675  Nothing selected
    676 
    677  > select #1:RCC
    678 
    679  100 atoms, 99 bonds, 1 residue, 1 model selected
    680 
    681  > select #2:GPC
    682 
    683  1800 atoms, 1760 bonds, 40 residues, 1 model selected
    684 
    685  > select #1:GPC
    686 
    687  4000 atoms, 3960 bonds, 40 residues, 1 model selected
    688 
    689  > select #2:GPC
    690 
    691  1800 atoms, 1760 bonds, 40 residues, 1 model selected
    692 
    693  > delete sel
    694 
    695  > ui tool show Shell
    696 
    697  /opt/UCSF/ChimeraX/lib/python3.7/site-
    698  packages/IPython/core/history.py:226:
    699  UserWarning: IPython History requires SQLite, your history will not be
    700  saved
    701  warn("IPython History requires SQLite, your history will not be saved")
    702 
    703  > delete #2:GP1
    704 
    705  > select #1:RCC
    706 
    707  100 atoms, 99 bonds, 1 residue, 1 model selected
    708 
    709  > select #1:RCC,GCC
    710 
    711  100 atoms, 99 bonds, 1 residue, 1 model selected
    712 
    713  > select #1:RCC,GPC
    714 
    715  4100 atoms, 4059 bonds, 41 residues, 1 model selected
    716 
    717  > close #1
    718 
    719  > addh
    720 
    721  Summary of feedback from adding hydrogens to
    722  working_noh_real_space_refined.pdb #2.2
    723  ---
    724  notes | No usable SEQRES records for working_noh_real_space_refined.pdb
    725  (#2.2)
    726  chain AA; guessing termini instead
    727  No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    728  chain
    729  AB; guessing termini instead
    730  No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    731  chain
    732  AC; guessing termini instead
    733  No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    734  chain
    735  AD; guessing termini instead
    736  No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    737  chain
    738  AE; guessing termini instead
    739  80 messages similar to the above omitted
    740  Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2,
    741  /AC
    742  HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2,
    743  /AJ
    744  HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2,
    745  /AQ
    746  HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2,
    747  /AX
    748  HIS 2, /BA GLY 6, /BB GLY 5, /BC GLY 6, /BD GLY 5, /BE GLY 5, /BF GLY 6,
    749  /BG
    750  GLY 6, /BH GLY 6, /BI GLY 5, /BJ GLY 6, /BK GLY 6, /BL GLY 6, /BM GLY 6,
    751  /BN
    752  GLY 6, /BO GLY 6, /BP GLY 6, /BQ GLY 6, /BR GLY 6, /BS GLY 6, /BT GLY 6,
    753  /BU
    754  GLY 6, /BV GLY 5, /BW GLY 5, /BX GLY 6, /C ALA 15, /H1 MET 1, /H2 SER 1,
    755  /L
    756  ALA 1, /M MET 1, /aa HIS 2, /ab MET 1, /ac MET 1, /ad MET 1, /ae MET 1,
    757  /af
    758  MET 1, /ag MET 1, /ah MET 1, /ai MET 1, /aj MET 1, /ak MET 1, /al MET 1,
    759  /am
    760  MET 1, /an MET 1, /ao MET 1, /ap MET 1, /ba GLY 6, /bb GLY 6, /bc GLY 6,
    761  /bd
    762  GLY 6, /be GLY 6, /bf GLY 6, /bg GLY 6, /bh GLY 6, /bi GLY 6, /bj GLY 6,
    763  /bk
    764  GLY 6, /bl GLY 6, /bm GLY 6, /bn GLY 5, /bo GLY 6, /bp GLY 6
    765  Chain-initial residues that are not actual N termini:
    766  Chain-final residues that are actual C termini: /BA PHE 44, /BB PHE 44,
    767  /BC
    768  PHE 44, /BD PHE 44, /BE PHE 44, /BF PHE 44, /BG PHE 44, /BH PHE 44, /BI
    769  PHE
    770  44, /BJ PHE 44, /BK PHE 44, /BL PHE 44, /BM PHE 44, /BN PHE 44, /BO PHE
    771  44,
    772  /BP PHE 44, /BQ PHE 44, /BR PHE 44, /BS PHE 44, /BT PHE 44, /BU PHE 44,
    773  /BV
    774  PHE 44, /BW PHE 44, /BX PHE 44, /C ARG 302, /H2 ILE 181, /L LYS 273, /ba
    775  PHE
    776  44, /bb PHE 44, /bc PHE 44, /bd PHE 44, /be PHE 44, /bf PHE 44, /bg PHE
    777  44,
    778  /bh PHE 44, /bi PHE 44, /bj PHE 44, /bk PHE 44, /bl PHE 44, /bm PHE 44,
    779  /bn
    780  PHE 44, /bo PHE 44, /bp PHE 44
    781  Chain-final residues that are not actual C termini: /AA TYR 46, /AB TYR
    782  46,
    783  /AC TYR 46, /AD TYR 46, /AE TYR 46, /AF TYR 46, /AG TYR 46, /AH TYR 46,
    784  /AI
    785  TYR 46, /AJ TYR 46, /AK TYR 46, /AL TYR 46, /AM TYR 46, /AN TYR 46, /AO
    786  TYR
    787  46, /AP TYR 46, /AQ TYR 46, /AR TYR 46, /AS TYR 46, /AT TYR 46, /AU TYR
    788  46,
    789  /AV TYR 46, /AW TYR 46, /AX TYR 46, /H1 LYS 53, /M TYR 324, /aa ALA 60,
    790  /ab
    791  ALA 60, /ac ALA 60, /ad ALA 60, /ae ALA 60, /af ALA 60, /ag ALA 60, /ah
    792  ALA
    793  60, /ai ALA 60, /aj ALA 60, /ak ALA 60, /al ALA 60, /am ALA 60, /an ALA
    794  60,
    795  /ao ALA 60, /ap ALA 60
    796  4864 hydrogen bonds
    797  /AA TYR 46 is not terminus, removing H atom from 'C'
    798  /AB TYR 46 is not terminus, removing H atom from 'C'
    799  /AC TYR 46 is not terminus, removing H atom from 'C'
    800  /AD TYR 46 is not terminus, removing H atom from 'C'
    801  /AE TYR 46 is not terminus, removing H atom from 'C'
    802  37 messages similar to the above omitted
    803  43714 hydrogens added
    804 
    805 
    806  > hide HC
    807 
    808  > select ~protein
    809 
    810  16594 atoms, 16919 bonds, 365 pseudobonds, 133 residues, 8 models selected
    811 
    812  > select clear
    813 
    814  > save old_model_in_map_1b.cxs
    815 
    816  opened ChimeraX session
    817 
    818  > isolde start
    819 
    820  > set selectionWidth 4
    821 
    822  Done loading forcefield
    823 
    824  > select :GPC
    825 
    826  4013 atoms, 3973 bonds, 40 residues, 1 model selected
    827 
    828  > ui tool show Shell
    829 
    830  /opt/UCSF/ChimeraX/lib/python3.7/site-
    831  packages/IPython/core/history.py:226:
    832  UserWarning: IPython History requires SQLite, your history will not be
    833  saved
    834  warn("IPython History requires SQLite, your history will not be saved")
    835 
    836  > select clear
    837 
    838  > delete sel
    839 
    840  > delete sel
    841 
    842  > delete sel
    843 
    844  > delete sel
    845 
    846  > save ready.cxs
    847 
    848  > select gpc
    849 
    850  Expected an objects specifier or a keyword
    851 
    852  > select :GPC
    853 
    854  4000 atoms, 3960 bonds, 40 residues, 1 model selected
    855 
    856  > select :GPC
    857 
    858  4000 atoms, 3960 bonds, 40 residues, 1 model selected
    859 
    860  > show sel
    861 
    862  > select clear
    863 
    864  > show sel
    865 
    866  > save ready.cxs
    867 
    868  > volume gaussian #1 bfactor 50
    869 
    870  > volume gaussian #2 bfactor 50
    871 
    872  > clipper associate #1 toModel #2
    873 
    874  > hide HC
    875 
    876  > select #1
    877 
    878  Nothing selected
    879 
    880  > select #2
    881 
    882  91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models
    883  selected
    884 
    885  > clipper set contourSensitivity 0.25
    886 
    887  > select clear
    888 
    889  > set bgColor white
    890 
    891  > select #1
    892 
    893  Nothing selected
    894 
    895  > select #2
    896 
    897  91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models
    898  selected
    899 
    900  > select clear
    901 
    902  > select #2
    903 
    904  91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models
    905  selected
    906 
    907  > select #1
    908 
    909  Nothing selected
    910 
    911  > select #2
    912 
    913  91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models
    914  selected
    915  Map is too large for fast cubic interpolation on the GPU! Switching to
    916  slower,
    917  more memory-efficient implementation.
    918  Map is too large for fast cubic interpolation on the GPU! Switching to
    919  slower,
    920  more memory-efficient implementation.
    921 
    922  > select clear
    923 
    924  > open
    925  >
    926  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb
    927 
    928  Summary of feedback from opening
    929  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb
    930  ---
    931  warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B
    932  5
    933  TYR B 9 1 5
    934  Start residue of secondary structure not found: HELIX 2 2 ARG B 22 ARG B
    935  52 1
    936  31
    937  Start residue of secondary structure not found: HELIX 3 3 VAL B 55 ARG B
    938  86 1
    939  32
    940 
    941  Chain information for assigned_sequence.pdb #1
    942  ---
    943  Chain | Description
    944  Ba | No description available
    945 
    946 
    947  > open
    948  >
    949  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb
    950 
    951  Summary of feedback from opening
    952  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb
    953  ---
    954  warnings | Start residue of secondary structure not found: HELIX 1 1 THR C
    955  19
    956  GLY C 21 1 3
    957  Start residue of secondary structure not found: HELIX 2 2 VAL C 28 VAL C
    958  31 1
    959  4
    960  Start residue of secondary structure not found: HELIX 3 3 VAL C 32 HIS C
    961  34 1
    962  3
    963  Start residue of secondary structure not found: HELIX 4 4 GLY C 61 ILE C
    964  64 1
    965  4
    966  Start residue of secondary structure not found: HELIX 5 5 MET C 71 LYS C
    967  74 1
    968  4
    969  3 messages similar to the above omitted
    970 
    971  Chain information for sequence_assigned.pdb #3
    972  ---
    973  Chain | Description
    974  C1 | No description available
    975 
    976 
    977  > open
    978  >
    979  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/rc-
    980  > dlh1-model1b_rearranged.pdb
    981 
    982  Chain information for rc-dlh1-model1b_rearranged.pdb #4
    983  ---
    984  Chain | Description
    985  AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX |
    986  No
    987  description available
    988  Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available
    989  Ag | No description available
    990  B | No description available
    991  BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX Ba
    992  Bb
    993  Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available
    994  C | No description available
    995  C1 | No description available
    996  H1 | No description available
    997  H2 | No description available
    998  L | No description available
    999  M | No description available
    1000 
    1001 
    1002  > hide #!4 models
    1003 
    1004  > select #3
    1005 
    1006  1472 atoms, 1487 bonds, 92 residues, 1 model selected
    1007 
    1008  > save working.cxs
    1009 
    1010  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    1011 
    1012  > hide #3 models
    1013 
    1014  > select #1
    1015 
    1016  1516 atoms, 1537 bonds, 99 residues, 1 model selected
    1017 
    1018  > select #2/Ba
    1019 
    1020  100 atoms, 99 bonds, 1 residue, 1 model selected
    1021 
    1022  > view sel
    1023 
    1024  > select #1
    1025 
    1026  1516 atoms, 1537 bonds, 99 residues, 1 model selected
    1027 
    1028  > select clear
    1029 
    1030  > select /AA
    1031 
    1032  1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected
    1033 
    1034  > select /BA
    1035 
    1036  1151 atoms, 1189 bonds, 4 pseudobonds, 79 residues, 3 models selected
    1037 
    1038  > isolde stepto /AA
    1039 
    1040  Multiple residues selected! Going to the first...
    1041 
    1042  > select /AA
    1043 
    1044  1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected
    1045 
    1046  > select clear
    1047 
    1048  > select clear
    1049 
    1050  > select /AA
    1051 
    1052  1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected
    1053 
    1054  > select clear
    1055 
    1056  > sequence chain /AA
    1057 
    1058  Chains must have same sequence
    1059 
    1060  > sequence chain #1/AA
    1061 
    1062  Chains must have same sequence
    1063 
    1064  > sequence chain #2/AA
    1065 
    1066  Alignment identifier is 2.2/AA
    1067 
    1068  > select /AA
    1069 
    1070  1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected
    1071 
    1072  > select clear
    1073 
    1074  > select clear
    1075 
    1076  > select /AA
    1077 
    1078  1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected
    1079 
    1080  > select clear
    1081 
    1082  > select clear
    1083 
    1084  > show #!4 models
    1085 
    1086  > select #4/AS
    1087 
    1088  540 atoms, 558 bonds, 4 pseudobonds, 49 residues, 2 models selected
    1089 
    1090  > select clear
    1091 
    1092  > select #4
    1093 
    1094  51294 atoms, 53027 bonds, 354 pseudobonds, 5083 residues, 3 models
    1095  selected
    1096 
    1097  > style sel stick
    1098 
    1099  Changed 51294 atom styles
    1100 
    1101  > select clear
    1102 
    1103  > hide #!4 models
    1104 
    1105  > select clear
    1106 
    1107  > isolde stepto /C
    1108 
    1109  Multiple residues selected! Going to the first...
    1110 
    1111  > select /C:15-200
    1112 
    1113  4296 atoms, 4372 bonds, 372 residues, 2 models selected
    1114 
    1115  > select clear
    1116 
    1117  > show #!4 models
    1118 
    1119  > hide #!4 models
    1120 
    1121  > show #!4 models
    1122 
    1123  > hide #!4 models
    1124 
    1125  > isolde stepto
    1126 
    1127  > isolde stepto
    1128 
    1129  > isolde stepto
    1130 
    1131  > show #!4 models
    1132 
    1133  > hide #!4 models
    1134 
    1135  reverting to start
    1136 
    1137  > select /C1
    1138 
    1139  4416 atoms, 4461 bonds, 276 residues, 3 models selected
    1140 
    1141  > isolde ignore /C1:30-300
    1142 
    1143  ISOLDE: currently ignoring 63 residues in model 2.2
    1144  ISOLDE: currently ignoring 63 residues in model 3
    1145  ISOLDE: currently ignoring 63 residues in model 4
    1146 
    1147  > select /C:15-200
    1148 
    1149  4296 atoms, 4372 bonds, 372 residues, 2 models selected
    1150 
    1151  > select /M:311-400
    1152 
    1153  359 atoms, 361 bonds, 28 residues, 2 models selected
    1154 
    1155  > select clear
    1156 
    1157  > isolde ~ignore
    1158 
    1159  > show #!4 models
    1160 
    1161  > hide #!4 models
    1162 
    1163  > save working.cxs
    1164 
    1165  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    1166 
    1167  > select /C:15-200
    1168 
    1169  4296 atoms, 4372 bonds, 372 residues, 2 models selected
    1170 
    1171  > select clear
    1172 
    1173  > isolde stepto
    1174 
    1175  > hide #1 models
    1176 
    1177  > isolde ignore /C2
    1178 
    1179  ISOLDE: currently ignoring 99 residues in model 2.2
    1180 
    1181  > select /H2:120-129
    1182 
    1183  241 atoms, 251 bonds, 20 residues, 2 models selected
    1184 
    1185  > select clear
    1186 
    1187  > select clear
    1188 
    1189  > isolde ~ignore
    1190 
    1191  > select up
    1192 
    1193  22 atoms, 21 bonds, 1 residue, 1 model selected
    1194 
    1195  > isolde ignore sel
    1196 
    1197  ISOLDE: currently ignoring 1 residues in model 2.2
    1198 
    1199  > isolde ~ignore
    1200 
    1201  > select clear
    1202 
    1203  > select up
    1204 
    1205  24 atoms, 23 bonds, 1 residue, 1 model selected
    1206 
    1207  > isolde ignore sel
    1208 
    1209  ISOLDE: currently ignoring 1 residues in model 2.2
    1210 
    1211  > isolde ~ignore
    1212 
    1213  > select up
    1214 
    1215  14 atoms, 13 bonds, 1 residue, 1 model selected
    1216 
    1217  > select up
    1218 
    1219  105 atoms, 108 bonds, 7 residues, 1 model selected
    1220 
    1221  > isolde ignore sel
    1222 
    1223  ISOLDE: currently ignoring 8 residues in model 2.2
    1224 
    1225  > select up
    1226 
    1227  10 atoms, 9 bonds, 1 residue, 1 model selected
    1228 
    1229  > select up
    1230 
    1231  939 atoms, 951 bonds, 60 residues, 1 model selected
    1232 
    1233  > select clear
    1234 
    1235  > show #!4 models
    1236 
    1237  > select clear
    1238 
    1239  > hide #!4 models
    1240 
    1241  > select clear
    1242 
    1243  > select clear
    1244 
    1245  > select clear
    1246 
    1247  > select clear
    1248 
    1249  > select clear
    1250 
    1251  > save working.cxs
    1252 
    1253  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    1254 
    1255  > select /C:15-200
    1256 
    1257  4296 atoms, 4372 bonds, 372 residues, 2 models selected
    1258 
    1259  > select clear
    1260 
    1261  > isolde stepto /C
    1262 
    1263  Multiple residues selected! Going to the first...
    1264 
    1265  > select clear
    1266 
    1267  > isolde stepto
    1268 
    1269  > isolde stepto
    1270 
    1271  > isolde stepto
    1272 
    1273  > select clear
    1274 
    1275  > show #!4 models
    1276 
    1277  > hide #!4 models
    1278 
    1279  > isolde stepto
    1280 
    1281  > isolde stepto
    1282 
    1283  > isolde stepto
    1284 
    1285  > show #!4 models
    1286 
    1287  > hide #!4 models
    1288 
    1289  > isolde stepto
    1290 
    1291  > isolde stepto
    1292 
    1293  > isolde stepto
    1294 
    1295  > isolde stepto
    1296 
    1297  > isolde stepto
    1298 
    1299  > isolde stepto
    1300 
    1301  > select clear
    1302 
    1303  > isolde stepto
    1304 
    1305  > isolde stepto
    1306 
    1307  > isolde stepto
    1308 
    1309  > isolde stepto
    1310 
    1311  > isolde stepto
    1312 
    1313  > isolde stepto
    1314 
    1315  > isolde stepto
    1316 
    1317  > isolde stepto
    1318 
    1319  > show #!4 models
    1320 
    1321  > hide #!4 models
    1322 
    1323  > show #!4 models
    1324 
    1325  > hide #!4 models
    1326 
    1327  > select clear
    1328 
    1329  > select up
    1330 
    1331  14 atoms, 14 bonds, 1 residue, 1 model selected
    1332 
    1333  > select up
    1334 
    1335  450 atoms, 459 bonds, 30 residues, 1 model selected
    1336 
    1337  > select clear
    1338 
    1339  > select clear
    1340 
    1341  > select /C:64-200
    1342 
    1343  3217 atoms, 3269 bonds, 274 residues, 2 models selected
    1344 
    1345  > select clear
    1346 
    1347  > select clear
    1348 
    1349  > select clear
    1350 
    1351  > isolde stepto /C:64
    1352 
    1353  Multiple residues selected! Going to the first...
    1354 
    1355  > isolde stepto
    1356 
    1357  > isolde stepto
    1358 
    1359  > isolde stepto
    1360 
    1361  > isolde stepto
    1362 
    1363  > isolde stepto
    1364 
    1365  > isolde stepto
    1366 
    1367  > isolde stepto
    1368 
    1369  > isolde stepto
    1370 
    1371  > isolde stepto
    1372 
    1373  > isolde stepto
    1374 
    1375  > isolde stepto
    1376 
    1377  > isolde stepto
    1378 
    1379  > isolde stepto
    1380 
    1381  > isolde stepto
    1382 
    1383  > isolde stepto
    1384 
    1385  > isolde stepto
    1386 
    1387  > isolde stepto
    1388 
    1389  > isolde stepto
    1390 
    1391  > isolde stepto
    1392 
    1393  > isolde stepto
    1394 
    1395  > isolde stepto
    1396 
    1397  > select clear
    1398 
    1399  > isolde stepto
    1400 
    1401  > isolde stepto
    1402 
    1403  > isolde stepto
    1404 
    1405  > isolde stepto
    1406 
    1407  > isolde stepto
    1408 
    1409  > isolde stepto
    1410 
    1411  > isolde stepto
    1412 
    1413  > isolde stepto
    1414 
    1415  > isolde stepto
    1416 
    1417  > isolde stepto
    1418 
    1419  > isolde stepto
    1420 
    1421  > isolde stepto
    1422 
    1423  > isolde stepto
    1424 
    1425  > isolde stepto
    1426 
    1427  > select clear
    1428 
    1429  > delete sel
    1430 
    1431  > select /C:99-200
    1432 
    1433  2415 atoms, 2455 bonds, 204 residues, 2 models selected
    1434 
    1435  > select clear
    1436 
    1437  > select clear
    1438 
    1439  > select clear
    1440 
    1441  > isolde stepto
    1442 
    1443  > isolde stepto
    1444 
    1445  > isolde stepto
    1446 
    1447  > isolde stepto
    1448 
    1449  > isolde stepto
    1450 
    1451  > isolde stepto
    1452 
    1453  > isolde stepto
    1454 
    1455  > isolde stepto
    1456 
    1457  > select clear
    1458 
    1459  > isolde stepto
    1460 
    1461  > isolde stepto
    1462 
    1463  > isolde stepto
    1464 
    1465  > isolde stepto
    1466 
    1467  > isolde stepto
    1468 
    1469  > isolde stepto
    1470 
    1471  > isolde stepto
    1472 
    1473  > isolde stepto
    1474 
    1475  > select clear
    1476 
    1477  > isolde stepto
    1478 
    1479  > isolde stepto
    1480 
    1481  > isolde stepto
    1482 
    1483  > isolde stepto
    1484 
    1485  > isolde stepto
    1486 
    1487  > isolde stepto
    1488 
    1489  > isolde stepto
    1490 
    1491  > isolde stepto
    1492 
    1493  > isolde stepto
    1494 
    1495  > isolde stepto
    1496 
    1497  > isolde stepto
    1498 
    1499  > isolde stepto
    1500 
    1501  > isolde stepto
    1502 
    1503  > isolde stepto
    1504 
    1505  > isolde stepto
    1506 
    1507  > isolde stepto
    1508 
    1509  > isolde stepto
    1510 
    1511  > isolde stepto
    1512 
    1513  > isolde stepto
    1514 
    1515  > isolde stepto
    1516 
    1517  > isolde stepto
    1518 
    1519  > isolde stepto
    1520 
    1521  > isolde stepto
    1522 
    1523  > isolde stepto
    1524 
    1525  > isolde stepto
    1526 
    1527  > isolde stepto
    1528 
    1529  > isolde stepto
    1530 
    1531  > isolde stepto
    1532 
    1533  > isolde stepto
    1534 
    1535  > isolde stepto
    1536 
    1537  > isolde stepto
    1538 
    1539  > isolde stepto
    1540 
    1541  > isolde stepto
    1542 
    1543  > isolde stepto
    1544 
    1545  > isolde stepto
    1546 
    1547  > isolde stepto
    1548 
    1549  > isolde stepto
    1550 
    1551  > isolde stepto
    1552 
    1553  > isolde stepto
    1554 
    1555  > isolde stepto
    1556 
    1557  > isolde stepto
    1558 
    1559  > isolde stepto
    1560 
    1561  > isolde stepto
    1562 
    1563  > isolde stepto
    1564 
    1565  > isolde stepto
    1566 
    1567  > isolde stepto
    1568 
    1569  > isolde stepto
    1570 
    1571  > show #!4 models
    1572 
    1573  > hide #!4 models
    1574 
    1575  > show #!4 models
    1576 
    1577  > hide #!4 models
    1578 
    1579  > isolde stepto
    1580 
    1581  > isolde stepto
    1582 
    1583  > isolde stepto
    1584 
    1585  > isolde stepto
    1586 
    1587  > isolde stepto
    1588 
    1589  > isolde stepto
    1590 
    1591  > isolde stepto
    1592 
    1593  > isolde stepto
    1594 
    1595  > isolde stepto
    1596 
    1597  > isolde stepto
    1598 
    1599  > isolde stepto
    1600 
    1601  > isolde stepto
    1602 
    1603  > show #!4 models
    1604 
    1605  > hide #!4 models
    1606 
    1607  > select /C:179-189
    1608 
    1609  241 atoms, 241 bonds, 22 residues, 2 models selected
    1610 
    1611  > select #2/C:179-189
    1612 
    1613  162 atoms, 162 bonds, 11 residues, 1 model selected
    1614 
    1615  > select clear
    1616 
    1617  > isolde stepto
    1618 
    1619  > isolde stepto
    1620 
    1621  > select clear
    1622 
    1623  > isolde stepto
    1624 
    1625  > isolde stepto
    1626 
    1627  > isolde stepto
    1628 
    1629  > isolde stepto
    1630 
    1631  > isolde stepto
    1632 
    1633  > isolde stepto
    1634 
    1635  > isolde stepto
    1636 
    1637  > select clear
    1638 
    1639  > isolde stepto
    1640 
    1641  > isolde stepto
    1642 
    1643  > isolde stepto
    1644 
    1645  > isolde stepto
    1646 
    1647  > isolde stepto
    1648 
    1649  > isolde stepto
    1650 
    1651  > isolde stepto
    1652 
    1653  > isolde stepto
    1654 
    1655  > isolde stepto
    1656 
    1657  > isolde stepto
    1658 
    1659  > isolde stepto
    1660 
    1661  > isolde stepto
    1662 
    1663  > isolde stepto
    1664 
    1665  > isolde stepto
    1666 
    1667  > isolde stepto
    1668 
    1669  > isolde stepto
    1670 
    1671  > isolde stepto
    1672 
    1673  > isolde stepto
    1674 
    1675  > isolde stepto
    1676 
    1677  > isolde stepto
    1678 
    1679  > isolde stepto
    1680 
    1681  > isolde stepto
    1682 
    1683  > isolde stepto
    1684 
    1685  > isolde stepto
    1686 
    1687  > isolde stepto
    1688 
    1689  > isolde stepto
    1690 
    1691  > isolde stepto
    1692 
    1693  > isolde stepto
    1694 
    1695  > save working.cxs
    1696 
    1697  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    1698 
    1699  > select /C:200-400
    1700 
    1701  2486 atoms, 2541 bonds, 217 residues, 2 models selected
    1702 
    1703  > select clear
    1704 
    1705  > select clear
    1706 
    1707  > isolde stepto
    1708 
    1709  > isolde stepto
    1710 
    1711  > isolde stepto
    1712 
    1713  > isolde stepto
    1714 
    1715  > isolde stepto
    1716 
    1717  > isolde stepto
    1718 
    1719  > isolde stepto
    1720 
    1721  > isolde stepto
    1722 
    1723  > isolde stepto
    1724 
    1725  > isolde stepto
    1726 
    1727  > isolde stepto
    1728 
    1729  > isolde stepto
    1730 
    1731  > isolde stepto
    1732 
    1733  > isolde stepto
    1734 
    1735  > isolde stepto
    1736 
    1737  > isolde stepto
    1738 
    1739  > isolde stepto
    1740 
    1741  > isolde stepto
    1742 
    1743  > isolde stepto
    1744 
    1745  > isolde stepto
    1746 
    1747  > isolde stepto
    1748 
    1749  > isolde stepto
    1750 
    1751  > isolde stepto
    1752 
    1753  > isolde stepto
    1754 
    1755  > isolde stepto
    1756 
    1757  > isolde stepto
    1758 
    1759  > isolde stepto
    1760 
    1761  > isolde stepto
    1762 
    1763  > isolde stepto
    1764 
    1765  > isolde stepto
    1766 
    1767  > isolde stepto
    1768 
    1769  > isolde stepto
    1770 
    1771  > isolde stepto
    1772 
    1773  > isolde stepto
    1774 
    1775  > isolde stepto
    1776 
    1777  > isolde stepto
    1778 
    1779  > isolde stepto
    1780 
    1781  > isolde stepto
    1782 
    1783  > isolde stepto
    1784 
    1785  > select clear
    1786 
    1787  > isolde stepto
    1788 
    1789  > isolde stepto
    1790 
    1791  > isolde stepto
    1792 
    1793  > isolde stepto
    1794 
    1795  > isolde stepto
    1796 
    1797  > isolde stepto
    1798 
    1799  > isolde stepto
    1800 
    1801  > isolde stepto
    1802 
    1803  > isolde stepto
    1804 
    1805  > isolde stepto
    1806 
    1807  > isolde stepto
    1808 
    1809  > isolde stepto
    1810 
    1811  > isolde stepto
    1812 
    1813  > isolde stepto
    1814 
    1815  > isolde stepto
    1816 
    1817  > isolde stepto
    1818 
    1819  > isolde stepto
    1820 
    1821  > isolde stepto
    1822 
    1823  > isolde stepto
    1824 
    1825  > isolde stepto
    1826 
    1827  > isolde stepto
    1828 
    1829  > isolde stepto
    1830 
    1831  > isolde stepto
    1832 
    1833  > isolde stepto
    1834 
    1835  > isolde stepto
    1836 
    1837  > isolde stepto
    1838 
    1839  > isolde stepto
    1840 
    1841  > select clear
    1842 
    1843  > isolde stepto
    1844 
    1845  > isolde stepto
    1846 
    1847  > isolde stepto
    1848 
    1849  > isolde stepto
    1850 
    1851  > isolde stepto
    1852 
    1853  > isolde stepto
    1854 
    1855  > isolde stepto
    1856 
    1857  > isolde stepto
    1858 
    1859  > isolde stepto
    1860 
    1861  > isolde stepto
    1862 
    1863  > isolde stepto
    1864 
    1865  > isolde stepto
    1866 
    1867  > isolde stepto
    1868 
    1869  > isolde stepto
    1870 
    1871  > isolde stepto
    1872 
    1873  > isolde stepto
    1874 
    1875  > isolde stepto
    1876 
    1877  > isolde stepto
    1878 
    1879  > isolde stepto
    1880 
    1881  > isolde stepto
    1882 
    1883  > isolde stepto
    1884 
    1885  > isolde stepto
    1886 
    1887  > isolde stepto
    1888 
    1889  > isolde stepto
    1890 
    1891  > show #!4 models
    1892 
    1893  > save working.cxs
    1894 
    1895  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    1896 
    1897  > select #4/C:303-313
    1898 
    1899  83 atoms, 87 bonds, 11 residues, 1 model selected
    1900 
    1901  > select clear
    1902 
    1903  > hide #!4 models
    1904 
    1905  > select #2/C:303-400
    1906 
    1907  83 atoms, 87 bonds, 11 residues, 1 model selected
    1908 
    1909  > show sel
    1910 
    1911  > delete sell
    1912 
    1913  Missing or invalid "atoms" argument: invalid atoms specifier
    1914 
    1915  > delete sel
    1916 
    1917  > addh #4
    1918 
    1919  Summary of feedback from adding hydrogens to rc-
    1920  dlh1-model1b_rearranged.pdb #4
    1921  ---
    1922  warning | Skipped 8 atom(s) with bad connectivities; see log for details
    1923  notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4)
    1924  chain
    1925  AA; guessing termini instead
    1926  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AB;
    1927  guessing termini instead
    1928  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AC;
    1929  guessing termini instead
    1930  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AD;
    1931  guessing termini instead
    1932  No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AE;
    1933  guessing termini instead
    1934  82 messages similar to the above omitted
    1935  Chain-initial residues that are actual N termini: rc-
    1936  dlh1-model1b_rearranged.pdb #4/AA HIS 2, rc-dlh1-model1b_rearranged.pdb
    1937  #4/AB
    1938  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AC HIS 2, rc-
    1939  dlh1-model1b_rearranged.pdb #4/AD HIS 2, rc-dlh1-model1b_rearranged.pdb
    1940  #4/AE
    1941  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AF HIS 2, rc-
    1942  dlh1-model1b_rearranged.pdb #4/AG HIS 2, rc-dlh1-model1b_rearranged.pdb
    1943  #4/AH
    1944  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AI HIS 2, rc-
    1945  dlh1-model1b_rearranged.pdb #4/AJ HIS 2, rc-dlh1-model1b_rearranged.pdb
    1946  #4/AK
    1947  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AL HIS 2, rc-
    1948  dlh1-model1b_rearranged.pdb #4/AM HIS 2, rc-dlh1-model1b_rearranged.pdb
    1949  #4/AN
    1950  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AO HIS 2, rc-
    1951  dlh1-model1b_rearranged.pdb #4/AP HIS 2, rc-dlh1-model1b_rearranged.pdb
    1952  #4/AQ
    1953  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AR HIS 2, rc-
    1954  dlh1-model1b_rearranged.pdb #4/AS HIS 2, rc-dlh1-model1b_rearranged.pdb
    1955  #4/AT
    1956  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AU HIS 2, rc-
    1957  dlh1-model1b_rearranged.pdb #4/AV HIS 2, rc-dlh1-model1b_rearranged.pdb
    1958  #4/AW
    1959  HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AX HIS 2, rc-
    1960  dlh1-model1b_rearranged.pdb #4/Aa MET 1, rc-dlh1-model1b_rearranged.pdb
    1961  #4/Ab
    1962  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ac MET 1, rc-
    1963  dlh1-model1b_rearranged.pdb #4/Ad MET 1, rc-dlh1-model1b_rearranged.pdb
    1964  #4/Ae
    1965  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Af MET 1, rc-
    1966  dlh1-model1b_rearranged.pdb #4/Ag MET 1, rc-dlh1-model1b_rearranged.pdb
    1967  #4/Ah
    1968  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ai MET 1, rc-
    1969  dlh1-model1b_rearranged.pdb #4/Aj MET 1, rc-dlh1-model1b_rearranged.pdb
    1970  #4/Ak
    1971  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Al MET 1, rc-
    1972  dlh1-model1b_rearranged.pdb #4/Am MET 1, rc-dlh1-model1b_rearranged.pdb
    1973  #4/An
    1974  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ao MET 1, rc-
    1975  dlh1-model1b_rearranged.pdb #4/Ap MET 1, rc-dlh1-model1b_rearranged.pdb
    1976  #4/B
    1977  PRO 25, rc-dlh1-model1b_rearranged.pdb #4/BA MET 1, rc-
    1978  dlh1-model1b_rearranged.pdb #4/BB MET 1, rc-dlh1-model1b_rearranged.pdb
    1979  #4/BC
    1980  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BD MET 1, rc-
    1981  dlh1-model1b_rearranged.pdb #4/BE MET 1, rc-dlh1-model1b_rearranged.pdb
    1982  #4/BF
    1983  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BG MET 1, rc-
    1984  dlh1-model1b_rearranged.pdb #4/BH MET 1, rc-dlh1-model1b_rearranged.pdb
    1985  #4/BI
    1986  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BJ MET 1, rc-
    1987  dlh1-model1b_rearranged.pdb #4/BK MET 1, rc-dlh1-model1b_rearranged.pdb
    1988  #4/BL
    1989  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BM MET 1, rc-
    1990  dlh1-model1b_rearranged.pdb #4/BN MET 1, rc-dlh1-model1b_rearranged.pdb
    1991  #4/BO
    1992  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BP MET 1, rc-
    1993  dlh1-model1b_rearranged.pdb #4/BQ MET 1, rc-dlh1-model1b_rearranged.pdb
    1994  #4/BR
    1995  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BS MET 1, rc-
    1996  dlh1-model1b_rearranged.pdb #4/BT MET 1, rc-dlh1-model1b_rearranged.pdb
    1997  #4/BU
    1998  MET 1, rc-dlh1-model1b_rearranged.pdb #4/BV MET 1, rc-
    1999  dlh1-model1b_rearranged.pdb #4/BW MET 1, rc-dlh1-model1b_rearranged.pdb
    2000  #4/BX
    2001  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ba MET 1, rc-
    2002  dlh1-model1b_rearranged.pdb #4/Bb MET 1, rc-dlh1-model1b_rearranged.pdb
    2003  #4/Bc
    2004  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bd MET 1, rc-
    2005  dlh1-model1b_rearranged.pdb #4/Be MET 1, rc-dlh1-model1b_rearranged.pdb
    2006  #4/Bf
    2007  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bg MET 1, rc-
    2008  dlh1-model1b_rearranged.pdb #4/Bh MET 1, rc-dlh1-model1b_rearranged.pdb
    2009  #4/Bi
    2010  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bj MET 1, rc-
    2011  dlh1-model1b_rearranged.pdb #4/Bk MET 1, rc-dlh1-model1b_rearranged.pdb
    2012  #4/Bl
    2013  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bm MET 1, rc-
    2014  dlh1-model1b_rearranged.pdb #4/Bn MET 1, rc-dlh1-model1b_rearranged.pdb
    2015  #4/Bo
    2016  MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bp MET 1, rc-
    2017  dlh1-model1b_rearranged.pdb #4/C ALA 15, rc-dlh1-model1b_rearranged.pdb
    2018  #4/H1
    2019  MET 1, rc-dlh1-model1b_rearranged.pdb #4/H2 SER 1, rc-
    2020  dlh1-model1b_rearranged.pdb #4/L ALA 1, rc-dlh1-model1b_rearranged.pdb
    2021  #4/M
    2022  MET 1
    2023  Chain-initial residues that are not actual N termini: rc-
    2024  dlh1-model1b_rearranged.pdb #4/C1 GLN 1, rc-dlh1-model1b_rearranged.pdb
    2025  #4/H2
    2026  ARG 38
    2027  Chain-final residues that are actual C termini: rc-
    2028  dlh1-model1b_rearranged.pdb
    2029  #4/BA PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BB PHE 38, rc-
    2030  dlh1-model1b_rearranged.pdb #4/BC PHE 38, rc-dlh1-model1b_rearranged.pdb
    2031  #4/BD
    2032  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BE PHE 38, rc-
    2033  dlh1-model1b_rearranged.pdb #4/BF PHE 38, rc-dlh1-model1b_rearranged.pdb
    2034  #4/BG
    2035  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BH PHE 38, rc-
    2036  dlh1-model1b_rearranged.pdb #4/BI PHE 38, rc-dlh1-model1b_rearranged.pdb
    2037  #4/BJ
    2038  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BK PHE 38, rc-
    2039  dlh1-model1b_rearranged.pdb #4/BL PHE 38, rc-dlh1-model1b_rearranged.pdb
    2040  #4/BM
    2041  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BN PHE 38, rc-
    2042  dlh1-model1b_rearranged.pdb #4/BO PHE 38, rc-dlh1-model1b_rearranged.pdb
    2043  #4/BP
    2044  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BQ PHE 38, rc-
    2045  dlh1-model1b_rearranged.pdb #4/BR PHE 38, rc-dlh1-model1b_rearranged.pdb
    2046  #4/BS
    2047  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BT PHE 38, rc-
    2048  dlh1-model1b_rearranged.pdb #4/BU PHE 38, rc-dlh1-model1b_rearranged.pdb
    2049  #4/BV
    2050  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BW PHE 38, rc-
    2051  dlh1-model1b_rearranged.pdb #4/BX PHE 38, rc-dlh1-model1b_rearranged.pdb
    2052  #4/Ba
    2053  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bb PHE 38, rc-
    2054  dlh1-model1b_rearranged.pdb #4/Bc PHE 38, rc-dlh1-model1b_rearranged.pdb
    2055  #4/Bd
    2056  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Be PHE 38, rc-
    2057  dlh1-model1b_rearranged.pdb #4/Bf PHE 38, rc-dlh1-model1b_rearranged.pdb
    2058  #4/Bg
    2059  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bh PHE 38, rc-
    2060  dlh1-model1b_rearranged.pdb #4/Bi PHE 38, rc-dlh1-model1b_rearranged.pdb
    2061  #4/Bj
    2062  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bk PHE 38, rc-
    2063  dlh1-model1b_rearranged.pdb #4/Bl PHE 38, rc-dlh1-model1b_rearranged.pdb
    2064  #4/Bm
    2065  PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bn PHE 38, rc-
    2066  dlh1-model1b_rearranged.pdb #4/Bo PHE 38, rc-dlh1-model1b_rearranged.pdb
    2067  #4/Bp
    2068  PHE 38
    2069  Chain-final residues that are not actual C termini: rc-
    2070  dlh1-model1b_rearranged.pdb #4/AA PRO 48, rc-dlh1-model1b_rearranged.pdb
    2071  #4/AB
    2072  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48, rc-
    2073  dlh1-model1b_rearranged.pdb #4/AD PRO 48, rc-dlh1-model1b_rearranged.pdb
    2074  #4/AE
    2075  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AF PRO 48, rc-
    2076  dlh1-model1b_rearranged.pdb #4/AG PRO 48, rc-dlh1-model1b_rearranged.pdb
    2077  #4/AH
    2078  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AI PRO 48, rc-
    2079  dlh1-model1b_rearranged.pdb #4/AJ PRO 48, rc-dlh1-model1b_rearranged.pdb
    2080  #4/AK
    2081  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AL PRO 48, rc-
    2082  dlh1-model1b_rearranged.pdb #4/AM PRO 48, rc-dlh1-model1b_rearranged.pdb
    2083  #4/AN
    2084  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AO PRO 48, rc-
    2085  dlh1-model1b_rearranged.pdb #4/AP PRO 48, rc-dlh1-model1b_rearranged.pdb
    2086  #4/AQ
    2087  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AR PRO 48, rc-
    2088  dlh1-model1b_rearranged.pdb #4/AS PRO 48, rc-dlh1-model1b_rearranged.pdb
    2089  #4/AT
    2090  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AU PRO 48, rc-
    2091  dlh1-model1b_rearranged.pdb #4/AV PRO 48, rc-dlh1-model1b_rearranged.pdb
    2092  #4/AW
    2093  PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AX PRO 48, rc-
    2094  dlh1-model1b_rearranged.pdb #4/Aa ALA 60, rc-dlh1-model1b_rearranged.pdb
    2095  #4/Ab
    2096  ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ac ALA 60, rc-
    2097  dlh1-model1b_rearranged.pdb #4/Ad ALA 60, rc-dlh1-model1b_rearranged.pdb
    2098  #4/Ae
    2099  ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Af ALA 60, rc-
    2100  dlh1-model1b_rearranged.pdb #4/Ag LEU 67, rc-dlh1-model1b_rearranged.pdb
    2101  #4/Ah
    2102  ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ai ALA 60, rc-
    2103  dlh1-model1b_rearranged.pdb #4/Aj ALA 60, rc-dlh1-model1b_rearranged.pdb
    2104  #4/Ak
    2105  ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Al ALA 60, rc-
    2106  dlh1-model1b_rearranged.pdb #4/Am ALA 60, rc-dlh1-model1b_rearranged.pdb
    2107  #4/An
    2108  ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ao ALA 60, rc-
    2109  dlh1-model1b_rearranged.pdb #4/Ap ALA 60, rc-dlh1-model1b_rearranged.pdb
    2110  #4/B
    2111  ILE 123, rc-dlh1-model1b_rearranged.pdb #4/C ILE 313, rc-
    2112  dlh1-model1b_rearranged.pdb #4/C1 LEU 92, rc-dlh1-model1b_rearranged.pdb
    2113  #4/H1
    2114  HIS 67, rc-dlh1-model1b_rearranged.pdb #4/H2 ILE 181, rc-
    2115  dlh1-model1b_rearranged.pdb #4/H2 ARG 36, rc-dlh1-model1b_rearranged.pdb
    2116  #4/L
    2117  TRP 272, rc-dlh1-model1b_rearranged.pdb #4/M TYR 324
    2118  Skipping possible acceptor with bad geometry: rc-
    2119  dlh1-model1b_rearranged.pdb
    2120  #4/C ARG 302 O
    2121  Wrong number of grandchild atoms for phi/psi acceptor rc-
    2122  dlh1-model1b_rearranged.pdb #4/C ARG 302 O
    2123 
    2124  Skipping possible acceptor with bad geometry: rc-
    2125  dlh1-model1b_rearranged.pdb
    2126  #4/C ARG 302 OXT
    2127  Wrong number of grandchild atoms for phi/psi acceptor rc-
    2128  dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT
    2129 
    2130  Skipping possible acceptor with bad geometry: rc-
    2131  dlh1-model1b_rearranged.pdb
    2132  #4/C ARG 302 OXT
    2133  Wrong number of grandchild atoms for phi/psi acceptor rc-
    2134  dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT
    2135 
    2136  Skipping possible acceptor with bad geometry: rc-
    2137  dlh1-model1b_rearranged.pdb
    2138  #4/C ARG 302 O
    2139  Wrong number of grandchild atoms for phi/psi acceptor rc-
    2140  dlh1-model1b_rearranged.pdb #4/C ARG 302 O
    2141 
    2142  Skipping possible acceptor with bad geometry: rc-
    2143  dlh1-model1b_rearranged.pdb
    2144  #4/C ARG 302 O
    2145  Wrong number of grandchild atoms for phi/psi acceptor rc-
    2146  dlh1-model1b_rearranged.pdb #4/C ARG 302 O
    2147 
    2148  3 messages similar to the above omitted
    2149  4768 hydrogen bonds
    2150  Adding 'H' to rc-dlh1-model1b_rearranged.pdb #4/H2 ARG 38
    2151  rc-dlh1-model1b_rearranged.pdb #4/AA PRO 48 is not terminus, removing H
    2152  atom
    2153  from 'C'
    2154  rc-dlh1-model1b_rearranged.pdb #4/AB PRO 48 is not terminus, removing H
    2155  atom
    2156  from 'C'
    2157  rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48 is not terminus, removing H
    2158  atom
    2159  from 'C'
    2160  rc-dlh1-model1b_rearranged.pdb #4/AD PRO 48 is not terminus, removing H
    2161  atom
    2162  from 'C'
    2163  rc-dlh1-model1b_rearranged.pdb #4/AE PRO 48 is not terminus, removing H
    2164  atom
    2165  from 'C'
    2166  42 messages similar to the above omitted
    2167  44090 hydrogens added
    2168 
    2169 
    2170  > select #2/C:303-400
    2171 
    2172  157 atoms, 161 bonds, 11 residues, 1 model selected
    2173 
    2174  > select clear
    2175 
    2176  > isolde stepto
    2177 
    2178  > isolde stepto
    2179 
    2180  > isolde stepto
    2181 
    2182  > isolde stepto
    2183 
    2184  > isolde stepto
    2185 
    2186  > isolde stepto
    2187 
    2188  > isolde stepto
    2189 
    2190  > isolde stepto
    2191 
    2192  > isolde stepto
    2193 
    2194  > isolde stepto
    2195 
    2196  > isolde stepto
    2197 
    2198  > isolde stepto
    2199 
    2200  > isolde stepto
    2201 
    2202  > show #!4 models
    2203 
    2204  > hide #!4 models
    2205 
    2206  > select up
    2207 
    2208  12 atoms, 11 bonds, 1 residue, 1 model selected
    2209 
    2210  > select up
    2211 
    2212  874 atoms, 890 bonds, 53 residues, 1 model selected
    2213 
    2214  > select #2/H1:3-100
    2215 
    2216  838 atoms, 854 bonds, 51 residues, 1 model selected
    2217 
    2218  > show #!4 models
    2219 
    2220  > hide #!4 models
    2221 
    2222  > isolde stepto
    2223 
    2224  > isolde stepto
    2225 
    2226  > isolde stepto
    2227 
    2228  > isolde stepto
    2229 
    2230  > isolde stepto
    2231 
    2232  > isolde stepto
    2233 
    2234  > isolde stepto
    2235 
    2236  > isolde stepto
    2237 
    2238  > isolde stepto
    2239 
    2240  > isolde stepto
    2241 
    2242  > isolde stepto
    2243 
    2244  > isolde stepto
    2245 
    2246  > isolde stepto
    2247 
    2248  > isolde stepto
    2249 
    2250  > isolde stepto
    2251 
    2252  > isolde stepto
    2253 
    2254  > isolde stepto
    2255 
    2256  > isolde stepto
    2257 
    2258  > isolde stepto
    2259 
    2260  > isolde stepto
    2261 
    2262  > isolde stepto
    2263 
    2264  > isolde stepto
    2265 
    2266  > isolde stepto
    2267 
    2268  > isolde stepto
    2269 
    2270  > isolde stepto
    2271 
    2272  > isolde stepto
    2273 
    2274  > isolde stepto
    2275 
    2276  > isolde stepto
    2277 
    2278  > isolde stepto
    2279 
    2280  > isolde stepto
    2281 
    2282  > isolde stepto
    2283 
    2284  > isolde stepto
    2285 
    2286  > isolde stepto
    2287 
    2288  > isolde stepto
    2289 
    2290  > isolde stepto
    2291 
    2292  > isolde stepto
    2293 
    2294  > isolde stepto
    2295 
    2296  > isolde stepto
    2297 
    2298  > isolde stepto
    2299 
    2300  > show #!4 models
    2301 
    2302  > hide #!4 models
    2303 
    2304  > select up
    2305 
    2306  38 atoms, 40 bonds, 2 residues, 1 model selected
    2307 
    2308  > select clear
    2309 
    2310  > select clear
    2311 
    2312  > select #1
    2313 
    2314  1516 atoms, 1537 bonds, 99 residues, 1 model selected
    2315 
    2316  > select #2
    2317 
    2318  94789 atoms, 96857 bonds, 14 pseudobonds, 5061 residues, 22 models
    2319  selected
    2320 
    2321  > style sel sphere
    2322 
    2323  Changed 94789 atom styles
    2324 
    2325  > select clear
    2326 
    2327  > style #!2.2 stick
    2328 
    2329  Changed 94789 atom styles
    2330 
    2331  > delete sel
    2332 
    2333  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2334  bonded heavy atom.
    2335 
    2336  > delete sel
    2337 
    2338  > delete sel
    2339 
    2340  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2341  bonded heavy atom.
    2342 
    2343  > delete sel
    2344 
    2345  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2346  bonded heavy atom.
    2347 
    2348  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2349  bonded heavy atom.
    2350 
    2351  > select #2/H2
    2352 
    2353  2777 atoms, 2816 bonds, 180 residues, 1 model selected
    2354 
    2355  > select clear
    2356 
    2357  > isolde jumpto
    2358 
    2359  > select #2/H2:3-100
    2360 
    2361  1476 atoms, 1499 bonds, 97 residues, 1 model selected
    2362 
    2363  > select clear
    2364 
    2365  > select clear
    2366 
    2367  > isolde stepto
    2368 
    2369  > isolde stepto
    2370 
    2371  > isolde stepto
    2372 
    2373  > isolde stepto
    2374 
    2375  > isolde stepto
    2376 
    2377  > isolde stepto
    2378 
    2379  > isolde stepto
    2380 
    2381  > isolde stepto
    2382 
    2383  > isolde stepto
    2384 
    2385  > isolde stepto
    2386 
    2387  > isolde stepto
    2388 
    2389  > isolde stepto
    2390 
    2391  > isolde stepto
    2392 
    2393  > isolde stepto
    2394 
    2395  > select #2/H2:3-100
    2396 
    2397  1476 atoms, 1499 bonds, 97 residues, 1 model selected
    2398 
    2399  > select clear
    2400 
    2401  > isolde stepto
    2402 
    2403  > isolde stepto
    2404 
    2405  > isolde stepto
    2406 
    2407  > isolde stepto
    2408 
    2409  > isolde stepto
    2410 
    2411  > isolde stepto
    2412 
    2413  > isolde stepto
    2414 
    2415  > isolde stepto
    2416 
    2417  > isolde stepto
    2418 
    2419  > isolde stepto
    2420 
    2421  > isolde stepto
    2422 
    2423  > isolde stepto
    2424 
    2425  > isolde stepto
    2426 
    2427  > isolde stepto
    2428 
    2429  > isolde stepto
    2430 
    2431  > isolde stepto
    2432 
    2433  > isolde stepto
    2434 
    2435  > isolde stepto
    2436 
    2437  > isolde stepto
    2438 
    2439  > isolde stepto
    2440 
    2441  > isolde stepto
    2442 
    2443  > isolde stepto
    2444 
    2445  > isolde stepto
    2446 
    2447  > isolde stepto
    2448 
    2449  > isolde stepto
    2450 
    2451  > isolde stepto
    2452 
    2453  > isolde stepto
    2454 
    2455  > isolde stepto
    2456 
    2457  > isolde stepto
    2458 
    2459  > isolde stepto
    2460 
    2461  > isolde stepto
    2462 
    2463  > isolde stepto
    2464 
    2465  > isolde stepto
    2466 
    2467  > isolde stepto
    2468 
    2469  > isolde stepto
    2470 
    2471  > isolde stepto
    2472 
    2473  > isolde stepto
    2474 
    2475  > isolde stepto
    2476 
    2477  > isolde stepto
    2478 
    2479  > isolde stepto
    2480 
    2481  > isolde stepto
    2482 
    2483  > isolde stepto
    2484 
    2485  > isolde stepto
    2486 
    2487  > isolde stepto
    2488 
    2489  > isolde stepto
    2490 
    2491  > isolde stepto
    2492 
    2493  > isolde stepto
    2494 
    2495  > isolde stepto
    2496 
    2497  > isolde stepto
    2498 
    2499  > isolde stepto
    2500 
    2501  > isolde stepto
    2502 
    2503  > isolde stepto
    2504 
    2505  > isolde stepto
    2506 
    2507  > isolde stepto
    2508 
    2509  > isolde stepto
    2510 
    2511  > isolde stepto
    2512 
    2513  > isolde stepto
    2514 
    2515  > isolde stepto
    2516 
    2517  > isolde stepto
    2518 
    2519  > isolde stepto
    2520 
    2521  > isolde stepto
    2522 
    2523  > isolde stepto
    2524 
    2525  > isolde stepto
    2526 
    2527  > isolde stepto
    2528 
    2529  > isolde stepto
    2530 
    2531  > isolde stepto
    2532 
    2533  > isolde stepto
    2534 
    2535  > isolde stepto
    2536 
    2537  > isolde stepto
    2538 
    2539  > isolde stepto
    2540 
    2541  > isolde stepto
    2542 
    2543  > isolde stepto
    2544 
    2545  > isolde stepto
    2546 
    2547  > isolde stepto
    2548 
    2549  > isolde stepto
    2550 
    2551  > isolde stepto
    2552 
    2553  > isolde stepto
    2554 
    2555  > isolde stepto
    2556 
    2557  > isolde stepto
    2558 
    2559  > select #2/H1:95-205
    2560 
    2561  Nothing selected
    2562 
    2563  > select #2/H1:95-205
    2564 
    2565  Nothing selected
    2566 
    2567  > select #2/H2:95-205
    2568 
    2569  1376 atoms, 1394 bonds, 87 residues, 1 model selected
    2570 
    2571  > select clear
    2572 
    2573  > isolde stepto
    2574 
    2575  > isolde stepto
    2576 
    2577  > isolde stepto
    2578 
    2579  > isolde stepto
    2580 
    2581  > isolde stepto
    2582 
    2583  > isolde stepto
    2584 
    2585  > isolde stepto
    2586 
    2587  > isolde stepto
    2588 
    2589  > isolde stepto
    2590 
    2591  > isolde stepto
    2592 
    2593  > select clear
    2594 
    2595  > isolde stepto
    2596 
    2597  > isolde stepto
    2598 
    2599  > isolde stepto
    2600 
    2601  > isolde stepto
    2602 
    2603  > isolde stepto
    2604 
    2605  > isolde stepto
    2606 
    2607  > isolde stepto
    2608 
    2609  > isolde stepto
    2610 
    2611  > isolde stepto
    2612 
    2613  > isolde stepto
    2614 
    2615  > isolde stepto
    2616 
    2617  > isolde stepto
    2618 
    2619  > isolde stepto
    2620 
    2621  > isolde stepto
    2622 
    2623  > isolde stepto
    2624 
    2625  > isolde stepto
    2626 
    2627  > isolde stepto
    2628 
    2629  > isolde stepto
    2630 
    2631  > isolde stepto
    2632 
    2633  > isolde stepto
    2634 
    2635  > isolde stepto
    2636 
    2637  > isolde stepto
    2638 
    2639  > isolde stepto
    2640 
    2641  > isolde stepto
    2642 
    2643  > isolde stepto
    2644 
    2645  > isolde stepto
    2646 
    2647  > isolde stepto
    2648 
    2649  > isolde stepto
    2650 
    2651  > isolde stepto
    2652 
    2653  > isolde stepto
    2654 
    2655  > isolde stepto
    2656 
    2657  > isolde stepto
    2658 
    2659  > isolde stepto
    2660 
    2661  > isolde stepto
    2662 
    2663  > isolde stepto
    2664 
    2665  > isolde stepto
    2666 
    2667  > isolde stepto
    2668 
    2669  > isolde stepto
    2670 
    2671  > isolde stepto
    2672 
    2673  > isolde stepto
    2674 
    2675  > isolde stepto
    2676 
    2677  > isolde stepto
    2678 
    2679  > isolde stepto
    2680 
    2681  > isolde stepto
    2682 
    2683  > isolde stepto
    2684 
    2685  > isolde stepto
    2686 
    2687  > isolde stepto
    2688 
    2689  > isolde stepto
    2690 
    2691  > isolde stepto
    2692 
    2693  > isolde stepto
    2694 
    2695  > isolde stepto
    2696 
    2697  > isolde stepto
    2698 
    2699  > isolde stepto
    2700 
    2701  > isolde stepto
    2702 
    2703  > isolde stepto
    2704 
    2705  > isolde stepto
    2706 
    2707  > isolde stepto
    2708 
    2709  > isolde stepto
    2710 
    2711  > isolde stepto
    2712 
    2713  > isolde stepto
    2714 
    2715  > isolde stepto
    2716 
    2717  > isolde stepto
    2718 
    2719  > isolde stepto
    2720 
    2721  > isolde stepto
    2722 
    2723  > isolde stepto
    2724 
    2725  > isolde stepto
    2726 
    2727  > isolde stepto
    2728 
    2729  > isolde stepto
    2730 
    2731  > isolde stepto
    2732 
    2733  > isolde stepto
    2734 
    2735  > isolde stepto
    2736 
    2737  > isolde stepto
    2738 
    2739  > isolde stepto
    2740 
    2741  > isolde stepto
    2742 
    2743  > isolde stepto
    2744 
    2745  > isolde stepto
    2746 
    2747  > isolde stepto
    2748 
    2749  > save working.cxs
    2750 
    2751  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    2752 
    2753  > isolde stepto
    2754 
    2755  > select #2/L:1-100
    2756 
    2757  1563 atoms, 1592 bonds, 100 residues, 1 model selected
    2758 
    2759  > select clear
    2760 
    2761  > isolde stepto
    2762 
    2763  > isolde stepto
    2764 
    2765  > isolde stepto
    2766 
    2767  > isolde stepto
    2768 
    2769  > isolde stepto
    2770 
    2771  > isolde stepto
    2772 
    2773  > isolde stepto
    2774 
    2775  > isolde stepto
    2776 
    2777  > isolde stepto
    2778 
    2779  > isolde stepto
    2780 
    2781  > select clear
    2782 
    2783  > isolde stepto
    2784 
    2785  > isolde stepto
    2786 
    2787  > isolde stepto
    2788 
    2789  > isolde stepto
    2790 
    2791  > isolde stepto
    2792 
    2793  > isolde stepto
    2794 
    2795  > isolde stepto
    2796 
    2797  > isolde stepto
    2798 
    2799  > isolde stepto
    2800 
    2801  > isolde stepto
    2802 
    2803  > isolde stepto
    2804 
    2805  > isolde stepto
    2806 
    2807  > isolde stepto
    2808 
    2809  > isolde stepto
    2810 
    2811  > isolde stepto
    2812 
    2813  > isolde stepto
    2814 
    2815  > isolde stepto
    2816 
    2817  > isolde stepto
    2818 
    2819  > isolde stepto
    2820 
    2821  > isolde stepto
    2822 
    2823  > isolde stepto
    2824 
    2825  > isolde stepto
    2826 
    2827  > isolde stepto
    2828 
    2829  > isolde stepto
    2830 
    2831  > isolde stepto
    2832 
    2833  > isolde stepto
    2834 
    2835  > isolde stepto
    2836 
    2837  > select clear
    2838 
    2839  > isolde stepto
    2840 
    2841  > isolde stepto
    2842 
    2843  > isolde stepto
    2844 
    2845  > isolde stepto
    2846 
    2847  > isolde stepto
    2848 
    2849  > isolde stepto
    2850 
    2851  > isolde stepto
    2852 
    2853  > isolde stepto
    2854 
    2855  > isolde stepto
    2856 
    2857  > isolde stepto
    2858 
    2859  > isolde stepto
    2860 
    2861  > isolde stepto
    2862 
    2863  > isolde stepto
    2864 
    2865  > isolde stepto
    2866 
    2867  > isolde stepto
    2868 
    2869  > isolde stepto
    2870 
    2871  > isolde stepto
    2872 
    2873  > isolde stepto
    2874 
    2875  > isolde stepto
    2876 
    2877  > isolde stepto
    2878 
    2879  > isolde stepto
    2880 
    2881  > isolde stepto
    2882 
    2883  > isolde stepto
    2884 
    2885  > isolde stepto
    2886 
    2887  > isolde stepto
    2888 
    2889  > isolde stepto
    2890 
    2891  > isolde stepto
    2892 
    2893  > isolde stepto
    2894 
    2895  > isolde stepto
    2896 
    2897  > isolde stepto
    2898 
    2899  > isolde stepto
    2900 
    2901  > isolde stepto
    2902 
    2903  > isolde stepto
    2904 
    2905  > isolde stepto
    2906 
    2907  > isolde stepto
    2908 
    2909  > isolde stepto
    2910 
    2911  > isolde stepto
    2912 
    2913  > isolde stepto
    2914 
    2915  > isolde stepto
    2916 
    2917  > isolde stepto
    2918 
    2919  > isolde stepto
    2920 
    2921  > isolde stepto
    2922 
    2923  > isolde stepto
    2924 
    2925  > isolde stepto
    2926 
    2927  > isolde stepto
    2928 
    2929  > isolde stepto
    2930 
    2931  > isolde stepto
    2932 
    2933  > isolde stepto
    2934 
    2935  > isolde stepto
    2936 
    2937  > isolde stepto
    2938 
    2939  > isolde stepto
    2940 
    2941  > isolde stepto
    2942 
    2943  > isolde stepto
    2944 
    2945  > isolde stepto
    2946 
    2947  > isolde stepto
    2948 
    2949  > isolde stepto
    2950 
    2951  > isolde stepto
    2952 
    2953  > isolde stepto
    2954 
    2955  > isolde stepto
    2956 
    2957  > isolde stepto
    2958 
    2959  > isolde stepto
    2960 
    2961  > isolde stepto
    2962 
    2963  > isolde stepto
    2964 
    2965  > isolde stepto
    2966 
    2967  > isolde stepto
    2968 
    2969  > isolde stepto
    2970 
    2971  > isolde stepto
    2972 
    2973  > isolde stepto
    2974 
    2975  > isolde stepto
    2976 
    2977  > isolde stepto
    2978 
    2979  > isolde stepto
    2980 
    2981  > isolde stepto
    2982 
    2983  > isolde stepto
    2984 
    2985  > select #2/L:100-300
    2986 
    2987  2756 atoms, 2816 bonds, 174 residues, 1 model selected
    2988 
    2989  > select clear
    2990 
    2991  > select clear
    2992 
    2993  > isolde stepto
    2994 
    2995  > isolde stepto
    2996 
    2997  > isolde stepto
    2998 
    2999  > select clear
    3000 
    3001  > isolde stepto
    3002 
    3003  > isolde stepto
    3004 
    3005  > isolde stepto
    3006 
    3007  > isolde stepto
    3008 
    3009  > isolde stepto
    3010 
    3011  > isolde stepto
    3012 
    3013  > isolde stepto
    3014 
    3015  > isolde stepto
    3016 
    3017  > isolde stepto
    3018 
    3019  > isolde stepto
    3020 
    3021  > isolde stepto
    3022 
    3023  > isolde stepto
    3024 
    3025  > isolde stepto
    3026 
    3027  > isolde stepto
    3028 
    3029  > isolde stepto
    3030 
    3031  > isolde stepto
    3032 
    3033  > isolde stepto
    3034 
    3035  > isolde stepto
    3036 
    3037  > isolde stepto
    3038 
    3039  > isolde stepto
    3040 
    3041  > isolde stepto
    3042 
    3043  > isolde stepto
    3044 
    3045  > isolde stepto
    3046 
    3047  > isolde stepto
    3048 
    3049  > isolde stepto
    3050 
    3051  > isolde stepto
    3052 
    3053  > isolde stepto
    3054 
    3055  > isolde stepto
    3056 
    3057  > isolde stepto
    3058 
    3059  > isolde stepto
    3060 
    3061  > isolde stepto
    3062 
    3063  > isolde stepto
    3064 
    3065  > isolde stepto
    3066 
    3067  > isolde stepto
    3068 
    3069  > isolde stepto
    3070 
    3071  > isolde stepto
    3072 
    3073  > isolde stepto
    3074 
    3075  > isolde stepto
    3076 
    3077  > isolde stepto
    3078 
    3079  > isolde stepto
    3080 
    3081  > isolde stepto
    3082 
    3083  > isolde stepto
    3084 
    3085  > isolde stepto
    3086 
    3087  > isolde stepto
    3088 
    3089  > isolde stepto
    3090 
    3091  > isolde stepto
    3092 
    3093  > isolde stepto
    3094 
    3095  > isolde stepto
    3096 
    3097  > isolde stepto
    3098 
    3099  > isolde stepto
    3100 
    3101  > isolde stepto
    3102 
    3103  > isolde stepto
    3104 
    3105  > isolde stepto
    3106 
    3107  > isolde stepto
    3108 
    3109  > isolde stepto
    3110 
    3111  > isolde stepto
    3112 
    3113  > isolde stepto
    3114 
    3115  > isolde stepto
    3116 
    3117  > isolde stepto
    3118 
    3119  > isolde stepto
    3120 
    3121  > isolde stepto
    3122 
    3123  > isolde stepto
    3124 
    3125  > isolde stepto
    3126 
    3127  > isolde stepto
    3128 
    3129  > isolde stepto
    3130 
    3131  > isolde stepto
    3132 
    3133  > isolde stepto
    3134 
    3135  > isolde stepto
    3136 
    3137  > isolde stepto
    3138 
    3139  > isolde stepto
    3140 
    3141  > isolde stepto
    3142 
    3143  > isolde stepto
    3144 
    3145  > isolde stepto
    3146 
    3147  > isolde stepto
    3148 
    3149  > isolde stepto
    3150 
    3151  > isolde stepto
    3152 
    3153  > isolde stepto
    3154 
    3155  > isolde stepto
    3156 
    3157  > isolde stepto
    3158 
    3159  > isolde stepto
    3160 
    3161  > isolde stepto
    3162 
    3163  > isolde stepto
    3164 
    3165  > isolde stepto
    3166 
    3167  > isolde stepto
    3168 
    3169  > isolde stepto
    3170 
    3171  > isolde stepto
    3172 
    3173  > isolde stepto
    3174 
    3175  > isolde stepto
    3176 
    3177  > isolde stepto
    3178 
    3179  > isolde stepto
    3180 
    3181  > select clear
    3182 
    3183  > isolde stepto
    3184 
    3185  > isolde stepto
    3186 
    3187  > isolde stepto
    3188 
    3189  > isolde stepto
    3190 
    3191  > select clear
    3192 
    3193  > isolde stepto
    3194 
    3195  > isolde stepto
    3196 
    3197  > isolde stepto
    3198 
    3199  > select clear
    3200 
    3201  > isolde stepto
    3202 
    3203  > isolde stepto
    3204 
    3205  > isolde stepto
    3206 
    3207  > isolde stepto
    3208 
    3209  > isolde stepto
    3210 
    3211  > isolde stepto
    3212 
    3213  > isolde stepto
    3214 
    3215  > isolde stepto
    3216 
    3217  > isolde stepto
    3218 
    3219  > isolde stepto
    3220 
    3221  > isolde stepto
    3222 
    3223  > isolde stepto
    3224 
    3225  > isolde stepto
    3226 
    3227  > isolde stepto
    3228 
    3229  > isolde stepto
    3230 
    3231  > swapaa mousemode sel ILE
    3232 
    3233  > select up
    3234 
    3235  19 atoms, 18 bonds, 1 residue, 1 model selected
    3236 
    3237  > color sel bychain
    3238 
    3239  > color sel byhetero
    3240 
    3241  > select #2/L:227-400
    3242 
    3243  777 atoms, 798 bonds, 47 residues, 1 model selected
    3244 
    3245  > hide HC
    3246 
    3247  > select up
    3248 
    3249  15 atoms, 14 bonds, 1 residue, 1 model selected
    3250 
    3251  > color sel byhetero
    3252 
    3253  > select clear
    3254 
    3255  > color bychain
    3256 
    3257  > color byhetero
    3258 
    3259  > hide HC
    3260 
    3261  > select #2/L:227-400
    3262 
    3263  777 atoms, 798 bonds, 47 residues, 1 model selected
    3264 
    3265  > select clear
    3266 
    3267  > isolde stepto
    3268 
    3269  > isolde stepto
    3270 
    3271  > isolde stepto
    3272 
    3273  > isolde stepto
    3274 
    3275  > isolde stepto
    3276 
    3277  > isolde stepto
    3278 
    3279  > isolde stepto
    3280 
    3281  > isolde stepto
    3282 
    3283  > isolde stepto
    3284 
    3285  > isolde stepto
    3286 
    3287  > isolde stepto
    3288 
    3289  > isolde stepto
    3290 
    3291  > isolde stepto
    3292 
    3293  > isolde stepto
    3294 
    3295  > isolde stepto
    3296 
    3297  > isolde stepto
    3298 
    3299  > isolde stepto
    3300 
    3301  > isolde stepto
    3302 
    3303  > isolde stepto
    3304 
    3305  > isolde stepto
    3306 
    3307  > select clear
    3308 
    3309  > show H&~HC
    3310 
    3311  > select clear
    3312 
    3313  > show H&~HC
    3314 
    3315  > show ~H
    3316 
    3317  > select #2/L:227-400
    3318 
    3319  777 atoms, 798 bonds, 47 residues, 1 model selected
    3320 
    3321  > select clear
    3322 
    3323  > select clear
    3324 
    3325  > isolde stepto
    3326 
    3327  > isolde stepto
    3328 
    3329  > isolde stepto
    3330 
    3331  > isolde stepto
    3332 
    3333  > isolde stepto
    3334 
    3335  > isolde stepto
    3336 
    3337  > isolde stepto
    3338 
    3339  > isolde stepto
    3340 
    3341  > isolde stepto
    3342 
    3343  > isolde stepto
    3344 
    3345  > isolde stepto
    3346 
    3347  > isolde stepto
    3348 
    3349  > isolde stepto
    3350 
    3351  > isolde stepto
    3352 
    3353  > isolde stepto
    3354 
    3355  > isolde stepto
    3356 
    3357  > isolde stepto
    3358 
    3359  > isolde stepto
    3360 
    3361  > isolde stepto
    3362 
    3363  > isolde stepto
    3364 
    3365  > isolde stepto
    3366 
    3367  > isolde stepto
    3368 
    3369  > isolde stepto
    3370 
    3371  > isolde stepto
    3372 
    3373  > isolde stepto
    3374 
    3375  > isolde stepto
    3376 
    3377  > isolde stepto
    3378 
    3379  > select #2/M
    3380 
    3381  5833 atoms, 5950 bonds, 6 pseudobonds, 330 residues, 2 models selected
    3382 
    3383  > select #2/M:1-50
    3384 
    3385  763 atoms, 772 bonds, 50 residues, 1 model selected
    3386 
    3387  > select clear
    3388 
    3389  > isolde stepto
    3390 
    3391  > isolde stepto
    3392 
    3393  > isolde stepto
    3394 
    3395  > isolde stepto
    3396 
    3397  > isolde stepto
    3398 
    3399  > isolde stepto
    3400 
    3401  > isolde stepto
    3402 
    3403  > isolde stepto
    3404 
    3405  > isolde stepto
    3406 
    3407  > isolde stepto
    3408 
    3409  > isolde stepto
    3410 
    3411  > isolde stepto
    3412 
    3413  > isolde stepto
    3414 
    3415  > isolde stepto
    3416 
    3417  > select clear
    3418 
    3419  > select clear
    3420 
    3421  > isolde stepto
    3422 
    3423  > isolde stepto
    3424 
    3425  > isolde stepto
    3426 
    3427  > isolde stepto
    3428 
    3429  > isolde stepto
    3430 
    3431  > isolde stepto
    3432 
    3433  > isolde stepto
    3434 
    3435  > isolde stepto
    3436 
    3437  > isolde stepto
    3438 
    3439  > isolde stepto
    3440 
    3441  > isolde stepto
    3442 
    3443  > isolde stepto
    3444 
    3445  > isolde stepto
    3446 
    3447  > isolde stepto
    3448 
    3449  > isolde stepto
    3450 
    3451  > isolde stepto
    3452 
    3453  > isolde stepto
    3454 
    3455  > isolde stepto
    3456 
    3457  > isolde stepto
    3458 
    3459  > isolde stepto
    3460 
    3461  > isolde stepto
    3462 
    3463  > isolde stepto
    3464 
    3465  > isolde stepto
    3466 
    3467  > isolde stepto
    3468 
    3469  > isolde stepto
    3470 
    3471  > isolde stepto
    3472 
    3473  > isolde stepto
    3474 
    3475  > isolde stepto
    3476 
    3477  > isolde stepto
    3478 
    3479  > isolde stepto
    3480 
    3481  > isolde stepto
    3482 
    3483  > isolde stepto
    3484 
    3485  > isolde stepto
    3486 
    3487  > isolde stepto
    3488 
    3489  > isolde stepto
    3490 
    3491  > isolde stepto
    3492 
    3493  > isolde stepto
    3494 
    3495  > isolde stepto
    3496 
    3497  > isolde stepto
    3498 
    3499  > isolde stepto
    3500 
    3501  > isolde stepto
    3502 
    3503  > isolde stepto
    3504 
    3505  > isolde stepto
    3506 
    3507  > select #2/M:58-158
    3508 
    3509  1664 atoms, 1698 bonds, 101 residues, 1 model selected
    3510 
    3511  > select clear
    3512 
    3513  > select #2/M:58-158
    3514 
    3515  1664 atoms, 1698 bonds, 101 residues, 1 model selected
    3516 
    3517  > select clear
    3518 
    3519  > isolde stepto
    3520 
    3521  > isolde stepto
    3522 
    3523  > isolde stepto
    3524 
    3525  > isolde stepto
    3526 
    3527  > isolde stepto
    3528 
    3529  > isolde stepto
    3530 
    3531  > isolde stepto
    3532 
    3533  > isolde stepto
    3534 
    3535  > select clear
    3536 
    3537  > isolde stepto
    3538 
    3539  > isolde stepto
    3540 
    3541  > isolde stepto
    3542 
    3543  > isolde stepto
    3544 
    3545  > sequence chain #2/M
    3546 
    3547  Alignment identifier is 2.2/M
    3548 
    3549  > select #2/M:58-158
    3550 
    3551  1665 atoms, 1699 bonds, 101 residues, 1 model selected
    3552 
    3553  > select clear
    3554 
    3555  > select clear
    3556 
    3557  > isolde stepto
    3558 
    3559  > isolde stepto
    3560 
    3561  > isolde stepto
    3562 
    3563  > isolde stepto
    3564 
    3565  > select clear
    3566 
    3567  > isolde stepto
    3568 
    3569  > isolde stepto
    3570 
    3571  > isolde stepto
    3572 
    3573  > isolde stepto
    3574 
    3575  > isolde stepto
    3576 
    3577  > isolde stepto
    3578 
    3579  > isolde stepto
    3580 
    3581  > select clear
    3582 
    3583  > isolde stepto
    3584 
    3585  > isolde stepto
    3586 
    3587  > isolde stepto
    3588 
    3589  > isolde stepto
    3590 
    3591  > isolde stepto
    3592 
    3593  > isolde stepto
    3594 
    3595  > isolde stepto
    3596 
    3597  > isolde stepto
    3598 
    3599  > isolde stepto
    3600 
    3601  > isolde stepto
    3602 
    3603  > isolde stepto
    3604 
    3605  > isolde stepto
    3606 
    3607  > isolde stepto
    3608 
    3609  > isolde stepto
    3610 
    3611  > isolde stepto
    3612 
    3613  > isolde stepto
    3614 
    3615  > isolde stepto
    3616 
    3617  > isolde stepto
    3618 
    3619  > isolde stepto
    3620 
    3621  > isolde stepto
    3622 
    3623  > isolde stepto
    3624 
    3625  > isolde stepto
    3626 
    3627  > isolde stepto
    3628 
    3629  > isolde stepto
    3630 
    3631  > isolde stepto
    3632 
    3633  > select clear
    3634 
    3635  > isolde stepto
    3636 
    3637  > isolde stepto
    3638 
    3639  > isolde stepto
    3640 
    3641  > isolde stepto
    3642 
    3643  > select clear
    3644 
    3645  > isolde stepto
    3646 
    3647  > isolde stepto
    3648 
    3649  > isolde stepto
    3650 
    3651  > isolde stepto
    3652 
    3653  > isolde stepto
    3654 
    3655  > isolde stepto
    3656 
    3657  > isolde stepto
    3658 
    3659  > isolde stepto
    3660 
    3661  > isolde stepto
    3662 
    3663  > isolde stepto
    3664 
    3665  > isolde stepto
    3666 
    3667  > isolde stepto
    3668 
    3669  > isolde stepto
    3670 
    3671  > isolde stepto
    3672 
    3673  > isolde stepto
    3674 
    3675  > isolde stepto
    3676 
    3677  > isolde stepto
    3678 
    3679  > isolde stepto
    3680 
    3681  > isolde stepto
    3682 
    3683  > isolde stepto
    3684 
    3685  > isolde stepto
    3686 
    3687  > isolde stepto
    3688 
    3689  > isolde stepto
    3690 
    3691  > isolde stepto
    3692 
    3693  > isolde stepto
    3694 
    3695  > isolde stepto
    3696 
    3697  > isolde stepto
    3698 
    3699  > isolde stepto
    3700 
    3701  > isolde stepto
    3702 
    3703  > isolde stepto
    3704 
    3705  > isolde stepto
    3706 
    3707  > isolde stepto
    3708 
    3709  > isolde stepto
    3710 
    3711  > isolde stepto
    3712 
    3713  > isolde stepto
    3714 
    3715  > isolde stepto
    3716 
    3717  > isolde stepto
    3718 
    3719  > isolde stepto
    3720 
    3721  > isolde stepto
    3722 
    3723  > isolde stepto
    3724 
    3725  > isolde stepto
    3726 
    3727  > isolde stepto
    3728 
    3729  > isolde stepto
    3730 
    3731  > isolde stepto
    3732 
    3733  > isolde stepto
    3734 
    3735  > isolde stepto
    3736 
    3737  > isolde stepto
    3738 
    3739  > isolde stepto
    3740 
    3741  > isolde stepto
    3742 
    3743  > isolde stepto
    3744 
    3745  > isolde stepto
    3746 
    3747  > isolde stepto
    3748 
    3749  > isolde stepto
    3750 
    3751  > isolde stepto
    3752 
    3753  > isolde stepto
    3754 
    3755  > isolde stepto
    3756 
    3757  > isolde stepto
    3758 
    3759  > isolde stepto
    3760 
    3761  > isolde stepto
    3762 
    3763  > isolde stepto
    3764 
    3765  > isolde stepto
    3766 
    3767  > isolde stepto
    3768 
    3769  > isolde stepto
    3770 
    3771  > isolde stepto
    3772 
    3773  > isolde stepto
    3774 
    3775  > isolde stepto
    3776 
    3777  > isolde stepto
    3778 
    3779  > isolde stepto
    3780 
    3781  > delete sel
    3782 
    3783  > select #2/M:178-400
    3784 
    3785  2337 atoms, 2378 bonds, 147 residues, 1 model selected
    3786 
    3787  > select clear
    3788 
    3789  > select clear
    3790 
    3791  > select clear
    3792 
    3793  > isolde stepto
    3794 
    3795  > isolde stepto
    3796 
    3797  > isolde stepto
    3798 
    3799  > isolde stepto
    3800 
    3801  > select clear
    3802 
    3803  > isolde stepto
    3804 
    3805  > isolde stepto
    3806 
    3807  > isolde stepto
    3808 
    3809  > isolde stepto
    3810 
    3811  > isolde stepto
    3812 
    3813  > isolde stepto
    3814 
    3815  > isolde stepto
    3816 
    3817  > isolde stepto
    3818 
    3819  > isolde stepto
    3820 
    3821  > isolde stepto
    3822 
    3823  > isolde stepto
    3824 
    3825  > isolde stepto
    3826 
    3827  > isolde stepto
    3828 
    3829  > isolde stepto
    3830 
    3831  > isolde stepto
    3832 
    3833  > isolde stepto
    3834 
    3835  > isolde stepto
    3836 
    3837  > isolde stepto
    3838 
    3839  > isolde stepto
    3840 
    3841  > isolde stepto
    3842 
    3843  > isolde stepto
    3844 
    3845  > isolde stepto
    3846 
    3847  > isolde stepto
    3848 
    3849  > isolde stepto
    3850 
    3851  > isolde stepto
    3852 
    3853  > isolde stepto
    3854 
    3855  > isolde stepto
    3856 
    3857  > isolde stepto
    3858 
    3859  > isolde stepto
    3860 
    3861  > isolde stepto
    3862 
    3863  > isolde stepto
    3864 
    3865  > isolde stepto
    3866 
    3867  > select clear
    3868 
    3869  > isolde stepto
    3870 
    3871  > select clear
    3872 
    3873  > isolde stepto
    3874 
    3875  > isolde stepto
    3876 
    3877  > isolde stepto
    3878 
    3879  > isolde stepto
    3880 
    3881  > isolde stepto
    3882 
    3883  > isolde stepto
    3884 
    3885  > isolde stepto
    3886 
    3887  > isolde stepto
    3888 
    3889  > isolde stepto
    3890 
    3891  > isolde stepto
    3892 
    3893  > isolde stepto
    3894 
    3895  > isolde stepto
    3896 
    3897  > isolde stepto
    3898 
    3899  > isolde stepto
    3900 
    3901  > isolde stepto
    3902 
    3903  > isolde stepto
    3904 
    3905  > isolde stepto
    3906 
    3907  > isolde stepto
    3908 
    3909  > isolde stepto
    3910 
    3911  > isolde stepto
    3912 
    3913  > isolde stepto
    3914 
    3915  > isolde stepto
    3916 
    3917  > isolde stepto
    3918 
    3919  > isolde stepto
    3920 
    3921  > isolde stepto
    3922 
    3923  > isolde stepto
    3924 
    3925  > isolde stepto
    3926 
    3927  > isolde stepto
    3928 
    3929  > isolde stepto
    3930 
    3931  > isolde stepto
    3932 
    3933  > isolde stepto
    3934 
    3935  > isolde stepto
    3936 
    3937  > isolde stepto
    3938 
    3939  > isolde stepto
    3940 
    3941  > isolde stepto
    3942 
    3943  > isolde stepto
    3944 
    3945  > isolde stepto
    3946 
    3947  > isolde stepto
    3948 
    3949  > isolde stepto
    3950 
    3951  > isolde stepto
    3952 
    3953  > isolde stepto
    3954 
    3955  > isolde stepto
    3956 
    3957  > isolde stepto
    3958 
    3959  > isolde stepto
    3960 
    3961  > isolde stepto
    3962 
    3963  > isolde stepto
    3964 
    3965  > isolde stepto
    3966 
    3967  > isolde stepto
    3968 
    3969  > isolde stepto
    3970 
    3971  > select clear
    3972 
    3973  > isolde stepto
    3974 
    3975  > isolde stepto
    3976 
    3977  > isolde stepto
    3978 
    3979  > isolde stepto
    3980 
    3981  > isolde stepto
    3982 
    3983  > isolde stepto
    3984 
    3985  > isolde stepto
    3986 
    3987  > isolde stepto
    3988 
    3989  > isolde stepto
    3990 
    3991  > isolde stepto
    3992 
    3993  > isolde stepto
    3994 
    3995  > isolde stepto
    3996 
    3997  > isolde stepto
    3998 
    3999  > isolde stepto
    4000 
    4001  > isolde stepto
    4002 
    4003  > isolde stepto
    4004 
    4005  > isolde stepto
    4006 
    4007  > isolde stepto
    4008 
    4009  > isolde stepto
    4010 
    4011  > isolde stepto
    4012 
    4013  > isolde stepto
    4014 
    4015  > isolde stepto
    4016 
    4017  > isolde stepto
    4018 
    4019  > isolde stepto
    4020 
    4021  > isolde stepto
    4022 
    4023  > isolde stepto
    4024 
    4025  > isolde stepto
    4026 
    4027  > isolde stepto
    4028 
    4029  > isolde stepto
    4030 
    4031  > isolde stepto
    4032 
    4033  > isolde stepto
    4034 
    4035  > select clear
    4036 
    4037  > isolde stepto
    4038 
    4039  > isolde stepto
    4040 
    4041  > isolde stepto
    4042 
    4043  > select clear
    4044 
    4045  > isolde stepto
    4046 
    4047  > isolde stepto
    4048 
    4049  > isolde stepto
    4050 
    4051  > isolde stepto
    4052 
    4053  > isolde stepto
    4054 
    4055  > isolde stepto
    4056 
    4057  > isolde stepto
    4058 
    4059  > isolde stepto
    4060 
    4061  > isolde stepto
    4062 
    4063  > isolde stepto
    4064 
    4065  > isolde stepto
    4066 
    4067  > isolde stepto
    4068 
    4069  > isolde stepto
    4070 
    4071  > isolde stepto
    4072 
    4073  > isolde stepto
    4074 
    4075  > select clear
    4076 
    4077  > isolde stepto
    4078 
    4079  > isolde stepto
    4080 
    4081  > isolde stepto
    4082 
    4083  > isolde stepto
    4084 
    4085  > isolde stepto
    4086 
    4087  > isolde stepto
    4088 
    4089  > select clear
    4090 
    4091  > isolde stepto
    4092 
    4093  > isolde stepto
    4094 
    4095  > isolde stepto
    4096 
    4097  > isolde stepto
    4098 
    4099  > isolde stepto
    4100 
    4101  > save working.cxs
    4102 
    4103  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4104 
    4105  > show #!4 models
    4106 
    4107  > hide #!4 models
    4108 
    4109  > swapaa mousemode sel GLY
    4110 
    4111  > select up
    4112 
    4113  16 atoms, 15 bonds, 1 residue, 1 model selected
    4114 
    4115  > select up
    4116 
    4117  255 atoms, 259 bonds, 18 residues, 1 model selected
    4118 
    4119  > isolde ignore sel
    4120 
    4121  ISOLDE: currently ignoring 26 residues in model 2.2
    4122 
    4123  > select clear
    4124 
    4125  > isolde ~ignore
    4126 
    4127  > select up
    4128 
    4129  23 atoms, 21 bonds, 2 residues, 1 model selected
    4130 
    4131  > select clear
    4132 
    4133  > delete sel
    4134 
    4135  > delete sel
    4136 
    4137  > select clear
    4138 
    4139  > save working.cxs
    4140 
    4141  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4142 
    4143  > ui tool show "Build Structure"
    4144 
    4145  > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    4146  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4147  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4148  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4149  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4150  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4151  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4152  > rotLib Dunbrack
    4153 
    4154  Chain information for custom built #5
    4155  ---
    4156  Chain | Description
    4157  A | No description available
    4158 
    4159 
    4160  > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    4161  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4162  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4163  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4164  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4165  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4166  > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    4167  > rotLib Dunbrack
    4168 
    4169  Chain information for custom built #6
    4170  ---
    4171  Chain | Description
    4172  A | No description available
    4173 
    4174 
    4175  > close #5
    4176 
    4177  > select #6
    4178 
    4179  258 atoms, 263 bonds, 36 residues, 1 model selected
    4180 
    4181  > show sel&:1
    4182 
    4183  > ui mousemode right "translate selected models"
    4184 
    4185  > ui mousemode right "rotate selected models"
    4186 
    4187  > ui mousemode right "translate selected models"
    4188 
    4189  > ui mousemode right "rotate selected models"
    4190 
    4191  > ui mousemode right "translate selected models"
    4192 
    4193  > hide #6 models
    4194 
    4195  > delete #2/M:332-367
    4196 
    4197  > addh #6
    4198 
    4199  Summary of feedback from adding hydrogens to custom built #6
    4200  ---
    4201  notes | No usable SEQRES records for custom built (#6) chain A; guessing
    4202  termini instead
    4203  Chain-initial residues that are actual N termini: custom built #6/A PHE 1
    4204  Chain-initial residues that are not actual N termini:
    4205  Chain-final residues that are actual C termini: custom built #6/A GLN 36
    4206  Chain-final residues that are not actual C termini:
    4207  37 hydrogen bonds
    4208  250 hydrogens added
    4209 
    4210 
    4211  > isolde ignore #2/C
    4212 
    4213  ISOLDE: currently ignoring 303 residues in model 2.2
    4214 
    4215  > select #2/M:332-367
    4216 
    4217  506 atoms, 511 bonds, 36 residues, 1 model selected
    4218 
    4219  > hide HC
    4220 
    4221  > delete #2/M:339-367
    4222 
    4223  > isolde ~ignore
    4224 
    4225  > select clear
    4226 
    4227  > select clear
    4228 
    4229  > select up
    4230 
    4231  11 atoms, 10 bonds, 1 residue, 1 model selected
    4232 
    4233  > select up
    4234 
    4235  92 atoms, 94 bonds, 6 residues, 1 model selected
    4236 
    4237  > select clear
    4238 
    4239  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    4240  bonded heavy atom.
    4241 
    4242  > select up
    4243 
    4244  14 atoms, 14 bonds, 1 residue, 1 model selected
    4245 
    4246  > delete sel
    4247 
    4248  > save ser_M331_O_glycan.jpg
    4249 
    4250  > open 3e80
    4251 
    4252  3e80 title:
    4253  Structure of Heparinase II complexed with heparan sulfate degradation
    4254  disaccharide product [more info...]
    4255 
    4256  Chain information for 3e80 #5
    4257  ---
    4258  Chain | Description
    4259  A B C | Heparinase II protein
    4260 
    4261  Non-standard residues in 3e80 #5
    4262  ---
    4263  GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid
    4264  GCU — alpha-D-glucopyranuronic acid
    4265  MAN — alpha-D-mannopyranose
    4266  NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose
    4267  PO4 — phosphate ion
    4268  RAM — alpha-L-rhamnopyranose
    4269  XYS — alpha-D-xylopyranose
    4270  ZN — zinc ion
    4271 
    4272  3e80 mmCIF Assemblies
    4273  ---
    4274  1| author_and_software_defined_assembly
    4275  2| author_and_software_defined_assembly
    4276  3| author_and_software_defined_assembly
    4277 
    4278 
    4279  > addh #5
    4280 
    4281  Summary of feedback from adding hydrogens to 3e80 #5
    4282  ---
    4283  warning | Not adding hydrogens to 3e80 #5/C LEU 732 CB because it is
    4284  missing
    4285  heavy-atom bond partners
    4286  notes | Termini for 3e80 (#5) chain A determined from SEQRES records
    4287  Termini for 3e80 (#5) chain B determined from SEQRES records
    4288  Termini for 3e80 (#5) chain C determined from SEQRES records
    4289  Chain-initial residues that are actual N termini:
    4290  Chain-initial residues that are not actual N termini: 3e80 #5/A PCA 26,
    4291  3e80
    4292  #5/B PCA 26, 3e80 #5/C PCA 26
    4293  Chain-final residues that are actual C termini: 3e80 #5/A ARG 772, 3e80
    4294  #5/B
    4295  ARG 772, 3e80 #5/C ARG 772
    4296  Chain-final residues that are not actual C termini:
    4297  Missing OXT added to C-terminal residue 3e80 #5/A ARG 772
    4298  Missing OXT added to C-terminal residue 3e80 #5/B ARG 772
    4299  Missing OXT added to C-terminal residue 3e80 #5/C ARG 772
    4300  3540 hydrogen bonds
    4301  Adding 'H' to 3e80 #5/A PCA 26
    4302  Adding 'H' to 3e80 #5/B PCA 26
    4303  Adding 'H' to 3e80 #5/C PCA 26
    4304  18911 hydrogens added
    4305 
    4306 
    4307  > select #5
    4308 
    4309  37630 atoms, 37586 bonds, 17 pseudobonds, 2807 residues, 2 models selected
    4310 
    4311  > hide #!2 models
    4312 
    4313  > select clear
    4314 
    4315  > select clear
    4316 
    4317  > select #5/B:134|(#5/E:1-4)
    4318 
    4319  90 atoms, 93 bonds, 5 residues, 1 model selected
    4320 
    4321  > hide #5&~sel
    4322 
    4323  > ~cartoon #5
    4324 
    4325  > show #!2 models
    4326 
    4327  > ui mousemode right "translate selected models"
    4328 
    4329  > ui mousemode right "rotate selected models"
    4330 
    4331  > ui mousemode right "translate selected models"
    4332 
    4333  > ui mousemode right "rotate selected models"
    4334 
    4335  > ui mousemode right "translate selected models"
    4336 
    4337  > select (#5/E:1-4)
    4338 
    4339  77 atoms, 80 bonds, 4 residues, 1 model selected
    4340 
    4341  > save working.cxs
    4342 
    4343  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4344  Restoring stepper: working_noh_real_space_refined.pdb
    4345  opened ChimeraX session
    4346 
    4347  > open
    4348  >
    4349  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb
    4350 
    4351  Summary of feedback from opening
    4352  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb
    4353  ---
    4354  warnings | End residue of secondary structure not found: HELIX 55 55 THR C
    4355  19
    4356  GLY C 21 1 3
    4357  Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C
    4358  34
    4359  1 7
    4360  Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C
    4361  55
    4362  1 3
    4363  Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C
    4364  69
    4365  1 6
    4366  Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C
    4367  81
    4368  1 7
    4369  Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C
    4370  91
    4371  1 3
    4372  5 messages similar to the above omitted
    4373  Cannot find LINK/SSBOND residue GCU (2 )
    4374  Cannot find LINK/SSBOND residue XYS (3 )
    4375  Cannot find LINK/SSBOND residue RAM (4 )
    4376  Cannot find LINK/SSBOND residue MAN (1 )
    4377  Cannot find LINK/SSBOND residue GCU (2 )
    4378  3 messages similar to the above omitted
    4379 
    4380  Chain information for working.pdb #7
    4381  ---
    4382  Chain | Description
    4383  AA | No description available
    4384  AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4385  description available
    4386  BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg
    4387  bh
    4388  bi bj bk bl bm bo bp | No description available
    4389  BB BD BE BI BV BW bn | No description available
    4390  C | No description available
    4391  C1 | No description available
    4392  C2 | No description available
    4393  H1 | No description available
    4394  H2 | No description available
    4395  L | No description available
    4396  M | No description available
    4397  aa | No description available
    4398  ab ac ad ae af ag ah ai aj am an ao ap | No description available
    4399  ak | No description available
    4400 
    4401 
    4402  > select clear
    4403 
    4404  > hide #7&protein
    4405 
    4406  > hide #!5 models
    4407 
    4408  > select #7/CG
    4409 
    4410  78 atoms, 81 bonds, 4 residues, 1 model selected
    4411 
    4412  > hide #!7 models
    4413 
    4414  > delete sel
    4415 
    4416  > select clear
    4417 
    4418  > select clear
    4419 
    4420  > view #2/M:330
    4421 
    4422  > show #!7 models
    4423 
    4424  > select #7/MG
    4425 
    4426  78 atoms, 81 bonds, 4 residues, 1 model selected
    4427 
    4428  > hide #!7 models
    4429 
    4430  > delete sel
    4431 
    4432  > select clear
    4433 
    4434  > select clear
    4435 
    4436  > save M331_glycan.jpg
    4437 
    4438  > save working.cxs
    4439 
    4440  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4441 
    4442  > select #2/ak
    4443 
    4444  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    4445 
    4446  > ui tool show "Build Structure"
    4447 
    4448  > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4449  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4450  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4451 
    4452  Chain information for custom built #8
    4453  ---
    4454  Chain | Description
    4455  A | No description available
    4456 
    4457 
    4458  > addh #8
    4459 
    4460  Summary of feedback from adding hydrogens to custom built #8
    4461  ---
    4462  notes | No usable SEQRES records for custom built (#8) chain A; guessing
    4463  termini instead
    4464  Chain-initial residues that are actual N termini: custom built #8/A ALA 1
    4465  Chain-initial residues that are not actual N termini:
    4466  Chain-final residues that are actual C termini: custom built #8/A ARG 11
    4467  Chain-final residues that are not actual C termini:
    4468  0 hydrogen bonds
    4469  80 hydrogens added
    4470 
    4471 
    4472  > select #8
    4473 
    4474  158 atoms, 160 bonds, 11 residues, 1 model selected
    4475 
    4476  > show sel
    4477 
    4478  > ui mousemode right "translate selected atoms"
    4479 
    4480  > ui mousemode right "rotate selected models"
    4481 
    4482  > ui mousemode right "translate selected models"
    4483 
    4484  > ui mousemode right "rotate selected models"
    4485 
    4486  > ui mousemode right "translate selected models"
    4487 
    4488  > ui mousemode right "rotate selected models"
    4489 
    4490  > ui mousemode right "translate selected models"
    4491 
    4492  > save working_2.cxs
    4493 
    4494  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4495  Restoring stepper: working_noh_real_space_refined.pdb
    4496  opened ChimeraX session
    4497 
    4498  > save
    4499  >
    4500  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4501  > models #2
    4502 
    4503  > close #2
    4504 
    4505  > open
    4506  >
    4507  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4508 
    4509  Summary of feedback from opening
    4510  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4511  ---
    4512  warnings | End residue of secondary structure not found: HELIX 55 55 THR C
    4513  19
    4514  GLY C 21 1 3
    4515  Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C
    4516  34
    4517  1 7
    4518  Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C
    4519  55
    4520  1 3
    4521  Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C
    4522  69
    4523  1 6
    4524  Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C
    4525  81
    4526  1 7
    4527  Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C
    4528  91
    4529  1 3
    4530  5 messages similar to the above omitted
    4531  Cannot find LINK/SSBOND residue GCU (2 )
    4532  Cannot find LINK/SSBOND residue XYS (3 )
    4533  Cannot find LINK/SSBOND residue RAM (4 )
    4534  Cannot find LINK/SSBOND residue MAN (1 )
    4535  Cannot find LINK/SSBOND residue GCU (2 )
    4536  3 messages similar to the above omitted
    4537 
    4538  Chain information for working_2.pdb #8
    4539  ---
    4540  Chain | Description
    4541  AA | No description available
    4542  AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4543  description available
    4544  BA BC BF BG BH BJ BK BL BM BN BO BP BQ BR BS BT BU BX ba bb bc bd be bf bg
    4545  bh
    4546  bi bj bk bl bm bo bp | No description available
    4547  BB BD BE BI BV BW bn | No description available
    4548  C | No description available
    4549  C1 | No description available
    4550  C2 | No description available
    4551  H1 | No description available
    4552  H2 | No description available
    4553  L | No description available
    4554  M | No description available
    4555  aa | No description available
    4556  ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available
    4557 
    4558 
    4559  > open
    4560  >
    4561  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    4562 
    4563  Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    4564  0.0224, step 2, values float32
    4565 
    4566  > clipper associate #9 toModel #8
    4567 
    4568  Chain information for working_2.pdb
    4569  ---
    4570  Chain | Description
    4571  8.2/AA | No description available
    4572  8.2/AB 8.2/AC 8.2/AD 8.2/AE 8.2/AF 8.2/AG 8.2/AH 8.2/AI 8.2/AJ 8.2/AK
    4573  8.2/AL
    4574  8.2/AM 8.2/AN 8.2/AO 8.2/AP 8.2/AQ 8.2/AR 8.2/AS 8.2/AT 8.2/AU 8.2/AV
    4575  8.2/AW
    4576  8.2/AX | No description available
    4577  8.2/BA 8.2/BC 8.2/BF 8.2/BG 8.2/BH 8.2/BJ 8.2/BK 8.2/BL 8.2/BM 8.2/BN
    4578  8.2/BO
    4579  8.2/BP 8.2/BQ 8.2/BR 8.2/BS 8.2/BT 8.2/BU 8.2/BX 8.2/ba 8.2/bb 8.2/bc
    4580  8.2/bd
    4581  8.2/be 8.2/bf 8.2/bg 8.2/bh 8.2/bi 8.2/bj 8.2/bk 8.2/bl 8.2/bm 8.2/bo
    4582  8.2/bp |
    4583  No description available
    4584  8.2/BB 8.2/BD 8.2/BE 8.2/BI 8.2/BV 8.2/BW 8.2/bn | No description
    4585  available
    4586  8.2/C | No description available
    4587  8.2/C1 | No description available
    4588  8.2/C2 | No description available
    4589  8.2/H1 | No description available
    4590  8.2/H2 | No description available
    4591  8.2/L | No description available
    4592  8.2/M | No description available
    4593  8.2/aa | No description available
    4594  8.2/ab 8.2/ac 8.2/ad 8.2/ae 8.2/af 8.2/ag 8.2/ah 8.2/ai 8.2/aj 8.2/ak
    4595  8.2/al
    4596  8.2/am 8.2/an 8.2/ao 8.2/ap | No description available
    4597 
    4598 
    4599  > close #1
    4600 
    4601  > close #2
    4602 
    4603  > select #3
    4604 
    4605  508 atoms, 513 bonds, 36 residues, 8 models selected
    4606 
    4607  > hide #!4 models
    4608 
    4609  > select #8/ak
    4610 
    4611  1079 atoms, 1095 bonds, 4 pseudobonds, 61 residues, 2 models selected
    4612 
    4613  > hide #!3 models
    4614 
    4615  > show #!3 models
    4616 
    4617  > close #4
    4618 
    4619  > view #3
    4620 
    4621  > show #3
    4622 
    4623  > hide #!3 models
    4624 
    4625  > show #!3 models
    4626 
    4627  > view #3
    4628 
    4629  > close #3
    4630 
    4631  > close #5
    4632 
    4633  > close #6
    4634 
    4635  > close #7
    4636 
    4637  > volume gaussian #8 bfactor 50
    4638 
    4639  > clipper associate #1 toModel #8
    4640 
    4641  > select clear
    4642 
    4643  > save reopened.cxs
    4644 
    4645  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4646  Traceback (most recent call last):
    4647  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4648  packages/chimerax/core/session.py", line 280, in process
    4649  data = sm.take_snapshot(obj, session, self.state_flags)
    4650  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4651  packages/chimerax/atomic/molobject.py", line 633, in take_snapshot
    4652  data = {'structure': self.structure,
    4653  File "cymol.pyx", line 1437, in
    4654  chimerax.atomic.cymol.CyResidue.structure.__get__
    4655  RuntimeError: Residue already deleted
    4656 
    4657  The above exception was the direct cause of the following exception:
    4658 
    4659  Traceback (most recent call last):
    4660  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4661  packages/chimerax/core/session.py", line 259, in discovery
    4662  self.processed[key] = self.process(obj, parents)
    4663  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4664  packages/chimerax/core/session.py", line 283, in process
    4665  raise RuntimeError(msg) from e
    4666  RuntimeError: Error while saving session data for 'isolde residue stepper
    4667  1'
    4668  -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4669  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4670 
    4671  During handling of the above exception, another exception occurred:
    4672 
    4673  Traceback (most recent call last):
    4674  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4675  packages/chimerax/core/session.py", line 826, in save
    4676  session.save(output, version=version, include_maps=include_maps)
    4677  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4678  packages/chimerax/core/session.py", line 583, in save
    4679  mgr.discovery(self._state_containers)
    4680  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4681  packages/chimerax/core/session.py", line 261, in discovery
    4682  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4683  e))
    4684  ValueError: error processing: 'isolde residue stepper 1' ->
    4685  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4686  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4687  saving session data for 'isolde residue stepper 1' ->
    4688  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4689  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4690 
    4691  ValueError: error processing: 'isolde residue stepper 1' -> -> : Error
    4692  while
    4693  saving session data for 'isolde residue stepper 1' -> ->
    4694 
    4695  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4696  packages/chimerax/core/session.py", line 261, in discovery
    4697  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4698  e))
    4699 
    4700  See log for complete Python traceback.
    4701 
    4702  Traceback (most recent call last):
    4703  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4704  packages/chimerax/core/session.py", line 280, in process
    4705  data = sm.take_snapshot(obj, session, self.state_flags)
    4706  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4707  packages/chimerax/atomic/molobject.py", line 633, in take_snapshot
    4708  data = {'structure': self.structure,
    4709  File "cymol.pyx", line 1437, in
    4710  chimerax.atomic.cymol.CyResidue.structure.__get__
    4711  RuntimeError: Residue already deleted
    4712 
    4713  The above exception was the direct cause of the following exception:
    4714 
    4715  Traceback (most recent call last):
    4716  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4717  packages/chimerax/core/session.py", line 259, in discovery
    4718  self.processed[key] = self.process(obj, parents)
    4719  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4720  packages/chimerax/core/session.py", line 283, in process
    4721  raise RuntimeError(msg) from e
    4722  RuntimeError: Error while saving session data for 'isolde residue stepper
    4723  1'
    4724  -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4725  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4726 
    4727  During handling of the above exception, another exception occurred:
    4728 
    4729  Traceback (most recent call last):
    4730  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4731  packages/chimerax/cmd_line/tool.py", line 275, in execute
    4732  cmd.run(cmd_text)
    4733  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4734  packages/chimerax/core/commands/cli.py", line 2805, in run
    4735  result = ci.function(session, **kw_args)
    4736  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4737  packages/chimerax/save_command/cmd.py", line 66, in cmd_save
    4738  Command(session, registry=registry).run(provider_cmd_text, log=log)
    4739  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4740  packages/chimerax/core/commands/cli.py", line 2805, in run
    4741  result = ci.function(session, **kw_args)
    4742  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4743  packages/chimerax/save_command/cmd.py", line 79, in provider_save
    4744  mgr).save(session, path, **provider_kw)
    4745  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4746  packages/chimerax/core_formats/__init__.py", line 79, in save
    4747  return cxs_save(session, path, **kw)
    4748  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4749  packages/chimerax/core/session.py", line 826, in save
    4750  session.save(output, version=version, include_maps=include_maps)
    4751  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4752  packages/chimerax/core/session.py", line 583, in save
    4753  mgr.discovery(self._state_containers)
    4754  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4755  packages/chimerax/core/session.py", line 261, in discovery
    4756  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4757  e))
    4758  ValueError: error processing: 'isolde residue stepper 1' ->
    4759  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4760  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4761  saving session data for 'isolde residue stepper 1' ->
    4762  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4763  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4764 
    4765  ValueError: error processing: 'isolde residue stepper 1' -> -> : Error
    4766  while
    4767  saving session data for 'isolde residue stepper 1' -> ->
    4768 
    4769  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4770  packages/chimerax/core/session.py", line 261, in discovery
    4771  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4772  e))
    4773 
    4774  See log for complete Python traceback.
    4775 
    4776 
    4777  > isolde stepto sel
    4778 
    4779  > select up
    4780 
    4781  10 atoms, 9 bonds, 1 residue, 1 model selected
    4782 
    4783  > save reopened.cxs
    4784 
    4785  Taking snapshot of stepper: working_2.pdb
    4786  Taking snapshot of stepper: working_noh_real_space_refined.pdb
    4787  Traceback (most recent call last):
    4788  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4789  packages/chimerax/core/session.py", line 280, in process
    4790  data = sm.take_snapshot(obj, session, self.state_flags)
    4791  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4792  packages/chimerax/atomic/molobject.py", line 633, in take_snapshot
    4793  data = {'structure': self.structure,
    4794  File "cymol.pyx", line 1437, in
    4795  chimerax.atomic.cymol.CyResidue.structure.__get__
    4796  RuntimeError: Residue already deleted
    4797 
    4798  The above exception was the direct cause of the following exception:
    4799 
    4800  Traceback (most recent call last):
    4801  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4802  packages/chimerax/core/session.py", line 259, in discovery
    4803  self.processed[key] = self.process(obj, parents)
    4804  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4805  packages/chimerax/core/session.py", line 283, in process
    4806  raise RuntimeError(msg) from e
    4807  RuntimeError: Error while saving session data for 'isolde residue stepper
    4808  1'
    4809  -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4810  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4811 
    4812  During handling of the above exception, another exception occurred:
    4813 
    4814  Traceback (most recent call last):
    4815  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4816  packages/chimerax/core/session.py", line 826, in save
    4817  session.save(output, version=version, include_maps=include_maps)
    4818  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4819  packages/chimerax/core/session.py", line 583, in save
    4820  mgr.discovery(self._state_containers)
    4821  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4822  packages/chimerax/core/session.py", line 261, in discovery
    4823  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4824  e))
    4825  ValueError: error processing: 'isolde residue stepper 1' ->
    4826  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4827  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4828  saving session data for 'isolde residue stepper 1' ->
    4829  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4830  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4831 
    4832  ValueError: error processing: 'isolde residue stepper 1' -> -> : Error
    4833  while
    4834  saving session data for 'isolde residue stepper 1' -> ->
    4835 
    4836  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4837  packages/chimerax/core/session.py", line 261, in discovery
    4838  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4839  e))
    4840 
    4841  See log for complete Python traceback.
    4842 
    4843  Traceback (most recent call last):
    4844  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4845  packages/chimerax/core/session.py", line 280, in process
    4846  data = sm.take_snapshot(obj, session, self.state_flags)
    4847  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4848  packages/chimerax/atomic/molobject.py", line 633, in take_snapshot
    4849  data = {'structure': self.structure,
    4850  File "cymol.pyx", line 1437, in
    4851  chimerax.atomic.cymol.CyResidue.structure.__get__
    4852  RuntimeError: Residue already deleted
    4853 
    4854  The above exception was the direct cause of the following exception:
    4855 
    4856  Traceback (most recent call last):
    4857  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4858  packages/chimerax/core/session.py", line 259, in discovery
    4859  self.processed[key] = self.process(obj, parents)
    4860  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4861  packages/chimerax/core/session.py", line 283, in process
    4862  raise RuntimeError(msg) from e
    4863  RuntimeError: Error while saving session data for 'isolde residue stepper
    4864  1'
    4865  -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4866  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4867 
    4868  During handling of the above exception, another exception occurred:
    4869 
    4870  Traceback (most recent call last):
    4871  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4872  packages/chimerax/cmd_line/tool.py", line 275, in execute
    4873  cmd.run(cmd_text)
    4874  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4875  packages/chimerax/core/commands/cli.py", line 2805, in run
    4876  result = ci.function(session, **kw_args)
    4877  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4878  packages/chimerax/save_command/cmd.py", line 66, in cmd_save
    4879  Command(session, registry=registry).run(provider_cmd_text, log=log)
    4880  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4881  packages/chimerax/core/commands/cli.py", line 2805, in run
    4882  result = ci.function(session, **kw_args)
    4883  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4884  packages/chimerax/save_command/cmd.py", line 79, in provider_save
    4885  mgr).save(session, path, **provider_kw)
    4886  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4887  packages/chimerax/core_formats/__init__.py", line 79, in save
    4888  return cxs_save(session, path, **kw)
    4889  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4890  packages/chimerax/core/session.py", line 826, in save
    4891  session.save(output, version=version, include_maps=include_maps)
    4892  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4893  packages/chimerax/core/session.py", line 583, in save
    4894  mgr.discovery(self._state_containers)
    4895  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4896  packages/chimerax/core/session.py", line 261, in discovery
    4897  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4898  e))
    4899  ValueError: error processing: 'isolde residue stepper 1' ->
    4900  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4901  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4902  saving session data for 'isolde residue stepper 1' ->
    4903  <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4904  <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>
    4905 
    4906  ValueError: error processing: 'isolde residue stepper 1' -> -> : Error
    4907  while
    4908  saving session data for 'isolde residue stepper 1' -> ->
    4909 
    4910  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4911  packages/chimerax/core/session.py", line 261, in discovery
    4912  raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj),
    4913  e))
    4914 
    4915  See log for complete Python traceback.
    4916 
    4917 
    4918  > save reopened.cxs
    4919 
    4920  Taking snapshot of stepper: working_2.pdb
    4921 
    4922  > ui tool show "Build Structure"
    4923 
    4924  > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4925  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4926  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4927 
    4928  Chain information for custom built #1
    4929  ---
    4930  Chain | Description
    4931  A | No description available
    4932 
    4933 
    4934  > addh #1
    4935 
    4936  Summary of feedback from adding hydrogens to custom built #1
    4937  ---
    4938  notes | No usable SEQRES records for custom built (#1) chain A; guessing
    4939  termini instead
    4940  Chain-initial residues that are actual N termini: custom built #1/A ALA 1
    4941  Chain-initial residues that are not actual N termini:
    4942  Chain-final residues that are actual C termini: custom built #1/A ARG 11
    4943  Chain-final residues that are not actual C termini:
    4944  0 hydrogen bonds
    4945  80 hydrogens added
    4946 
    4947 
    4948  > select #1
    4949 
    4950  158 atoms, 160 bonds, 11 residues, 1 model selected
    4951 
    4952  > show sel
    4953 
    4954  > ui mousemode right "translate selected models"
    4955 
    4956  > ui mousemode right "rotate selected models"
    4957 
    4958  > ui mousemode right "translate selected models"
    4959 
    4960  > save reopened.cxs
    4961 
    4962  Taking snapshot of stepper: working_2.pdb
    4963  Restoring stepper: working_2.pdb
    4964  opened ChimeraX session
    4965 
    4966  > ui tool show Shell
    4967 
    4968  /opt/UCSF/ChimeraX/lib/python3.7/site-
    4969  packages/IPython/core/history.py:226:
    4970  UserWarning: IPython History requires SQLite, your history will not be
    4971  saved
    4972  warn("IPython History requires SQLite, your history will not be saved")
    4973 
    4974  > isolde start
    4975 
    4976  > set selectionWidth 4
    4977 
    4978  Done loading forcefield
    4979 
    4980  > select clear
    4981 
    4982  > select clear
    4983 
    4984  > select ~protein
    4985 
    4986  16729 atoms, 17062 bonds, 366 pseudobonds, 140 residues, 23 models
    4987  selected
    4988 
    4989  > select /ak
    4990 
    4991  1238 atoms, 1261 bonds, 72 residues, 1 model selected
    4992 
    4993  > hide #!1 models
    4994 
    4995  > select up
    4996 
    4997  45 atoms, 44 bonds, 2 residues, 1 model selected
    4998 
    4999  > select up
    5000 
    5001  71 atoms, 71 bonds, 4 residues, 1 model selected
    5002 
    5003  > isolde ignore sel
    5004 
    5005  ISOLDE: currently ignoring 4 residues in model 8.2
    5006 
    5007  > select up
    5008 
    5009  11 atoms, 10 bonds, 1 residue, 1 model selected
    5010 
    5011  > select up
    5012 
    5013  939 atoms, 951 bonds, 60 residues, 1 model selected
    5014 
    5015  > select up
    5016 
    5017  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    5018 
    5019  > select up
    5020 
    5021  1179 atoms, 1198 bonds, 62 residues, 1 model selected
    5022 
    5023  > isolde ignore sel
    5024 
    5025  ISOLDE: currently ignoring 66 residues in model 8.2
    5026 
    5027  > select up
    5028 
    5029  20 atoms, 19 bonds, 1 residue, 1 model selected
    5030 
    5031  > select up
    5032 
    5033  159 atoms, 161 bonds, 11 residues, 1 model selected
    5034 
    5035  Chain CG, residue 1 specifies more than one residue! The simulation can
    5036  still
    5037  run, but this will probably cause problems later if not rectified by
    5038  renumbering.
    5039 
    5040  Chain CG, residue 2 specifies more than one residue! The simulation can
    5041  still
    5042  run, but this will probably cause problems later if not rectified by
    5043  renumbering.
    5044 
    5045  Chain CG, residue 3 specifies more than one residue! The simulation can
    5046  still
    5047  run, but this will probably cause problems later if not rectified by
    5048  renumbering.
    5049 
    5050  Chain ak, residue 67 specifies more than one residue! The simulation can
    5051  still
    5052  run, but this will probably cause problems later if not rectified by
    5053  renumbering.
    5054 
    5055  Chain CG, residue 1 specifies more than one residue! The simulation can
    5056  still
    5057  run, but this will probably cause problems later if not rectified by
    5058  renumbering.
    5059 
    5060  Chain CG, residue 2 specifies more than one residue! The simulation can
    5061  still
    5062  run, but this will probably cause problems later if not rectified by
    5063  renumbering.
    5064 
    5065  Chain CG, residue 3 specifies more than one residue! The simulation can
    5066  still
    5067  run, but this will probably cause problems later if not rectified by
    5068  renumbering.
    5069 
    5070  Chain ak, residue 67 specifies more than one residue! The simulation can
    5071  still
    5072  run, but this will probably cause problems later if not rectified by
    5073  renumbering.
    5074 
    5075  > delete sel
    5076 
    5077  > delete sel
    5078 
    5079  > delete sel
    5080 
    5081  > delete sel
    5082 
    5083  > select up
    5084 
    5085  99 atoms, 102 bonds, 4 residues, 1 model selected
    5086 
    5087  > select clear
    5088 
    5089  Chain ak, residue 67 specifies more than one residue! The simulation can
    5090  still
    5091  run, but this will probably cause problems later if not rectified by
    5092  renumbering.
    5093 
    5094  > select /ak
    5095 
    5096  1234 atoms, 1257 bonds, 72 residues, 1 model selected
    5097 
    5098  > select up
    5099 
    5100  10 atoms, 9 bonds, 1 residue, 1 model selected
    5101 
    5102  > select up
    5103 
    5104  155 atoms, 157 bonds, 11 residues, 1 model selected
    5105 
    5106  Chain ak, residue 67 specifies more than one residue! The simulation can
    5107  still
    5108  run, but this will probably cause problems later if not rectified by
    5109  renumbering.
    5110 
    5111  Chain ak, residue 67 specifies more than one residue! The simulation can
    5112  still
    5113  run, but this will probably cause problems later if not rectified by
    5114  renumbering.
    5115 
    5116  > select /MG
    5117 
    5118  99 atoms, 102 bonds, 4 residues, 1 model selected
    5119 
    5120  > select up
    5121 
    5122  42 atoms, 42 bonds, 1 residue, 1 model selected
    5123 
    5124  > select clear
    5125 
    5126  > select sel&:MG
    5127 
    5128  Nothing selected
    5129 
    5130  > select sel&/MG
    5131 
    5132  21 atoms, 21 bonds, 1 residue, 1 model selected
    5133 
    5134  > select up
    5135 
    5136  42 atoms, 42 bonds, 1 residue, 1 model selected
    5137 
    5138  > select clear
    5139 
    5140  > select up
    5141 
    5142  99 atoms, 102 bonds, 4 residues, 1 model selected
    5143 
    5144  > select clear
    5145 
    5146  > select up
    5147 
    5148  42 atoms, 42 bonds, 1 residue, 1 model selected
    5149 
    5150  > delete sel
    5151 
    5152  > isolde add ligand RAM
    5153 
    5154  Deleted the following atoms from residue RAM CG4: O1, HO1
    5155 
    5156  > ui mousemode right "translate selected atoms"
    5157 
    5158  > clipper set contourSensitivity 0.25
    5159 
    5160  > select clear
    5161 
    5162  > isolde add ligand RAM
    5163 
    5164  Deleted the following atoms from residue RAM MG4: HO1, O1
    5165 
    5166  > delete sel
    5167 
    5168  > isolde add ligand RAM
    5169 
    5170  Deleted the following atoms from residue RAM MG4: HO1, O1
    5171 
    5172  > ui mousemode right "translate selected atoms"
    5173 
    5174  > select clear
    5175 
    5176  > select /ak
    5177 
    5178  1234 atoms, 1257 bonds, 72 residues, 1 model selected
    5179 
    5180  > select up
    5181 
    5182  10 atoms, 9 bonds, 1 residue, 1 model selected
    5183 
    5184  > select up
    5185 
    5186  155 atoms, 157 bonds, 11 residues, 1 model selected
    5187 
    5188  Chain ak, residue 67 specifies more than one residue! The simulation can
    5189  still
    5190  run, but this will probably cause problems later if not rectified by
    5191  renumbering.
    5192 
    5193  > select clear
    5194 
    5195  > select up
    5196 
    5197  15 atoms, 14 bonds, 1 residue, 1 model selected
    5198 
    5199  > select up
    5200 
    5201  155 atoms, 157 bonds, 11 residues, 1 model selected
    5202 
    5203  Chain ak, residue 67 specifies more than one residue! The simulation can
    5204  still
    5205  run, but this will probably cause problems later if not rectified by
    5206  renumbering.
    5207 
    5208  > select clear
    5209 
    5210  Chain ak, residue 67 specifies more than one residue! The simulation can
    5211  still
    5212  run, but this will probably cause problems later if not rectified by
    5213  renumbering.
    5214 
    5215  > select clear
    5216 
    5217  > isolde ~ignore
    5218 
    5219  > save working_3.cxs
    5220 
    5221  Taking snapshot of stepper: working_2.pdb
    5222  Restoring stepper: working_2.pdb
    5223  opened ChimeraX session
    5224 
    5225  > select /ak
    5226 
    5227  1234 atoms, 1257 bonds, 72 residues, 1 model selected
    5228 
    5229  > select clear
    5230 
    5231  > dssp
    5232 
    5233  > select /AA
    5234 
    5235  981 atoms, 1002 bonds, 48 residues, 1 model selected
    5236 
    5237  > isolde stepto /AB
    5238 
    5239  Multiple residues selected! Going to the first...
    5240 
    5241  > clipper set contourSensitivity 0.25
    5242 
    5243  > select /AB
    5244 
    5245  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5246 
    5247  > select clear
    5248 
    5249  > isolde stepto
    5250 
    5251  > isolde stepto
    5252 
    5253  > isolde stepto
    5254 
    5255  > isolde stepto
    5256 
    5257  > isolde stepto
    5258 
    5259  > isolde stepto
    5260 
    5261  > isolde stepto
    5262 
    5263  > isolde stepto
    5264 
    5265  > isolde stepto
    5266 
    5267  > isolde stepto
    5268 
    5269  > isolde stepto
    5270 
    5271  > isolde stepto
    5272 
    5273  > isolde stepto
    5274 
    5275  > isolde stepto
    5276 
    5277  > isolde stepto
    5278 
    5279  > isolde stepto
    5280 
    5281  > isolde stepto
    5282 
    5283  > isolde stepto
    5284 
    5285  > isolde stepto
    5286 
    5287  > isolde stepto
    5288 
    5289  > isolde stepto
    5290 
    5291  > isolde stepto
    5292 
    5293  > isolde stepto
    5294 
    5295  > isolde stepto
    5296 
    5297  > isolde stepto
    5298 
    5299  > isolde stepto
    5300 
    5301  > isolde stepto
    5302 
    5303  > isolde stepto
    5304 
    5305  > isolde stepto
    5306 
    5307  > isolde stepto
    5308 
    5309  > isolde stepto
    5310 
    5311  > isolde stepto
    5312 
    5313  > isolde stepto
    5314 
    5315  > isolde stepto
    5316 
    5317  > isolde stepto
    5318 
    5319  > isolde stepto
    5320 
    5321  > isolde stepto
    5322 
    5323  > isolde stepto
    5324 
    5325  > isolde stepto
    5326 
    5327  > isolde stepto
    5328 
    5329  > isolde stepto
    5330 
    5331  > isolde stepto
    5332 
    5333  > isolde stepto
    5334 
    5335  > isolde stepto
    5336 
    5337  > select clear
    5338 
    5339  > select clear
    5340 
    5341  > isolde stepto
    5342 
    5343  > isolde stepto
    5344 
    5345  > isolde stepto
    5346 
    5347  > isolde stepto
    5348 
    5349  > select /AC
    5350 
    5351  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5352 
    5353  > select clear
    5354 
    5355  > isolde stepto
    5356 
    5357  > isolde stepto
    5358 
    5359  > isolde stepto
    5360 
    5361  > isolde stepto
    5362 
    5363  > isolde stepto
    5364 
    5365  > isolde stepto
    5366 
    5367  > isolde stepto
    5368 
    5369  > isolde stepto
    5370 
    5371  > isolde stepto
    5372 
    5373  > isolde stepto
    5374 
    5375  > isolde stepto
    5376 
    5377  > isolde stepto
    5378 
    5379  > isolde stepto
    5380 
    5381  > isolde stepto
    5382 
    5383  > isolde stepto
    5384 
    5385  > isolde stepto
    5386 
    5387  > isolde stepto
    5388 
    5389  > isolde stepto
    5390 
    5391  > isolde stepto
    5392 
    5393  > isolde stepto
    5394 
    5395  > isolde stepto
    5396 
    5397  > isolde stepto
    5398 
    5399  > isolde stepto
    5400 
    5401  > isolde stepto
    5402 
    5403  > isolde stepto
    5404 
    5405  > isolde stepto
    5406 
    5407  > isolde stepto
    5408 
    5409  > isolde stepto
    5410 
    5411  > isolde stepto
    5412 
    5413  > isolde stepto
    5414 
    5415  > isolde stepto
    5416 
    5417  > isolde stepto
    5418 
    5419  > isolde stepto
    5420 
    5421  > isolde stepto
    5422 
    5423  > isolde stepto
    5424 
    5425  > isolde stepto
    5426 
    5427  > isolde stepto
    5428 
    5429  > isolde stepto
    5430 
    5431  > isolde stepto
    5432 
    5433  > isolde stepto
    5434 
    5435  > select clear
    5436 
    5437  > isolde stepto
    5438 
    5439  > isolde stepto
    5440 
    5441  > isolde stepto
    5442 
    5443  > isolde stepto
    5444 
    5445  > isolde stepto
    5446 
    5447  > isolde stepto prev
    5448 
    5449  > isolde ignore sel
    5450 
    5451  ISOLDE: currently ignoring 1 residues in model 8.2
    5452 
    5453  > select clear
    5454 
    5455  > isolde stepto
    5456 
    5457  > isolde stepto
    5458 
    5459  > isolde stepto
    5460 
    5461  > select /AD
    5462 
    5463  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5464 
    5465  > select clear
    5466 
    5467  > isolde stepto
    5468 
    5469  > isolde stepto
    5470 
    5471  > isolde stepto
    5472 
    5473  > isolde stepto
    5474 
    5475  > isolde stepto
    5476 
    5477  > isolde stepto
    5478 
    5479  > isolde stepto
    5480 
    5481  > isolde stepto
    5482 
    5483  > isolde stepto
    5484 
    5485  > isolde stepto
    5486 
    5487  > isolde stepto
    5488 
    5489  > isolde stepto
    5490 
    5491  > isolde stepto
    5492 
    5493  > isolde stepto
    5494 
    5495  > isolde stepto
    5496 
    5497  > isolde stepto
    5498 
    5499  > isolde stepto
    5500 
    5501  > isolde stepto
    5502 
    5503  > isolde stepto
    5504 
    5505  > isolde stepto
    5506 
    5507  > isolde stepto
    5508 
    5509  > isolde stepto
    5510 
    5511  > isolde stepto
    5512 
    5513  > isolde stepto
    5514 
    5515  > isolde stepto
    5516 
    5517  > isolde stepto
    5518 
    5519  > isolde stepto
    5520 
    5521  > isolde stepto
    5522 
    5523  > isolde stepto
    5524 
    5525  > isolde stepto
    5526 
    5527  > isolde stepto
    5528 
    5529  > isolde stepto
    5530 
    5531  > isolde stepto
    5532 
    5533  > isolde stepto
    5534 
    5535  > isolde stepto
    5536 
    5537  > isolde stepto
    5538 
    5539  > isolde stepto
    5540 
    5541  > isolde stepto
    5542 
    5543  > isolde stepto
    5544 
    5545  > isolde stepto
    5546 
    5547  > isolde stepto
    5548 
    5549  > isolde stepto
    5550 
    5551  > isolde stepto
    5552 
    5553  > isolde stepto
    5554 
    5555  > select clear
    5556 
    5557  > isolde stepto
    5558 
    5559  > isolde stepto
    5560 
    5561  > isolde stepto
    5562 
    5563  > select /AE
    5564 
    5565  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5566 
    5567  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5568  bonded heavy atom.
    5569 
    5570  > select clear
    5571 
    5572  > isolde stepto
    5573 
    5574  > isolde stepto
    5575 
    5576  > isolde stepto
    5577 
    5578  > isolde stepto
    5579 
    5580  > isolde stepto
    5581 
    5582  > isolde stepto
    5583 
    5584  > isolde stepto
    5585 
    5586  > isolde stepto
    5587 
    5588  > isolde stepto
    5589 
    5590  > isolde stepto
    5591 
    5592  > isolde stepto
    5593 
    5594  > isolde stepto
    5595 
    5596  > isolde stepto
    5597 
    5598  > isolde stepto
    5599 
    5600  > isolde stepto
    5601 
    5602  > isolde stepto
    5603 
    5604  > isolde stepto
    5605 
    5606  > isolde stepto
    5607 
    5608  > isolde stepto
    5609 
    5610  > isolde stepto
    5611 
    5612  > isolde stepto
    5613 
    5614  > isolde stepto
    5615 
    5616  > isolde stepto
    5617 
    5618  > isolde stepto
    5619 
    5620  > isolde stepto
    5621 
    5622  > isolde stepto
    5623 
    5624  > isolde stepto
    5625 
    5626  > isolde stepto
    5627 
    5628  > isolde stepto
    5629 
    5630  > isolde stepto
    5631 
    5632  > isolde stepto
    5633 
    5634  > isolde stepto
    5635 
    5636  > isolde stepto
    5637 
    5638  > isolde stepto
    5639 
    5640  > isolde stepto
    5641 
    5642  > isolde stepto
    5643 
    5644  > isolde stepto
    5645 
    5646  > isolde stepto
    5647 
    5648  > isolde stepto
    5649 
    5650  > select clear
    5651 
    5652  > isolde stepto
    5653 
    5654  > isolde stepto
    5655 
    5656  > isolde stepto
    5657 
    5658  > isolde stepto
    5659 
    5660  > isolde stepto
    5661 
    5662  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5663  bonded heavy atom.
    5664 
    5665  > select clear
    5666 
    5667  > select clear
    5668 
    5669  > isolde stepto
    5670 
    5671  > isolde stepto
    5672 
    5673  > isolde stepto
    5674 
    5675  > isolde stepto
    5676 
    5677  > select /AF
    5678 
    5679  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5680 
    5681  > select clear
    5682 
    5683  > isolde stepto
    5684 
    5685  > isolde stepto
    5686 
    5687  > isolde stepto
    5688 
    5689  > isolde stepto
    5690 
    5691  > isolde stepto
    5692 
    5693  > isolde stepto
    5694 
    5695  > isolde stepto
    5696 
    5697  > isolde stepto
    5698 
    5699  > isolde stepto
    5700 
    5701  > isolde stepto
    5702 
    5703  > isolde stepto
    5704 
    5705  > isolde stepto
    5706 
    5707  > isolde stepto
    5708 
    5709  > isolde stepto
    5710 
    5711  > isolde stepto
    5712 
    5713  > isolde stepto
    5714 
    5715  > isolde stepto
    5716 
    5717  > isolde stepto
    5718 
    5719  > isolde stepto
    5720 
    5721  > isolde stepto
    5722 
    5723  > isolde stepto
    5724 
    5725  > isolde stepto
    5726 
    5727  > isolde stepto
    5728 
    5729  > isolde stepto
    5730 
    5731  > isolde stepto
    5732 
    5733  > isolde stepto
    5734 
    5735  > isolde stepto
    5736 
    5737  > isolde stepto
    5738 
    5739  > isolde stepto
    5740 
    5741  > isolde stepto
    5742 
    5743  > isolde stepto
    5744 
    5745  > isolde stepto
    5746 
    5747  > isolde stepto
    5748 
    5749  > isolde stepto
    5750 
    5751  > isolde stepto
    5752 
    5753  > isolde stepto
    5754 
    5755  > isolde stepto
    5756 
    5757  > isolde stepto
    5758 
    5759  > isolde stepto
    5760 
    5761  > isolde stepto
    5762 
    5763  > isolde stepto
    5764 
    5765  > isolde stepto
    5766 
    5767  > isolde stepto
    5768 
    5769  > isolde stepto
    5770 
    5771  > swapaa mousemode sel PRO
    5772 
    5773  Traceback (most recent call last):
    5774  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5775  packages/chimerax/isolde/isolde.py", line 2707, in
    5776  _start_sim_or_toggle_pause
    5777  self.start_sim()
    5778  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5779  packages/chimerax/isolde/isolde.py", line 2724, in start_sim
    5780  main_sel = self._last_main_sel = self._get_main_sim_selection()
    5781  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5782  packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
    5783  raise TypeError('You must select at least one atom from the current '
    5784  TypeError: You must select at least one atom from the current working
    5785  model
    5786  prior to starting a simulation!
    5787 
    5788  TypeError: You must select at least one atom from the current working
    5789  model
    5790  prior to starting a simulation!
    5791 
    5792  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5793  packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
    5794  raise TypeError('You must select at least one atom from the current '
    5795 
    5796  See log for complete Python traceback.
    5797 
    5798 
    5799  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5800  bonded heavy atom.
    5801 
    5802  > select clear
    5803 
    5804  > isolde stepto
    5805 
    5806  > isolde stepto
    5807 
    5808  > isolde stepto
    5809 
    5810  > isolde stepto
    5811 
    5812  > select /AG
    5813 
    5814  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5815 
    5816  > select clear
    5817 
    5818  > isolde stepto
    5819 
    5820  > isolde stepto
    5821 
    5822  > isolde stepto
    5823 
    5824  > isolde stepto
    5825 
    5826  > isolde stepto
    5827 
    5828  > isolde stepto
    5829 
    5830  > isolde stepto
    5831 
    5832  > isolde stepto
    5833 
    5834  > isolde stepto
    5835 
    5836  > isolde stepto
    5837 
    5838  > isolde stepto
    5839 
    5840  > isolde stepto
    5841 
    5842  > isolde stepto
    5843 
    5844  > select /AG
    5845 
    5846  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5847 
    5848  > select /AG, ak
    5849 
    5850  2214 atoms, 2258 bonds, 120 residues, 1 model selected
    5851 
    5852  > select /AG
    5853 
    5854  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5855 
    5856  > select clear
    5857 
    5858  > isolde stepto
    5859 
    5860  > isolde stepto
    5861 
    5862  > isolde stepto
    5863 
    5864  > isolde stepto
    5865 
    5866  > isolde stepto
    5867 
    5868  > isolde stepto
    5869 
    5870  > isolde stepto
    5871 
    5872  > isolde stepto
    5873 
    5874  > isolde stepto
    5875 
    5876  > isolde stepto
    5877 
    5878  > isolde stepto
    5879 
    5880  > isolde stepto
    5881 
    5882  > isolde stepto
    5883 
    5884  > isolde stepto
    5885 
    5886  > isolde stepto
    5887 
    5888  > isolde stepto
    5889 
    5890  > isolde stepto
    5891 
    5892  > isolde stepto
    5893 
    5894  > isolde stepto
    5895 
    5896  > isolde stepto
    5897 
    5898  > isolde stepto
    5899 
    5900  > isolde stepto
    5901 
    5902  > isolde stepto
    5903 
    5904  > isolde stepto
    5905 
    5906  > isolde stepto
    5907 
    5908  > isolde stepto
    5909 
    5910  > isolde stepto
    5911 
    5912  > select clear
    5913 
    5914  > isolde stepto
    5915 
    5916  > isolde stepto
    5917 
    5918  > isolde stepto
    5919 
    5920  > isolde stepto
    5921 
    5922  > select clear
    5923 
    5924  > select clear
    5925 
    5926  > isolde stepto
    5927 
    5928  > isolde stepto
    5929 
    5930  > isolde stepto
    5931 
    5932  > isolde stepto
    5933 
    5934  > select /AH
    5935 
    5936  980 atoms, 1001 bonds, 48 residues, 1 model selected
    5937 
    5938  > select clear
    5939 
    5940  > isolde stepto
    5941 
    5942  > isolde stepto
    5943 
    5944  > isolde stepto
    5945 
    5946  > isolde stepto
    5947 
    5948  > isolde stepto
    5949 
    5950  > isolde stepto
    5951 
    5952  > isolde stepto
    5953 
    5954  > isolde stepto
    5955 
    5956  > isolde stepto
    5957 
    5958  > isolde stepto
    5959 
    5960  > isolde stepto
    5961 
    5962  > isolde stepto
    5963 
    5964  > isolde stepto
    5965 
    5966  > isolde stepto
    5967 
    5968  > isolde stepto
    5969 
    5970  > isolde stepto
    5971 
    5972  > isolde stepto
    5973 
    5974  > isolde stepto
    5975 
    5976  > isolde stepto
    5977 
    5978  > isolde stepto
    5979 
    5980  > isolde stepto
    5981 
    5982  > isolde stepto
    5983 
    5984  > isolde stepto
    5985 
    5986  > isolde stepto
    5987 
    5988  > isolde stepto
    5989 
    5990  > isolde stepto
    5991 
    5992  > isolde stepto
    5993 
    5994  > isolde stepto
    5995 
    5996  > isolde stepto
    5997 
    5998  > isolde stepto
    5999 
    6000  > isolde stepto
    6001 
    6002  > isolde stepto
    6003 
    6004  > isolde stepto
    6005 
    6006  > isolde stepto
    6007 
    6008  > isolde stepto
    6009 
    6010  > isolde stepto
    6011 
    6012  > isolde stepto
    6013 
    6014  > isolde stepto
    6015 
    6016  > isolde stepto
    6017 
    6018  > isolde stepto
    6019 
    6020  > isolde stepto
    6021 
    6022  > isolde stepto
    6023 
    6024  > isolde stepto
    6025 
    6026  > isolde stepto
    6027 
    6028  > select clear
    6029 
    6030  > isolde stepto
    6031 
    6032  > isolde stepto
    6033 
    6034  > isolde stepto
    6035 
    6036  > isolde stepto
    6037 
    6038  > select /AI
    6039 
    6040  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6041 
    6042  > select clear
    6043 
    6044  > isolde stepto
    6045 
    6046  > isolde stepto
    6047 
    6048  > isolde stepto
    6049 
    6050  > isolde stepto
    6051 
    6052  > isolde stepto
    6053 
    6054  > isolde stepto
    6055 
    6056  > isolde stepto
    6057 
    6058  > isolde stepto
    6059 
    6060  > isolde stepto
    6061 
    6062  > isolde stepto
    6063 
    6064  > isolde stepto
    6065 
    6066  > isolde stepto
    6067 
    6068  > isolde stepto
    6069 
    6070  > isolde stepto
    6071 
    6072  > isolde stepto
    6073 
    6074  > isolde stepto
    6075 
    6076  > isolde stepto
    6077 
    6078  > isolde stepto
    6079 
    6080  > isolde stepto
    6081 
    6082  > isolde stepto
    6083 
    6084  > isolde stepto
    6085 
    6086  > isolde stepto
    6087 
    6088  > isolde stepto
    6089 
    6090  > isolde stepto
    6091 
    6092  > isolde stepto
    6093 
    6094  > isolde stepto
    6095 
    6096  > isolde stepto
    6097 
    6098  > isolde stepto
    6099 
    6100  > isolde stepto
    6101 
    6102  > isolde stepto
    6103 
    6104  > isolde stepto
    6105 
    6106  > isolde stepto
    6107 
    6108  > isolde stepto
    6109 
    6110  > isolde stepto
    6111 
    6112  > isolde stepto
    6113 
    6114  > isolde stepto
    6115 
    6116  > isolde stepto
    6117 
    6118  > isolde stepto
    6119 
    6120  > isolde stepto
    6121 
    6122  > isolde stepto
    6123 
    6124  > isolde stepto
    6125 
    6126  > isolde stepto
    6127 
    6128  > isolde stepto
    6129 
    6130  > isolde stepto
    6131 
    6132  > select clear
    6133 
    6134  > isolde stepto
    6135 
    6136  > isolde stepto
    6137 
    6138  > isolde stepto
    6139 
    6140  > isolde stepto
    6141 
    6142  > save working_4.cxs
    6143 
    6144  Taking snapshot of stepper: working_2.pdb
    6145 
    6146  > select /AJ
    6147 
    6148  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6149 
    6150  > select clear
    6151 
    6152  > select clear
    6153 
    6154  > select clear
    6155 
    6156  > isolde stepto
    6157 
    6158  > isolde stepto
    6159 
    6160  > isolde stepto
    6161 
    6162  > isolde stepto
    6163 
    6164  > isolde stepto
    6165 
    6166  > isolde stepto
    6167 
    6168  > isolde stepto
    6169 
    6170  > isolde stepto
    6171 
    6172  > isolde stepto
    6173 
    6174  > isolde stepto
    6175 
    6176  > isolde stepto
    6177 
    6178  > isolde stepto
    6179 
    6180  > isolde stepto
    6181 
    6182  > isolde stepto
    6183 
    6184  > isolde stepto
    6185 
    6186  > isolde stepto
    6187 
    6188  > isolde stepto
    6189 
    6190  > isolde stepto
    6191 
    6192  > isolde stepto
    6193 
    6194  > select clear
    6195 
    6196  > isolde stepto
    6197 
    6198  > isolde stepto
    6199 
    6200  > isolde stepto
    6201 
    6202  > isolde stepto
    6203 
    6204  > isolde stepto
    6205 
    6206  > isolde stepto
    6207 
    6208  > isolde stepto
    6209 
    6210  > isolde stepto
    6211 
    6212  > isolde stepto
    6213 
    6214  > isolde stepto
    6215 
    6216  > isolde stepto
    6217 
    6218  > isolde stepto
    6219 
    6220  > isolde stepto
    6221 
    6222  > isolde stepto
    6223 
    6224  > isolde stepto
    6225 
    6226  > isolde stepto
    6227 
    6228  > isolde stepto
    6229 
    6230  > isolde stepto
    6231 
    6232  > isolde stepto
    6233 
    6234  > isolde stepto
    6235 
    6236  > isolde stepto
    6237 
    6238  > isolde stepto
    6239 
    6240  > isolde stepto
    6241 
    6242  > isolde stepto
    6243 
    6244  > isolde stepto
    6245 
    6246  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6247  bonded heavy atom.
    6248 
    6249  > select clear
    6250 
    6251  > isolde stepto
    6252 
    6253  > isolde stepto
    6254 
    6255  > isolde stepto
    6256 
    6257  > isolde stepto
    6258 
    6259  > select /AK
    6260 
    6261  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6262 
    6263  > select clear
    6264 
    6265  > select /AK
    6266 
    6267  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6268 
    6269  > select clear
    6270 
    6271  > isolde stepto
    6272 
    6273  > isolde stepto
    6274 
    6275  > isolde stepto
    6276 
    6277  > isolde stepto
    6278 
    6279  > isolde stepto
    6280 
    6281  > isolde stepto
    6282 
    6283  > isolde stepto
    6284 
    6285  > isolde stepto
    6286 
    6287  > isolde stepto
    6288 
    6289  > isolde stepto
    6290 
    6291  > isolde stepto
    6292 
    6293  > isolde stepto
    6294 
    6295  > isolde stepto
    6296 
    6297  > isolde stepto
    6298 
    6299  > isolde stepto
    6300 
    6301  > isolde stepto
    6302 
    6303  > isolde stepto
    6304 
    6305  > isolde stepto
    6306 
    6307  > isolde stepto
    6308 
    6309  > isolde stepto
    6310 
    6311  > isolde stepto
    6312 
    6313  > isolde stepto
    6314 
    6315  > isolde stepto
    6316 
    6317  > isolde stepto
    6318 
    6319  > isolde stepto
    6320 
    6321  > isolde stepto
    6322 
    6323  > isolde stepto
    6324 
    6325  > isolde stepto
    6326 
    6327  > isolde stepto
    6328 
    6329  > isolde stepto
    6330 
    6331  > isolde stepto
    6332 
    6333  > isolde stepto
    6334 
    6335  > isolde stepto
    6336 
    6337  > isolde stepto
    6338 
    6339  > isolde stepto
    6340 
    6341  > isolde stepto
    6342 
    6343  > isolde stepto
    6344 
    6345  > isolde stepto
    6346 
    6347  > isolde stepto
    6348 
    6349  > isolde stepto
    6350 
    6351  > isolde stepto
    6352 
    6353  > isolde stepto
    6354 
    6355  > isolde stepto
    6356 
    6357  > isolde stepto
    6358 
    6359  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6360  bonded heavy atom.
    6361 
    6362  > select clear
    6363 
    6364  > isolde stepto
    6365 
    6366  > isolde stepto
    6367 
    6368  > isolde stepto
    6369 
    6370  > isolde stepto
    6371 
    6372  > select /AL
    6373 
    6374  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6375 
    6376  > select clear
    6377 
    6378  > isolde stepto
    6379 
    6380  > isolde stepto
    6381 
    6382  > isolde stepto
    6383 
    6384  > isolde stepto
    6385 
    6386  > isolde stepto
    6387 
    6388  > isolde stepto
    6389 
    6390  > isolde stepto
    6391 
    6392  > isolde stepto
    6393 
    6394  > isolde stepto
    6395 
    6396  > isolde stepto
    6397 
    6398  > isolde stepto
    6399 
    6400  > isolde stepto
    6401 
    6402  > isolde stepto
    6403 
    6404  > isolde stepto
    6405 
    6406  > isolde stepto
    6407 
    6408  > isolde stepto
    6409 
    6410  > isolde stepto
    6411 
    6412  > isolde stepto
    6413 
    6414  > isolde stepto
    6415 
    6416  > isolde stepto
    6417 
    6418  > isolde stepto
    6419 
    6420  > isolde stepto
    6421 
    6422  > isolde stepto
    6423 
    6424  > isolde stepto
    6425 
    6426  > select clear
    6427 
    6428  > isolde stepto
    6429 
    6430  > isolde stepto
    6431 
    6432  > isolde stepto
    6433 
    6434  > isolde stepto
    6435 
    6436  > isolde stepto
    6437 
    6438  > isolde stepto
    6439 
    6440  > isolde stepto
    6441 
    6442  > isolde stepto
    6443 
    6444  > isolde stepto
    6445 
    6446  > isolde stepto
    6447 
    6448  > isolde stepto
    6449 
    6450  > isolde stepto
    6451 
    6452  > isolde stepto
    6453 
    6454  > isolde stepto
    6455 
    6456  > isolde stepto
    6457 
    6458  > isolde stepto
    6459 
    6460  > isolde stepto
    6461 
    6462  > isolde stepto
    6463 
    6464  > isolde stepto
    6465 
    6466  > isolde stepto
    6467 
    6468  > select clear
    6469 
    6470  > isolde stepto
    6471 
    6472  > isolde stepto
    6473 
    6474  > isolde stepto
    6475 
    6476  > isolde stepto
    6477 
    6478  > select /AM
    6479 
    6480  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6481 
    6482  > select clear
    6483 
    6484  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6485  bonded heavy atom.
    6486 
    6487  > select clear
    6488 
    6489  > select /AM
    6490 
    6491  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6492 
    6493  > select clear
    6494 
    6495  > isolde stepto
    6496 
    6497  > isolde stepto
    6498 
    6499  > isolde stepto
    6500 
    6501  > isolde stepto
    6502 
    6503  > isolde stepto
    6504 
    6505  > isolde stepto
    6506 
    6507  > isolde stepto
    6508 
    6509  > isolde stepto
    6510 
    6511  > isolde stepto
    6512 
    6513  > isolde stepto
    6514 
    6515  > isolde stepto
    6516 
    6517  > isolde stepto
    6518 
    6519  > isolde stepto
    6520 
    6521  > isolde stepto
    6522 
    6523  > isolde stepto
    6524 
    6525  > isolde stepto
    6526 
    6527  > isolde stepto
    6528 
    6529  > isolde stepto
    6530 
    6531  > isolde stepto
    6532 
    6533  > isolde stepto
    6534 
    6535  > isolde stepto
    6536 
    6537  > isolde stepto
    6538 
    6539  > isolde stepto
    6540 
    6541  > isolde stepto
    6542 
    6543  > isolde stepto
    6544 
    6545  > isolde stepto
    6546 
    6547  > isolde stepto
    6548 
    6549  > isolde stepto
    6550 
    6551  > isolde stepto
    6552 
    6553  > isolde stepto
    6554 
    6555  > isolde stepto
    6556 
    6557  > isolde stepto
    6558 
    6559  > isolde stepto
    6560 
    6561  > isolde stepto
    6562 
    6563  > isolde stepto
    6564 
    6565  > isolde stepto
    6566 
    6567  > isolde stepto
    6568 
    6569  > isolde stepto
    6570 
    6571  > isolde stepto
    6572 
    6573  > isolde stepto
    6574 
    6575  > isolde stepto
    6576 
    6577  > isolde stepto
    6578 
    6579  > isolde stepto
    6580 
    6581  > isolde stepto
    6582 
    6583  > isolde stepto
    6584 
    6585  > isolde stepto
    6586 
    6587  > isolde stepto
    6588 
    6589  > isolde stepto
    6590 
    6591  > select /AN
    6592 
    6593  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6594 
    6595  > select clear
    6596 
    6597  > isolde stepto
    6598 
    6599  > isolde stepto
    6600 
    6601  > isolde stepto
    6602 
    6603  > isolde stepto
    6604 
    6605  > isolde stepto
    6606 
    6607  > isolde stepto
    6608 
    6609  > isolde stepto
    6610 
    6611  > isolde stepto
    6612 
    6613  > isolde stepto
    6614 
    6615  > isolde stepto
    6616 
    6617  > isolde stepto
    6618 
    6619  > isolde stepto
    6620 
    6621  > isolde stepto
    6622 
    6623  > isolde stepto
    6624 
    6625  > isolde stepto
    6626 
    6627  > isolde stepto
    6628 
    6629  > isolde stepto
    6630 
    6631  > isolde stepto
    6632 
    6633  > isolde stepto
    6634 
    6635  > isolde stepto
    6636 
    6637  > isolde stepto
    6638 
    6639  > isolde stepto
    6640 
    6641  > isolde stepto
    6642 
    6643  > isolde stepto
    6644 
    6645  > isolde stepto
    6646 
    6647  > isolde stepto
    6648 
    6649  > isolde stepto
    6650 
    6651  > isolde stepto
    6652 
    6653  > isolde stepto
    6654 
    6655  > isolde stepto
    6656 
    6657  > isolde stepto
    6658 
    6659  > isolde stepto
    6660 
    6661  > isolde stepto
    6662 
    6663  > isolde stepto
    6664 
    6665  > isolde stepto
    6666 
    6667  > isolde stepto
    6668 
    6669  > isolde stepto
    6670 
    6671  > isolde stepto
    6672 
    6673  > isolde stepto
    6674 
    6675  > isolde stepto
    6676 
    6677  > isolde stepto
    6678 
    6679  > isolde stepto
    6680 
    6681  > isolde stepto
    6682 
    6683  > isolde stepto
    6684 
    6685  > isolde ignore sel
    6686 
    6687  ISOLDE: currently ignoring 2 residues in model 8.2
    6688 
    6689  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6690  bonded heavy atom.
    6691 
    6692  > select clear
    6693 
    6694  > isolde ~ignore
    6695 
    6696  > isolde stepto
    6697 
    6698  > isolde stepto
    6699 
    6700  > isolde stepto
    6701 
    6702  > isolde stepto
    6703 
    6704  > select /AO
    6705 
    6706  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6707 
    6708  > select clear
    6709 
    6710  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6711  bonded heavy atom.
    6712 
    6713  > isolde stepto
    6714 
    6715  > isolde stepto
    6716 
    6717  > isolde stepto
    6718 
    6719  > isolde stepto
    6720 
    6721  > isolde stepto
    6722 
    6723  > isolde stepto
    6724 
    6725  > isolde stepto
    6726 
    6727  > isolde stepto
    6728 
    6729  > isolde stepto
    6730 
    6731  > isolde stepto
    6732 
    6733  > isolde stepto
    6734 
    6735  > isolde stepto
    6736 
    6737  > isolde stepto
    6738 
    6739  > isolde stepto
    6740 
    6741  > isolde stepto
    6742 
    6743  > isolde stepto
    6744 
    6745  > isolde stepto
    6746 
    6747  > isolde stepto
    6748 
    6749  > isolde stepto
    6750 
    6751  > isolde stepto
    6752 
    6753  > isolde stepto
    6754 
    6755  > isolde stepto
    6756 
    6757  > isolde stepto
    6758 
    6759  > isolde stepto
    6760 
    6761  > isolde stepto
    6762 
    6763  > isolde stepto
    6764 
    6765  > isolde stepto
    6766 
    6767  > isolde stepto
    6768 
    6769  > isolde stepto
    6770 
    6771  > isolde stepto
    6772 
    6773  > isolde stepto
    6774 
    6775  > isolde stepto
    6776 
    6777  > isolde stepto
    6778 
    6779  > isolde stepto
    6780 
    6781  > isolde stepto
    6782 
    6783  > isolde stepto
    6784 
    6785  > isolde stepto
    6786 
    6787  > isolde stepto
    6788 
    6789  > isolde stepto
    6790 
    6791  > isolde stepto
    6792 
    6793  > isolde stepto
    6794 
    6795  > isolde stepto
    6796 
    6797  > isolde stepto
    6798 
    6799  > select clear
    6800 
    6801  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6802  bonded heavy atom.
    6803 
    6804  > select clear
    6805 
    6806  > isolde stepto
    6807 
    6808  > isolde stepto
    6809 
    6810  > isolde stepto
    6811 
    6812  > isolde stepto
    6813 
    6814  > isolde stepto
    6815 
    6816  > select /AP
    6817 
    6818  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6819 
    6820  > select clear
    6821 
    6822  > select clear
    6823 
    6824  > isolde stepto
    6825 
    6826  > isolde stepto
    6827 
    6828  > isolde stepto
    6829 
    6830  > isolde stepto
    6831 
    6832  > isolde stepto
    6833 
    6834  > isolde stepto
    6835 
    6836  > isolde stepto
    6837 
    6838  > isolde stepto
    6839 
    6840  > isolde stepto
    6841 
    6842  > isolde stepto
    6843 
    6844  > isolde stepto
    6845 
    6846  > isolde stepto
    6847 
    6848  > isolde stepto
    6849 
    6850  > isolde stepto
    6851 
    6852  > isolde stepto
    6853 
    6854  > isolde stepto
    6855 
    6856  > isolde stepto
    6857 
    6858  > isolde stepto
    6859 
    6860  > isolde stepto
    6861 
    6862  > isolde stepto
    6863 
    6864  > isolde stepto
    6865 
    6866  > isolde stepto
    6867 
    6868  > isolde stepto
    6869 
    6870  > isolde stepto
    6871 
    6872  > isolde stepto
    6873 
    6874  > isolde stepto
    6875 
    6876  > isolde stepto
    6877 
    6878  > isolde stepto
    6879 
    6880  > isolde stepto
    6881 
    6882  > isolde stepto
    6883 
    6884  > isolde stepto
    6885 
    6886  > isolde stepto
    6887 
    6888  > isolde stepto
    6889 
    6890  > isolde stepto
    6891 
    6892  > isolde stepto
    6893 
    6894  > isolde stepto
    6895 
    6896  > isolde stepto
    6897 
    6898  > isolde stepto
    6899 
    6900  > isolde stepto
    6901 
    6902  > isolde stepto
    6903 
    6904  > isolde stepto
    6905 
    6906  > isolde stepto
    6907 
    6908  > isolde stepto
    6909 
    6910  > isolde stepto
    6911 
    6912  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6913  bonded heavy atom.
    6914 
    6915  > select clear
    6916 
    6917  > isolde stepto
    6918 
    6919  > isolde stepto
    6920 
    6921  > isolde stepto
    6922 
    6923  > isolde stepto
    6924 
    6925  > select /AQ
    6926 
    6927  980 atoms, 1001 bonds, 48 residues, 1 model selected
    6928 
    6929  > select clear
    6930 
    6931  > select clear
    6932 
    6933  > isolde stepto
    6934 
    6935  > isolde stepto
    6936 
    6937  > isolde stepto
    6938 
    6939  > isolde stepto
    6940 
    6941  > isolde stepto
    6942 
    6943  > isolde stepto
    6944 
    6945  > isolde stepto
    6946 
    6947  > isolde stepto
    6948 
    6949  > isolde stepto
    6950 
    6951  > isolde stepto
    6952 
    6953  > isolde stepto
    6954 
    6955  > isolde stepto
    6956 
    6957  > isolde stepto
    6958 
    6959  > isolde stepto
    6960 
    6961  > isolde stepto
    6962 
    6963  > isolde stepto
    6964 
    6965  > isolde stepto
    6966 
    6967  > isolde stepto
    6968 
    6969  > isolde stepto
    6970 
    6971  > isolde stepto
    6972 
    6973  > isolde stepto
    6974 
    6975  > isolde stepto
    6976 
    6977  > isolde stepto
    6978 
    6979  > isolde stepto
    6980 
    6981  > isolde stepto
    6982 
    6983  > isolde stepto
    6984 
    6985  > isolde stepto
    6986 
    6987  > isolde stepto
    6988 
    6989  > isolde stepto
    6990 
    6991  > isolde stepto
    6992 
    6993  > isolde stepto
    6994 
    6995  > isolde stepto
    6996 
    6997  > isolde stepto
    6998 
    6999  > isolde stepto
    7000 
    7001  > isolde stepto
    7002 
    7003  > isolde stepto
    7004 
    7005  > isolde stepto
    7006 
    7007  > isolde stepto
    7008 
    7009  > isolde stepto
    7010 
    7011  > isolde stepto
    7012 
    7013  > isolde stepto
    7014 
    7015  > isolde stepto
    7016 
    7017  > isolde stepto
    7018 
    7019  > isolde stepto
    7020 
    7021  > select clear
    7022 
    7023  > isolde stepto
    7024 
    7025  > isolde stepto
    7026 
    7027  > isolde stepto
    7028 
    7029  > isolde stepto
    7030 
    7031  > select /AR
    7032 
    7033  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7034 
    7035  > select clear
    7036 
    7037  > isolde stepto
    7038 
    7039  > isolde stepto
    7040 
    7041  > isolde stepto
    7042 
    7043  > isolde stepto
    7044 
    7045  > isolde stepto
    7046 
    7047  > isolde stepto
    7048 
    7049  > isolde stepto
    7050 
    7051  > isolde stepto
    7052 
    7053  > isolde stepto
    7054 
    7055  > isolde stepto
    7056 
    7057  > isolde stepto
    7058 
    7059  > isolde stepto
    7060 
    7061  > isolde stepto
    7062 
    7063  > isolde stepto
    7064 
    7065  > isolde stepto
    7066 
    7067  > isolde stepto
    7068 
    7069  > isolde stepto
    7070 
    7071  > isolde stepto
    7072 
    7073  > isolde stepto
    7074 
    7075  > isolde stepto
    7076 
    7077  > isolde stepto
    7078 
    7079  > isolde stepto
    7080 
    7081  > isolde stepto
    7082 
    7083  > isolde stepto
    7084 
    7085  > isolde stepto
    7086 
    7087  > isolde stepto
    7088 
    7089  > isolde stepto
    7090 
    7091  > isolde stepto
    7092 
    7093  > isolde stepto
    7094 
    7095  > isolde stepto
    7096 
    7097  > isolde stepto
    7098 
    7099  > isolde stepto
    7100 
    7101  > isolde stepto
    7102 
    7103  > isolde stepto
    7104 
    7105  > isolde stepto
    7106 
    7107  > isolde stepto
    7108 
    7109  > isolde stepto
    7110 
    7111  > isolde stepto
    7112 
    7113  > isolde stepto
    7114 
    7115  > isolde stepto
    7116 
    7117  > isolde stepto
    7118 
    7119  > isolde stepto
    7120 
    7121  > isolde stepto
    7122 
    7123  > isolde stepto
    7124 
    7125  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7126  bonded heavy atom.
    7127 
    7128  > select clear
    7129 
    7130  > isolde stepto
    7131 
    7132  > isolde stepto
    7133 
    7134  > isolde stepto
    7135 
    7136  > isolde stepto
    7137 
    7138  > select /AS
    7139 
    7140  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7141 
    7142  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7143  bonded heavy atom.
    7144 
    7145  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7146  bonded heavy atom.
    7147 
    7148  > isolde stepto
    7149 
    7150  > isolde stepto
    7151 
    7152  > select clear
    7153 
    7154  > isolde stepto
    7155 
    7156  > isolde stepto
    7157 
    7158  > isolde stepto
    7159 
    7160  > isolde stepto
    7161 
    7162  > isolde stepto
    7163 
    7164  > isolde stepto
    7165 
    7166  > isolde stepto
    7167 
    7168  > isolde stepto
    7169 
    7170  > isolde stepto
    7171 
    7172  > isolde stepto
    7173 
    7174  > isolde stepto
    7175 
    7176  > isolde stepto
    7177 
    7178  > isolde stepto
    7179 
    7180  > isolde stepto
    7181 
    7182  > isolde stepto
    7183 
    7184  > isolde stepto
    7185 
    7186  > isolde stepto
    7187 
    7188  > isolde stepto
    7189 
    7190  > isolde stepto
    7191 
    7192  > isolde stepto
    7193 
    7194  > isolde stepto
    7195 
    7196  > isolde stepto
    7197 
    7198  > isolde stepto
    7199 
    7200  > isolde stepto
    7201 
    7202  > isolde stepto
    7203 
    7204  > isolde stepto
    7205 
    7206  > select clear
    7207 
    7208  > isolde stepto
    7209 
    7210  > isolde stepto
    7211 
    7212  > isolde stepto
    7213 
    7214  > isolde stepto
    7215 
    7216  > isolde stepto
    7217 
    7218  > isolde stepto
    7219 
    7220  > isolde stepto
    7221 
    7222  > isolde stepto
    7223 
    7224  > isolde stepto
    7225 
    7226  > isolde stepto
    7227 
    7228  > isolde stepto
    7229 
    7230  > isolde stepto
    7231 
    7232  > isolde stepto
    7233 
    7234  > isolde stepto
    7235 
    7236  > isolde stepto
    7237 
    7238  > isolde stepto
    7239 
    7240  > select clear
    7241 
    7242  > isolde stepto
    7243 
    7244  > isolde stepto
    7245 
    7246  > isolde stepto
    7247 
    7248  > isolde stepto
    7249 
    7250  > select /AT
    7251 
    7252  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7253 
    7254  > select clear
    7255 
    7256  > select clear
    7257 
    7258  > isolde stepto
    7259 
    7260  > isolde stepto
    7261 
    7262  > isolde stepto
    7263 
    7264  > isolde stepto
    7265 
    7266  > isolde stepto
    7267 
    7268  > isolde stepto
    7269 
    7270  > isolde stepto
    7271 
    7272  > isolde stepto
    7273 
    7274  > isolde stepto
    7275 
    7276  > isolde stepto
    7277 
    7278  > isolde stepto
    7279 
    7280  > isolde stepto
    7281 
    7282  > isolde stepto
    7283 
    7284  > isolde stepto
    7285 
    7286  > isolde stepto
    7287 
    7288  > isolde stepto
    7289 
    7290  > isolde stepto
    7291 
    7292  > isolde stepto
    7293 
    7294  > isolde stepto
    7295 
    7296  > isolde stepto
    7297 
    7298  > isolde stepto
    7299 
    7300  > isolde stepto
    7301 
    7302  > isolde stepto
    7303 
    7304  > isolde stepto
    7305 
    7306  > isolde stepto
    7307 
    7308  > isolde stepto
    7309 
    7310  > isolde stepto
    7311 
    7312  > isolde stepto
    7313 
    7314  > isolde stepto
    7315 
    7316  > isolde stepto
    7317 
    7318  > isolde stepto
    7319 
    7320  > isolde stepto
    7321 
    7322  > isolde stepto
    7323 
    7324  > isolde stepto
    7325 
    7326  > isolde stepto
    7327 
    7328  > isolde stepto
    7329 
    7330  > isolde stepto
    7331 
    7332  > isolde stepto
    7333 
    7334  > isolde stepto
    7335 
    7336  > isolde stepto
    7337 
    7338  > isolde stepto
    7339 
    7340  > isolde stepto
    7341 
    7342  > isolde stepto
    7343 
    7344  > isolde stepto
    7345 
    7346  > select clear
    7347 
    7348  > select clear
    7349 
    7350  > isolde stepto
    7351 
    7352  > isolde stepto
    7353 
    7354  > isolde stepto
    7355 
    7356  > isolde stepto
    7357 
    7358  > select /AU
    7359 
    7360  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7361 
    7362  > select clear
    7363 
    7364  > isolde stepto
    7365 
    7366  > isolde stepto
    7367 
    7368  > isolde stepto
    7369 
    7370  > isolde stepto
    7371 
    7372  > isolde stepto
    7373 
    7374  > isolde stepto
    7375 
    7376  > isolde stepto
    7377 
    7378  > isolde stepto
    7379 
    7380  > isolde stepto
    7381 
    7382  > isolde stepto
    7383 
    7384  > isolde stepto
    7385 
    7386  > select clear
    7387 
    7388  > isolde stepto
    7389 
    7390  > isolde stepto
    7391 
    7392  > isolde stepto
    7393 
    7394  > isolde stepto
    7395 
    7396  > isolde stepto
    7397 
    7398  > isolde stepto
    7399 
    7400  > isolde stepto
    7401 
    7402  > isolde stepto
    7403 
    7404  > isolde stepto
    7405 
    7406  > isolde stepto
    7407 
    7408  > isolde stepto
    7409 
    7410  > isolde stepto
    7411 
    7412  > isolde stepto
    7413 
    7414  > isolde stepto
    7415 
    7416  > isolde stepto
    7417 
    7418  > isolde stepto
    7419 
    7420  > isolde stepto
    7421 
    7422  > isolde stepto
    7423 
    7424  > isolde stepto
    7425 
    7426  > isolde stepto
    7427 
    7428  > isolde stepto
    7429 
    7430  > isolde stepto
    7431 
    7432  > isolde stepto
    7433 
    7434  > isolde stepto
    7435 
    7436  > isolde stepto
    7437 
    7438  > isolde stepto
    7439 
    7440  > isolde stepto
    7441 
    7442  > isolde stepto
    7443 
    7444  > isolde stepto
    7445 
    7446  > isolde stepto
    7447 
    7448  > isolde stepto
    7449 
    7450  > isolde stepto
    7451 
    7452  > isolde stepto
    7453 
    7454  > isolde stepto
    7455 
    7456  > isolde stepto prev
    7457 
    7458  > select clear
    7459 
    7460  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7461  bonded heavy atom.
    7462 
    7463  > isolde stepto
    7464 
    7465  > isolde stepto
    7466 
    7467  > isolde stepto
    7468 
    7469  > isolde stepto
    7470 
    7471  > select /AV
    7472 
    7473  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7474 
    7475  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7476  bonded heavy atom.
    7477 
    7478  > isolde stepto
    7479 
    7480  > isolde stepto
    7481 
    7482  > isolde stepto
    7483 
    7484  > isolde stepto
    7485 
    7486  > isolde stepto
    7487 
    7488  > isolde stepto
    7489 
    7490  > isolde stepto
    7491 
    7492  > isolde stepto
    7493 
    7494  > isolde stepto
    7495 
    7496  > isolde stepto
    7497 
    7498  > isolde stepto
    7499 
    7500  > isolde stepto
    7501 
    7502  > select clear
    7503 
    7504  > isolde stepto
    7505 
    7506  > isolde stepto
    7507 
    7508  > isolde stepto
    7509 
    7510  > isolde stepto
    7511 
    7512  > isolde stepto
    7513 
    7514  > isolde stepto
    7515 
    7516  > isolde stepto
    7517 
    7518  > isolde stepto
    7519 
    7520  > isolde stepto
    7521 
    7522  > isolde stepto
    7523 
    7524  > isolde stepto
    7525 
    7526  > isolde stepto
    7527 
    7528  > isolde stepto
    7529 
    7530  > isolde stepto
    7531 
    7532  > isolde stepto
    7533 
    7534  > isolde stepto
    7535 
    7536  > isolde stepto
    7537 
    7538  > isolde stepto
    7539 
    7540  > isolde stepto
    7541 
    7542  > isolde stepto
    7543 
    7544  > isolde stepto
    7545 
    7546  > isolde stepto
    7547 
    7548  > isolde stepto
    7549 
    7550  > isolde stepto
    7551 
    7552  > isolde stepto
    7553 
    7554  > isolde stepto
    7555 
    7556  > isolde stepto
    7557 
    7558  > isolde stepto
    7559 
    7560  > isolde stepto
    7561 
    7562  > isolde stepto
    7563 
    7564  > isolde stepto
    7565 
    7566  > isolde stepto
    7567 
    7568  > select clear
    7569 
    7570  > select clear
    7571 
    7572  > isolde stepto
    7573 
    7574  > isolde stepto
    7575 
    7576  > isolde stepto
    7577 
    7578  > isolde stepto
    7579 
    7580  > select /AW
    7581 
    7582  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7583 
    7584  > select clear
    7585 
    7586  > isolde stepto
    7587 
    7588  > isolde stepto
    7589 
    7590  > isolde stepto
    7591 
    7592  > isolde stepto
    7593 
    7594  > isolde stepto
    7595 
    7596  > isolde stepto
    7597 
    7598  > select clear
    7599 
    7600  > isolde stepto
    7601 
    7602  > isolde stepto
    7603 
    7604  > isolde stepto
    7605 
    7606  > isolde stepto
    7607 
    7608  > isolde stepto
    7609 
    7610  > isolde stepto
    7611 
    7612  > isolde stepto
    7613 
    7614  > isolde stepto
    7615 
    7616  > isolde stepto
    7617 
    7618  > isolde stepto
    7619 
    7620  > isolde stepto
    7621 
    7622  > isolde stepto
    7623 
    7624  > isolde stepto
    7625 
    7626  > isolde stepto
    7627 
    7628  > isolde stepto
    7629 
    7630  > isolde stepto
    7631 
    7632  > isolde stepto
    7633 
    7634  > isolde stepto
    7635 
    7636  > isolde stepto
    7637 
    7638  > isolde stepto
    7639 
    7640  > isolde stepto
    7641 
    7642  > isolde stepto
    7643 
    7644  > isolde stepto
    7645 
    7646  > isolde stepto
    7647 
    7648  > isolde stepto
    7649 
    7650  > isolde stepto
    7651 
    7652  > isolde stepto
    7653 
    7654  > isolde stepto
    7655 
    7656  > isolde stepto
    7657 
    7658  > isolde stepto
    7659 
    7660  > isolde stepto
    7661 
    7662  > isolde stepto
    7663 
    7664  > isolde stepto
    7665 
    7666  > isolde stepto
    7667 
    7668  > isolde stepto
    7669 
    7670  > isolde stepto
    7671 
    7672  > isolde stepto
    7673 
    7674  > isolde stepto
    7675 
    7676  > isolde stepto
    7677 
    7678  > isolde stepto
    7679 
    7680  > isolde stepto
    7681 
    7682  > isolde stepto
    7683 
    7684  > select /AX
    7685 
    7686  980 atoms, 1001 bonds, 48 residues, 1 model selected
    7687 
    7688  > select clear
    7689 
    7690  > isolde stepto
    7691 
    7692  > isolde stepto
    7693 
    7694  > isolde stepto
    7695 
    7696  > isolde stepto
    7697 
    7698  > isolde stepto
    7699 
    7700  > isolde stepto
    7701 
    7702  > isolde stepto
    7703 
    7704  > isolde stepto
    7705 
    7706  > isolde stepto
    7707 
    7708  > isolde stepto
    7709 
    7710  > isolde stepto
    7711 
    7712  > isolde stepto
    7713 
    7714  > isolde stepto
    7715 
    7716  > isolde stepto
    7717 
    7718  > isolde stepto
    7719 
    7720  > isolde stepto
    7721 
    7722  > isolde stepto
    7723 
    7724  > isolde stepto
    7725 
    7726  > isolde stepto
    7727 
    7728  > isolde stepto
    7729 
    7730  > isolde stepto
    7731 
    7732  > isolde stepto
    7733 
    7734  > isolde stepto
    7735 
    7736  > isolde stepto
    7737 
    7738  > isolde stepto
    7739 
    7740  > isolde stepto
    7741 
    7742  > isolde stepto
    7743 
    7744  > isolde stepto
    7745 
    7746  > isolde stepto
    7747 
    7748  > isolde stepto
    7749 
    7750  > isolde stepto
    7751 
    7752  > isolde stepto
    7753 
    7754  > isolde stepto
    7755 
    7756  > isolde stepto
    7757 
    7758  > isolde stepto
    7759 
    7760  > isolde stepto
    7761 
    7762  > isolde stepto
    7763 
    7764  > isolde stepto
    7765 
    7766  > isolde stepto
    7767 
    7768  > isolde stepto
    7769 
    7770  > isolde stepto
    7771 
    7772  > isolde stepto
    7773 
    7774  > isolde stepto
    7775 
    7776  > isolde stepto
    7777 
    7778  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7779  bonded heavy atom.
    7780 
    7781  > select clear
    7782 
    7783  > select /AA
    7784 
    7785  981 atoms, 1002 bonds, 48 residues, 1 model selected
    7786 
    7787  > select clear
    7788 
    7789  > save working.cxs
    7790 
    7791  Taking snapshot of stepper: working_2.pdb
    7792 
    7793  > isolde stepto
    7794 
    7795  > isolde stepto
    7796 
    7797  > isolde stepto
    7798 
    7799  > isolde stepto
    7800 
    7801  > isolde stepto
    7802 
    7803  > select /BA
    7804 
    7805  766 atoms, 787 bonds, 40 residues, 1 model selected
    7806 
    7807  > select clear
    7808 
    7809  > isolde stepto
    7810 
    7811  > isolde stepto
    7812 
    7813  > isolde stepto
    7814 
    7815  > isolde stepto
    7816 
    7817  > isolde stepto
    7818 
    7819  > isolde stepto
    7820 
    7821  > isolde stepto
    7822 
    7823  > isolde stepto
    7824 
    7825  > isolde stepto
    7826 
    7827  > isolde stepto
    7828 
    7829  > isolde stepto
    7830 
    7831  > isolde stepto
    7832 
    7833  > isolde stepto
    7834 
    7835  > isolde stepto
    7836 
    7837  > isolde stepto
    7838 
    7839  > isolde stepto
    7840 
    7841  > isolde stepto
    7842 
    7843  > isolde stepto
    7844 
    7845  > isolde stepto
    7846 
    7847  > isolde stepto
    7848 
    7849  > isolde stepto
    7850 
    7851  > isolde stepto
    7852 
    7853  > isolde stepto
    7854 
    7855  > isolde stepto
    7856 
    7857  > isolde stepto
    7858 
    7859  > isolde stepto
    7860 
    7861  > isolde stepto
    7862 
    7863  > isolde stepto
    7864 
    7865  > isolde stepto
    7866 
    7867  > isolde stepto
    7868 
    7869  > isolde stepto
    7870 
    7871  > isolde stepto
    7872 
    7873  > isolde stepto
    7874 
    7875  > isolde stepto
    7876 
    7877  > isolde stepto
    7878 
    7879  > isolde stepto
    7880 
    7881  > isolde stepto
    7882 
    7883  > isolde stepto
    7884 
    7885  > select /BB
    7886 
    7887  773 atoms, 794 bonds, 41 residues, 1 model selected
    7888 
    7889  > select clear
    7890 
    7891  > isolde stepto
    7892 
    7893  > isolde stepto
    7894 
    7895  > isolde stepto
    7896 
    7897  > isolde stepto
    7898 
    7899  > isolde stepto
    7900 
    7901  > isolde stepto
    7902 
    7903  > isolde stepto
    7904 
    7905  > isolde stepto
    7906 
    7907  > isolde stepto
    7908 
    7909  > isolde stepto
    7910 
    7911  > isolde stepto
    7912 
    7913  > isolde stepto
    7914 
    7915  > isolde stepto
    7916 
    7917  > isolde stepto
    7918 
    7919  > isolde stepto
    7920 
    7921  > isolde stepto
    7922 
    7923  > isolde stepto
    7924 
    7925  > isolde stepto
    7926 
    7927  > isolde stepto
    7928 
    7929  > isolde stepto
    7930 
    7931  > isolde stepto
    7932 
    7933  > isolde stepto
    7934 
    7935  > isolde stepto
    7936 
    7937  > isolde stepto
    7938 
    7939  > isolde stepto
    7940 
    7941  > isolde stepto
    7942 
    7943  > isolde stepto
    7944 
    7945  > isolde stepto
    7946 
    7947  > isolde stepto
    7948 
    7949  > isolde stepto
    7950 
    7951  > isolde stepto
    7952 
    7953  > isolde stepto
    7954 
    7955  > isolde stepto
    7956 
    7957  > isolde stepto
    7958 
    7959  > isolde stepto
    7960 
    7961  > isolde stepto
    7962 
    7963  > isolde stepto
    7964 
    7965  > isolde stepto
    7966 
    7967  > isolde stepto
    7968 
    7969  > isolde stepto
    7970 
    7971  > select up
    7972 
    7973  9 atoms, 8 bonds, 1 residue, 1 model selected
    7974 
    7975  > select up
    7976 
    7977  40 atoms, 39 bonds, 3 residues, 1 model selected
    7978 
    7979  > select up
    7980 
    7981  766 atoms, 787 bonds, 40 residues, 1 model selected
    7982 
    7983  > select clear
    7984 
    7985  > select clear
    7986 
    7987  > isolde stepto
    7988 
    7989  > isolde stepto
    7990 
    7991  > isolde stepto
    7992 
    7993  > isolde stepto
    7994 
    7995  > isolde stepto
    7996 
    7997  > isolde stepto
    7998 
    7999  > isolde stepto
    8000 
    8001  > isolde stepto
    8002 
    8003  > isolde stepto
    8004 
    8005  > isolde stepto
    8006 
    8007  > isolde stepto
    8008 
    8009  > isolde stepto
    8010 
    8011  > isolde stepto
    8012 
    8013  > isolde stepto
    8014 
    8015  > isolde stepto
    8016 
    8017  > isolde stepto
    8018 
    8019  > isolde stepto
    8020 
    8021  > isolde stepto
    8022 
    8023  > isolde stepto
    8024 
    8025  > isolde stepto
    8026 
    8027  > isolde stepto
    8028 
    8029  > isolde stepto
    8030 
    8031  > isolde stepto
    8032 
    8033  > isolde stepto
    8034 
    8035  > isolde stepto
    8036 
    8037  > isolde stepto
    8038 
    8039  > isolde stepto
    8040 
    8041  > isolde stepto
    8042 
    8043  > isolde stepto
    8044 
    8045  > isolde stepto
    8046 
    8047  > isolde stepto
    8048 
    8049  > isolde stepto
    8050 
    8051  > isolde stepto
    8052 
    8053  > isolde stepto
    8054 
    8055  > isolde stepto
    8056 
    8057  > isolde stepto
    8058 
    8059  > isolde stepto
    8060 
    8061  > isolde stepto
    8062 
    8063  > isolde stepto
    8064 
    8065  > select clear
    8066 
    8067  > isolde stepto
    8068 
    8069  > isolde stepto
    8070 
    8071  > clipper spotlight radius 13.00
    8072 
    8073  > clipper spotlight radius 14.00
    8074 
    8075  > clipper spotlight radius 15.00
    8076 
    8077  > isolde stepto
    8078 
    8079  > isolde stepto
    8080 
    8081  > save working.cxs
    8082 
    8083  Taking snapshot of stepper: working_2.pdb
    8084 
    8085  > isolde add ligand LMT
    8086 
    8087  place_ligand() was called with use_md_template=True, but no suitable
    8088  template
    8089  was found. This command has been ignored.
    8090 
    8091  Chain ak, residue 67 specifies more than one residue! The simulation can
    8092  still
    8093  run, but this will probably cause problems later if not rectified by
    8094  renumbering.
    8095 
    8096  Chain ak, residue 67 specifies more than one residue! The simulation can
    8097  still
    8098  run, but this will probably cause problems later if not rectified by
    8099  renumbering.
    8100 
    8101  > select up
    8102 
    8103  140 atoms, 148 bonds, 1 residue, 1 model selected
    8104 
    8105  > isolde ignore sel
    8106 
    8107  ISOLDE: currently ignoring 1 residues in model 8.2
    8108 
    8109  > isolde ~ignore
    8110 
    8111  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    8112  bonded heavy atom.
    8113 
    8114  > select clear
    8115 
    8116  > select up
    8117 
    8118  81 atoms, 82 bonds, 1 residue, 1 model selected
    8119 
    8120  > delete sel
    8121 
    8122  > save working.cxs
    8123 
    8124  Taking snapshot of stepper: working_2.pdb
    8125  opened ChimeraX session
    8126 
    8127  > isolde start
    8128 
    8129  > set selectionWidth 4
    8130 
    8131  Done loading forcefield
    8132 
    8133  > isolde stepto
    8134 
    8135  > clipper set contourSensitivity 0.25
    8136 
    8137  > select /AA
    8138 
    8139  1019 atoms, 1041 bonds, 51 residues, 1 model selected
    8140 
    8141  > show #!1 models
    8142 
    8143  > select #1
    8144 
    8145  158 atoms, 160 bonds, 11 residues, 8 models selected
    8146 
    8147  > select #1
    8148 
    8149  158 atoms, 160 bonds, 11 residues, 8 models selected
    8150 
    8151  > close #1
    8152 
    8153  > isolde stepto /BA
    8154 
    8155  Multiple residues selected! Going to the first...
    8156 
    8157  > isolde stepto /BB
    8158 
    8159  Multiple residues selected! Going to the first...
    8160 
    8161  > select clear
    8162 
    8163  > select /BB
    8164 
    8165  773 atoms, 794 bonds, 41 residues, 1 model selected
    8166 
    8167  > select clear
    8168 
    8169  > select clear
    8170 
    8171  > isolde stepto
    8172 
    8173  > isolde stepto
    8174 
    8175  > isolde stepto
    8176 
    8177  > isolde stepto
    8178 
    8179  > isolde stepto
    8180 
    8181  > isolde stepto
    8182 
    8183  > isolde stepto
    8184 
    8185  > isolde stepto
    8186 
    8187  > isolde stepto
    8188 
    8189  > isolde stepto
    8190 
    8191  > isolde stepto
    8192 
    8193  > isolde stepto
    8194 
    8195  > isolde stepto
    8196 
    8197  > isolde stepto
    8198 
    8199  > isolde stepto
    8200 
    8201  > isolde stepto
    8202 
    8203  > isolde stepto
    8204 
    8205  > isolde stepto
    8206 
    8207  > isolde stepto
    8208 
    8209  > isolde stepto
    8210 
    8211  > isolde stepto
    8212 
    8213  > isolde stepto
    8214 
    8215  > isolde stepto
    8216 
    8217  > isolde stepto
    8218 
    8219  > isolde stepto
    8220 
    8221  > isolde stepto
    8222 
    8223  > isolde stepto
    8224 
    8225  > isolde stepto
    8226 
    8227  > isolde stepto
    8228 
    8229  > isolde stepto
    8230 
    8231  > isolde stepto
    8232 
    8233  > isolde stepto
    8234 
    8235  > isolde stepto
    8236 
    8237  > isolde stepto
    8238 
    8239  > isolde stepto
    8240 
    8241  > isolde stepto
    8242 
    8243  > isolde stepto
    8244 
    8245  > isolde stepto
    8246 
    8247  > isolde stepto
    8248 
    8249  > isolde stepto
    8250 
    8251  > select up
    8252 
    8253  17 atoms, 16 bonds, 1 residue, 1 model selected
    8254 
    8255  > select up
    8256 
    8257  40 atoms, 39 bonds, 3 residues, 1 model selected
    8258 
    8259  > select up
    8260 
    8261  766 atoms, 787 bonds, 40 residues, 1 model selected
    8262 
    8263  > select clear
    8264 
    8265  > isolde stepto
    8266 
    8267  > isolde stepto
    8268 
    8269  > isolde stepto
    8270 
    8271  > isolde stepto
    8272 
    8273  > isolde stepto
    8274 
    8275  > isolde stepto
    8276 
    8277  > isolde stepto
    8278 
    8279  > isolde stepto
    8280 
    8281  > isolde stepto
    8282 
    8283  > isolde stepto
    8284 
    8285  > isolde stepto
    8286 
    8287  > isolde stepto
    8288 
    8289  > isolde stepto
    8290 
    8291  > isolde stepto
    8292 
    8293  > isolde stepto
    8294 
    8295  > isolde stepto
    8296 
    8297  > isolde stepto
    8298 
    8299  > isolde stepto
    8300 
    8301  > isolde stepto
    8302 
    8303  > isolde stepto
    8304 
    8305  > isolde stepto
    8306 
    8307  > isolde stepto
    8308 
    8309  > isolde stepto
    8310 
    8311  > isolde stepto
    8312 
    8313  > isolde stepto
    8314 
    8315  > isolde stepto
    8316 
    8317  > isolde stepto
    8318 
    8319  > isolde stepto
    8320 
    8321  > isolde stepto
    8322 
    8323  > isolde stepto
    8324 
    8325  > isolde stepto
    8326 
    8327  > isolde stepto
    8328 
    8329  > isolde stepto
    8330 
    8331  > isolde stepto
    8332 
    8333  > isolde stepto
    8334 
    8335  > isolde stepto
    8336 
    8337  > isolde stepto
    8338 
    8339  > isolde stepto
    8340 
    8341  > isolde stepto
    8342 
    8343  > select clear
    8344 
    8345  > select up
    8346 
    8347  14 atoms, 13 bonds, 1 residue, 1 model selected
    8348 
    8349  > select up
    8350 
    8351  47 atoms, 46 bonds, 4 residues, 1 model selected
    8352 
    8353  > select up
    8354 
    8355  773 atoms, 794 bonds, 41 residues, 1 model selected
    8356 
    8357  > select clear
    8358 
    8359  > isolde stepto
    8360 
    8361  > isolde stepto
    8362 
    8363  > isolde stepto
    8364 
    8365  > isolde stepto
    8366 
    8367  > isolde stepto
    8368 
    8369  > isolde stepto
    8370 
    8371  > isolde stepto
    8372 
    8373  > isolde stepto
    8374 
    8375  > isolde stepto
    8376 
    8377  > isolde stepto
    8378 
    8379  > isolde stepto
    8380 
    8381  > isolde stepto
    8382 
    8383  > isolde stepto
    8384 
    8385  > isolde stepto
    8386 
    8387  > isolde stepto
    8388 
    8389  > isolde stepto
    8390 
    8391  > isolde stepto
    8392 
    8393  > isolde stepto
    8394 
    8395  > isolde stepto
    8396 
    8397  > isolde stepto
    8398 
    8399  > isolde stepto
    8400 
    8401  > isolde stepto
    8402 
    8403  > isolde stepto
    8404 
    8405  > isolde stepto
    8406 
    8407  > isolde stepto
    8408 
    8409  > isolde stepto
    8410 
    8411  > isolde stepto
    8412 
    8413  > isolde stepto
    8414 
    8415  > isolde stepto
    8416 
    8417  > isolde stepto
    8418 
    8419  > isolde stepto
    8420 
    8421  > isolde stepto
    8422 
    8423  > isolde stepto
    8424 
    8425  > isolde stepto
    8426 
    8427  > isolde stepto
    8428 
    8429  > isolde stepto
    8430 
    8431  > isolde stepto
    8432 
    8433  > isolde stepto
    8434 
    8435  > isolde stepto
    8436 
    8437  > isolde stepto
    8438 
    8439  > select up
    8440 
    8441  9 atoms, 8 bonds, 1 residue, 1 model selected
    8442 
    8443  > select up
    8444 
    8445  47 atoms, 46 bonds, 4 residues, 1 model selected
    8446 
    8447  > select up
    8448 
    8449  773 atoms, 794 bonds, 41 residues, 1 model selected
    8450 
    8451  > select clear
    8452 
    8453  > isolde stepto
    8454 
    8455  > isolde stepto
    8456 
    8457  > isolde stepto
    8458 
    8459  > isolde stepto
    8460 
    8461  > isolde stepto
    8462 
    8463  > isolde stepto
    8464 
    8465  > isolde stepto
    8466 
    8467  > isolde stepto
    8468 
    8469  > isolde stepto
    8470 
    8471  > isolde stepto
    8472 
    8473  > isolde stepto
    8474 
    8475  > isolde stepto
    8476 
    8477  > isolde stepto
    8478 
    8479  > isolde stepto
    8480 
    8481  > isolde stepto
    8482 
    8483  > isolde stepto
    8484 
    8485  > isolde stepto
    8486 
    8487  > isolde stepto
    8488 
    8489  > isolde stepto
    8490 
    8491  > isolde stepto
    8492 
    8493  > isolde stepto
    8494 
    8495  > isolde stepto
    8496 
    8497  > isolde stepto
    8498 
    8499  > isolde stepto
    8500 
    8501  > isolde stepto
    8502 
    8503  > isolde stepto
    8504 
    8505  > isolde stepto
    8506 
    8507  > isolde stepto
    8508 
    8509  > isolde stepto
    8510 
    8511  > isolde stepto
    8512 
    8513  > isolde stepto
    8514 
    8515  > isolde stepto
    8516 
    8517  > isolde stepto
    8518 
    8519  > isolde stepto
    8520 
    8521  > isolde stepto
    8522 
    8523  > isolde stepto
    8524 
    8525  > isolde stepto
    8526 
    8527  > isolde stepto
    8528 
    8529  > isolde stepto
    8530 
    8531  > isolde stepto
    8532 
    8533  > select up
    8534 
    8535  9 atoms, 8 bonds, 1 residue, 1 model selected
    8536 
    8537  > select up
    8538 
    8539  40 atoms, 39 bonds, 3 residues, 1 model selected
    8540 
    8541  > select up
    8542 
    8543  766 atoms, 787 bonds, 40 residues, 1 model selected
    8544 
    8545  > select clear
    8546 
    8547  > isolde stepto
    8548 
    8549  > isolde stepto
    8550 
    8551  > isolde stepto
    8552 
    8553  > isolde stepto
    8554 
    8555  > isolde stepto
    8556 
    8557  > select clear
    8558 
    8559  > isolde stepto
    8560 
    8561  > isolde stepto
    8562 
    8563  > isolde stepto
    8564 
    8565  > isolde stepto
    8566 
    8567  > isolde stepto
    8568 
    8569  > isolde stepto
    8570 
    8571  > isolde stepto
    8572 
    8573  > isolde stepto
    8574 
    8575  > isolde stepto
    8576 
    8577  > isolde stepto
    8578 
    8579  > isolde stepto
    8580 
    8581  > isolde stepto
    8582 
    8583  > isolde stepto
    8584 
    8585  > isolde stepto
    8586 
    8587  > isolde stepto
    8588 
    8589  > isolde stepto
    8590 
    8591  > isolde stepto
    8592 
    8593  > isolde stepto
    8594 
    8595  > isolde stepto
    8596 
    8597  > isolde stepto
    8598 
    8599  > isolde stepto
    8600 
    8601  > isolde stepto
    8602 
    8603  > isolde stepto
    8604 
    8605  > isolde stepto
    8606 
    8607  > isolde stepto
    8608 
    8609  > isolde stepto
    8610 
    8611  > isolde stepto
    8612 
    8613  > isolde stepto
    8614 
    8615  > isolde stepto
    8616 
    8617  > isolde stepto
    8618 
    8619  > select clear
    8620 
    8621  > isolde stepto
    8622 
    8623  > isolde stepto
    8624 
    8625  > isolde stepto
    8626 
    8627  > isolde stepto
    8628 
    8629  > select up
    8630 
    8631  9 atoms, 8 bonds, 1 residue, 1 model selected
    8632 
    8633  > select up
    8634 
    8635  40 atoms, 39 bonds, 3 residues, 1 model selected
    8636 
    8637  > select up
    8638 
    8639  766 atoms, 787 bonds, 40 residues, 1 model selected
    8640 
    8641  > select up
    8642 
    8643  96639 atoms, 98747 bonds, 5194 residues, 1 model selected
    8644 
    8645  Chain ak, residue 67 specifies more than one residue! The simulation can
    8646  still
    8647  run, but this will probably cause problems later if not rectified by
    8648  renumbering.
    8649 
    8650  Map is too large for fast cubic interpolation on the GPU! Switching to
    8651  slower,
    8652  more memory-efficient implementation.
    8653  Map is too large for fast cubic interpolation on the GPU! Switching to
    8654  slower,
    8655  more memory-efficient implementation.
    8656 
    8657  > select clear
    8658 
    8659  > select clear
    8660 
    8661  > select up
    8662 
    8663  17 atoms, 16 bonds, 1 residue, 1 model selected
    8664 
    8665  > select up
    8666 
    8667  40 atoms, 39 bonds, 3 residues, 1 model selected
    8668 
    8669  > select up
    8670 
    8671  766 atoms, 787 bonds, 40 residues, 1 model selected
    8672 
    8673  > select up
    8674 
    8675  96639 atoms, 98747 bonds, 5194 residues, 1 model selected
    8676 
    8677  > select down
    8678 
    8679  766 atoms, 787 bonds, 40 residues, 1 model selected
    8680 
    8681  > select clear
    8682 
    8683  > isolde stepto
    8684 
    8685  > isolde stepto
    8686 
    8687  > isolde stepto
    8688 
    8689  > isolde stepto
    8690 
    8691  > isolde stepto
    8692 
    8693  > isolde stepto
    8694 
    8695  > isolde stepto
    8696 
    8697  > isolde stepto
    8698 
    8699  > isolde stepto
    8700 
    8701  > isolde stepto
    8702 
    8703  > isolde stepto
    8704 
    8705  > isolde stepto
    8706 
    8707  > isolde stepto
    8708 
    8709  > isolde stepto
    8710 
    8711  > isolde stepto
    8712 
    8713  > isolde stepto
    8714 
    8715  > isolde stepto
    8716 
    8717  > isolde stepto
    8718 
    8719  > isolde stepto
    8720 
    8721  > isolde stepto
    8722 
    8723  > isolde stepto
    8724 
    8725  > isolde stepto
    8726 
    8727  > isolde stepto
    8728 
    8729  > isolde stepto
    8730 
    8731  > isolde stepto
    8732 
    8733  > isolde stepto
    8734 
    8735  > isolde stepto
    8736 
    8737  > isolde stepto
    8738 
    8739  > isolde stepto
    8740 
    8741  > isolde stepto
    8742 
    8743  > isolde stepto
    8744 
    8745  > isolde stepto
    8746 
    8747  > isolde stepto
    8748 
    8749  > isolde stepto
    8750 
    8751  > isolde stepto
    8752 
    8753  > isolde stepto
    8754 
    8755  > isolde stepto
    8756 
    8757  > isolde stepto
    8758 
    8759  > isolde stepto
    8760 
    8761  > select up
    8762 
    8763  9 atoms, 8 bonds, 1 residue, 1 model selected
    8764 
    8765  > select up
    8766 
    8767  40 atoms, 39 bonds, 3 residues, 1 model selected
    8768 
    8769  > select up
    8770 
    8771  766 atoms, 787 bonds, 40 residues, 1 model selected
    8772 
    8773  > select clear
    8774 
    8775  > isolde stepto
    8776 
    8777  > isolde stepto
    8778 
    8779  > isolde stepto
    8780 
    8781  > isolde stepto
    8782 
    8783  > isolde stepto
    8784 
    8785  > isolde stepto
    8786 
    8787  > isolde stepto
    8788 
    8789  > isolde stepto
    8790 
    8791  > isolde stepto
    8792 
    8793  > isolde stepto
    8794 
    8795  > isolde stepto
    8796 
    8797  > isolde stepto
    8798 
    8799  > isolde stepto
    8800 
    8801  > isolde stepto
    8802 
    8803  > isolde stepto
    8804 
    8805  > isolde stepto
    8806 
    8807  > isolde stepto
    8808 
    8809  > isolde stepto
    8810 
    8811  > isolde stepto
    8812 
    8813  > isolde stepto
    8814 
    8815  > isolde stepto
    8816 
    8817  > isolde stepto
    8818 
    8819  > isolde stepto
    8820 
    8821  > isolde stepto
    8822 
    8823  > isolde stepto
    8824 
    8825  > isolde stepto
    8826 
    8827  > isolde stepto
    8828 
    8829  > isolde stepto
    8830 
    8831  > isolde stepto
    8832 
    8833  > isolde stepto
    8834 
    8835  > isolde stepto
    8836 
    8837  > isolde stepto
    8838 
    8839  > isolde stepto
    8840 
    8841  > isolde stepto
    8842 
    8843  > isolde stepto
    8844 
    8845  > isolde stepto
    8846 
    8847  > isolde stepto
    8848 
    8849  > isolde stepto
    8850 
    8851  > isolde stepto
    8852 
    8853  > select up
    8854 
    8855  9 atoms, 8 bonds, 1 residue, 1 model selected
    8856 
    8857  > select up
    8858 
    8859  47 atoms, 46 bonds, 4 residues, 1 model selected
    8860 
    8861  > select up
    8862 
    8863  773 atoms, 794 bonds, 41 residues, 1 model selected
    8864 
    8865  > select clear
    8866 
    8867  > isolde stepto
    8868 
    8869  > isolde stepto
    8870 
    8871  > isolde stepto
    8872 
    8873  > isolde stepto
    8874 
    8875  > isolde stepto
    8876 
    8877  > isolde stepto
    8878 
    8879  > isolde stepto
    8880 
    8881  > isolde stepto
    8882 
    8883  > isolde stepto
    8884 
    8885  > isolde stepto
    8886 
    8887  > isolde stepto
    8888 
    8889  > isolde stepto
    8890 
    8891  > isolde stepto
    8892 
    8893  > isolde stepto
    8894 
    8895  > isolde stepto
    8896 
    8897  > isolde stepto
    8898 
    8899  > isolde stepto
    8900 
    8901  > isolde stepto
    8902 
    8903  > isolde stepto
    8904 
    8905  > isolde stepto
    8906 
    8907  > isolde stepto
    8908 
    8909  > isolde stepto
    8910 
    8911  > isolde stepto
    8912 
    8913  > isolde stepto
    8914 
    8915  > isolde stepto
    8916 
    8917  > isolde stepto
    8918 
    8919  > isolde stepto
    8920 
    8921  > isolde stepto
    8922 
    8923  > isolde stepto
    8924 
    8925  > isolde stepto
    8926 
    8927  > isolde stepto
    8928 
    8929  > isolde stepto
    8930 
    8931  > isolde stepto
    8932 
    8933  > isolde stepto
    8934 
    8935  > isolde stepto
    8936 
    8937  > isolde stepto
    8938 
    8939  > isolde stepto
    8940 
    8941  > isolde stepto
    8942 
    8943  > isolde stepto
    8944 
    8945  > isolde stepto
    8946 
    8947  > select up
    8948 
    8949  9 atoms, 8 bonds, 1 residue, 1 model selected
    8950 
    8951  > select up
    8952 
    8953  40 atoms, 39 bonds, 3 residues, 1 model selected
    8954 
    8955  > select up
    8956 
    8957  766 atoms, 787 bonds, 40 residues, 1 model selected
    8958 
    8959  > select clear
    8960 
    8961  > isolde stepto
    8962 
    8963  > isolde stepto
    8964 
    8965  > isolde stepto
    8966 
    8967  > isolde stepto
    8968 
    8969  > isolde stepto
    8970 
    8971  > isolde stepto
    8972 
    8973  > isolde stepto
    8974 
    8975  > isolde stepto
    8976 
    8977  > isolde stepto
    8978 
    8979  > isolde stepto
    8980 
    8981  > isolde stepto
    8982 
    8983  > isolde stepto
    8984 
    8985  > isolde stepto
    8986 
    8987  > isolde stepto
    8988 
    8989  > isolde stepto
    8990 
    8991  > isolde stepto
    8992 
    8993  > isolde stepto
    8994 
    8995  > isolde stepto
    8996 
    8997  > isolde stepto
    8998 
    8999  > isolde stepto
    9000 
    9001  > isolde stepto
    9002 
    9003  > isolde stepto
    9004 
    9005  > isolde stepto
    9006 
    9007  > isolde stepto
    9008 
    9009  > isolde stepto
    9010 
    9011  > isolde stepto
    9012 
    9013  > isolde stepto
    9014 
    9015  > isolde stepto
    9016 
    9017  > isolde stepto
    9018 
    9019  > isolde stepto
    9020 
    9021  > isolde stepto
    9022 
    9023  > isolde stepto
    9024 
    9025  > isolde stepto
    9026 
    9027  > isolde stepto
    9028 
    9029  > isolde stepto
    9030 
    9031  > isolde stepto
    9032 
    9033  > isolde stepto
    9034 
    9035  > isolde stepto
    9036 
    9037  > isolde stepto
    9038 
    9039  > select up
    9040 
    9041  9 atoms, 8 bonds, 1 residue, 1 model selected
    9042 
    9043  > select up
    9044 
    9045  40 atoms, 39 bonds, 3 residues, 1 model selected
    9046 
    9047  > select up
    9048 
    9049  766 atoms, 787 bonds, 40 residues, 1 model selected
    9050 
    9051  > select clear
    9052 
    9053  > isolde stepto
    9054 
    9055  > isolde stepto
    9056 
    9057  > isolde stepto
    9058 
    9059  > isolde stepto
    9060 
    9061  > isolde stepto
    9062 
    9063  > isolde stepto
    9064 
    9065  > isolde stepto
    9066 
    9067  > isolde stepto
    9068 
    9069  > isolde stepto
    9070 
    9071  > isolde stepto
    9072 
    9073  > isolde stepto
    9074 
    9075  > isolde stepto
    9076 
    9077  > isolde stepto
    9078 
    9079  > isolde stepto
    9080 
    9081  > isolde stepto
    9082 
    9083  > isolde stepto
    9084 
    9085  > isolde stepto
    9086 
    9087  > isolde stepto
    9088 
    9089  > isolde stepto
    9090 
    9091  > isolde stepto
    9092 
    9093  > isolde stepto
    9094 
    9095  > isolde stepto
    9096 
    9097  > isolde stepto
    9098 
    9099  > isolde stepto
    9100 
    9101  > isolde stepto
    9102 
    9103  > isolde stepto
    9104 
    9105  > isolde stepto
    9106 
    9107  > isolde stepto
    9108 
    9109  > isolde stepto
    9110 
    9111  > isolde stepto
    9112 
    9113  > isolde stepto
    9114 
    9115  > isolde stepto
    9116 
    9117  > isolde stepto
    9118 
    9119  > isolde stepto
    9120 
    9121  > isolde stepto
    9122 
    9123  > isolde stepto
    9124 
    9125  > isolde stepto
    9126 
    9127  > isolde stepto
    9128 
    9129  > isolde stepto
    9130 
    9131  > select up
    9132 
    9133  9 atoms, 8 bonds, 1 residue, 1 model selected
    9134 
    9135  > select up
    9136 
    9137  40 atoms, 39 bonds, 3 residues, 1 model selected
    9138 
    9139  > select up
    9140 
    9141  766 atoms, 787 bonds, 40 residues, 1 model selected
    9142 
    9143  > select clear
    9144 
    9145  > isolde stepto
    9146 
    9147  > isolde stepto
    9148 
    9149  > isolde stepto
    9150 
    9151  > isolde stepto
    9152 
    9153  > isolde stepto
    9154 
    9155  > isolde stepto
    9156 
    9157  > isolde stepto
    9158 
    9159  > isolde stepto
    9160 
    9161  > isolde stepto
    9162 
    9163  > isolde stepto
    9164 
    9165  > isolde stepto
    9166 
    9167  > isolde stepto
    9168 
    9169  > isolde stepto
    9170 
    9171  > isolde stepto
    9172 
    9173  > isolde stepto
    9174 
    9175  > isolde stepto
    9176 
    9177  > isolde stepto
    9178 
    9179  > isolde stepto
    9180 
    9181  > select clear
    9182 
    9183  > isolde stepto
    9184 
    9185  > isolde stepto
    9186 
    9187  > isolde stepto
    9188 
    9189  > isolde stepto
    9190 
    9191  > isolde stepto
    9192 
    9193  > isolde stepto
    9194 
    9195  > isolde stepto
    9196 
    9197  > isolde stepto
    9198 
    9199  > isolde stepto
    9200 
    9201  > isolde stepto
    9202 
    9203  > isolde stepto
    9204 
    9205  > isolde stepto
    9206 
    9207  > isolde stepto
    9208 
    9209  > isolde stepto
    9210 
    9211  > isolde stepto
    9212 
    9213  > isolde stepto
    9214 
    9215  > isolde stepto
    9216 
    9217  > isolde stepto
    9218 
    9219  > isolde stepto
    9220 
    9221  > isolde stepto
    9222 
    9223  > isolde stepto
    9224 
    9225  > select up
    9226 
    9227  9 atoms, 8 bonds, 1 residue, 1 model selected
    9228 
    9229  > select up
    9230 
    9231  40 atoms, 39 bonds, 3 residues, 1 model selected
    9232 
    9233  > select up
    9234 
    9235  766 atoms, 787 bonds, 40 residues, 1 model selected
    9236 
    9237  > select clear
    9238 
    9239  > isolde stepto
    9240 
    9241  > isolde stepto
    9242 
    9243  > isolde stepto
    9244 
    9245  > isolde stepto
    9246 
    9247  > isolde stepto
    9248 
    9249  > isolde stepto
    9250 
    9251  > isolde stepto
    9252 
    9253  > isolde stepto
    9254 
    9255  > isolde stepto
    9256 
    9257  > isolde stepto
    9258 
    9259  > isolde stepto
    9260 
    9261  > isolde stepto
    9262 
    9263  > isolde stepto
    9264 
    9265  > isolde stepto
    9266 
    9267  > isolde stepto
    9268 
    9269  > isolde stepto
    9270 
    9271  > isolde stepto
    9272 
    9273  > isolde stepto
    9274 
    9275  > isolde stepto
    9276 
    9277  > isolde stepto
    9278 
    9279  > isolde stepto
    9280 
    9281  > isolde stepto
    9282 
    9283  > isolde stepto
    9284 
    9285  > isolde stepto
    9286 
    9287  > isolde stepto
    9288 
    9289  > isolde stepto
    9290 
    9291  > isolde stepto
    9292 
    9293  > isolde stepto
    9294 
    9295  > isolde stepto
    9296 
    9297  > isolde stepto
    9298 
    9299  > isolde stepto
    9300 
    9301  > isolde stepto
    9302 
    9303  > isolde stepto
    9304 
    9305  > isolde stepto
    9306 
    9307  > isolde stepto
    9308 
    9309  > isolde stepto
    9310 
    9311  > isolde stepto
    9312 
    9313  > isolde stepto
    9314 
    9315  > isolde stepto
    9316 
    9317  > select up
    9318 
    9319  9 atoms, 8 bonds, 1 residue, 1 model selected
    9320 
    9321  > select up
    9322 
    9323  40 atoms, 39 bonds, 3 residues, 1 model selected
    9324 
    9325  > select up
    9326 
    9327  766 atoms, 787 bonds, 40 residues, 1 model selected
    9328 
    9329  > select clear
    9330 
    9331  > isolde stepto
    9332 
    9333  > isolde stepto
    9334 
    9335  > isolde stepto
    9336 
    9337  > isolde stepto
    9338 
    9339  > isolde stepto
    9340 
    9341  > isolde stepto
    9342 
    9343  > isolde stepto
    9344 
    9345  > isolde stepto
    9346 
    9347  > select up
    9348 
    9349  100 atoms, 99 bonds, 1 residue, 1 model selected
    9350 
    9351  > show sel
    9352 
    9353  > select clear
    9354 
    9355  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9356  bonded heavy atom.
    9357 
    9358  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9359  bonded heavy atom.
    9360 
    9361  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9362  bonded heavy atom.
    9363 
    9364  > select clear
    9365 
    9366  > isolde stepto
    9367 
    9368  > isolde stepto
    9369 
    9370  > isolde stepto
    9371 
    9372  > isolde stepto
    9373 
    9374  > isolde stepto
    9375 
    9376  > isolde stepto
    9377 
    9378  > isolde stepto
    9379 
    9380  > isolde stepto
    9381 
    9382  > isolde stepto
    9383 
    9384  > isolde stepto
    9385 
    9386  > isolde stepto
    9387 
    9388  > isolde stepto
    9389 
    9390  > isolde stepto
    9391 
    9392  > isolde stepto
    9393 
    9394  > isolde stepto
    9395 
    9396  > isolde stepto
    9397 
    9398  > isolde stepto
    9399 
    9400  > isolde stepto
    9401 
    9402  > isolde stepto
    9403 
    9404  > isolde stepto
    9405 
    9406  > isolde stepto
    9407 
    9408  > isolde stepto
    9409 
    9410  > isolde stepto
    9411 
    9412  > isolde stepto
    9413 
    9414  > isolde stepto
    9415 
    9416  > isolde stepto
    9417 
    9418  > isolde stepto
    9419 
    9420  > isolde stepto
    9421 
    9422  > isolde stepto
    9423 
    9424  > isolde stepto
    9425 
    9426  > isolde stepto
    9427 
    9428  > select up
    9429 
    9430  17 atoms, 16 bonds, 1 residue, 1 model selected
    9431 
    9432  > select up
    9433 
    9434  40 atoms, 39 bonds, 3 residues, 1 model selected
    9435 
    9436  > select up
    9437 
    9438  766 atoms, 787 bonds, 40 residues, 1 model selected
    9439 
    9440  > select clear
    9441 
    9442  > isolde stepto
    9443 
    9444  > isolde stepto
    9445 
    9446  > isolde stepto
    9447 
    9448  > isolde stepto
    9449 
    9450  > isolde stepto
    9451 
    9452  > isolde stepto
    9453 
    9454  > isolde stepto
    9455 
    9456  > isolde stepto
    9457 
    9458  > isolde stepto
    9459 
    9460  > isolde stepto
    9461 
    9462  > isolde stepto
    9463 
    9464  > isolde stepto
    9465 
    9466  > isolde stepto
    9467 
    9468  > isolde stepto
    9469 
    9470  > isolde stepto
    9471 
    9472  > isolde stepto
    9473 
    9474  > isolde stepto
    9475 
    9476  > isolde stepto
    9477 
    9478  > isolde stepto
    9479 
    9480  > isolde stepto
    9481 
    9482  > isolde stepto
    9483 
    9484  > isolde stepto
    9485 
    9486  > isolde stepto
    9487 
    9488  > isolde stepto
    9489 
    9490  > isolde stepto
    9491 
    9492  > isolde stepto
    9493 
    9494  > isolde stepto
    9495 
    9496  > isolde stepto
    9497 
    9498  > isolde stepto
    9499 
    9500  > isolde stepto
    9501 
    9502  > isolde stepto
    9503 
    9504  > isolde stepto
    9505 
    9506  > isolde stepto
    9507 
    9508  > isolde stepto
    9509 
    9510  > isolde stepto
    9511 
    9512  > isolde stepto
    9513 
    9514  > isolde stepto
    9515 
    9516  > isolde stepto
    9517 
    9518  > isolde stepto
    9519 
    9520  > select up
    9521 
    9522  9 atoms, 8 bonds, 1 residue, 1 model selected
    9523 
    9524  > select up
    9525 
    9526  40 atoms, 39 bonds, 3 residues, 1 model selected
    9527 
    9528  > select clear
    9529 
    9530  > isolde stepto
    9531 
    9532  > isolde stepto
    9533 
    9534  > isolde stepto
    9535 
    9536  > isolde stepto
    9537 
    9538  > isolde stepto
    9539 
    9540  > isolde stepto
    9541 
    9542  > isolde stepto
    9543 
    9544  > isolde stepto
    9545 
    9546  > isolde stepto
    9547 
    9548  > isolde stepto
    9549 
    9550  > isolde stepto
    9551 
    9552  > isolde stepto
    9553 
    9554  > isolde stepto
    9555 
    9556  > isolde stepto
    9557 
    9558  > select up
    9559 
    9560  16 atoms, 15 bonds, 1 residue, 1 model selected
    9561 
    9562  > select up
    9563 
    9564  503 atoms, 512 bonds, 32 residues, 1 model selected
    9565 
    9566  > select up
    9567 
    9568  766 atoms, 787 bonds, 40 residues, 1 model selected
    9569 
    9570  > select clear
    9571 
    9572  > isolde stepto
    9573 
    9574  > isolde stepto
    9575 
    9576  > isolde stepto
    9577 
    9578  > isolde stepto
    9579 
    9580  > isolde stepto
    9581 
    9582  > isolde stepto
    9583 
    9584  > isolde stepto
    9585 
    9586  > isolde stepto
    9587 
    9588  > isolde stepto
    9589 
    9590  > isolde stepto
    9591 
    9592  > isolde stepto
    9593 
    9594  > isolde stepto
    9595 
    9596  > isolde stepto
    9597 
    9598  > isolde stepto
    9599 
    9600  > isolde stepto
    9601 
    9602  > isolde stepto
    9603 
    9604  > isolde stepto
    9605 
    9606  > isolde stepto
    9607 
    9608  > isolde stepto
    9609 
    9610  > isolde stepto
    9611 
    9612  > isolde stepto
    9613 
    9614  > isolde stepto
    9615 
    9616  > isolde stepto
    9617 
    9618  > isolde stepto
    9619 
    9620  > isolde stepto
    9621 
    9622  > select up
    9623 
    9624  9 atoms, 8 bonds, 1 residue, 1 model selected
    9625 
    9626  > select up
    9627 
    9628  40 atoms, 39 bonds, 3 residues, 1 model selected
    9629 
    9630  > select up
    9631 
    9632  766 atoms, 787 bonds, 40 residues, 1 model selected
    9633 
    9634  > ui tool show Shell
    9635 
    9636  /opt/UCSF/ChimeraX/lib/python3.7/site-
    9637  packages/IPython/core/history.py:226:
    9638  UserWarning: IPython History requires SQLite, your history will not be
    9639  saved
    9640  warn("IPython History requires SQLite, your history will not be saved")
    9641 
    9642  > select up
    9643 
    9644  7 atoms, 6 bonds, 1 residue, 1 model selected
    9645 
    9646  > select up
    9647 
    9648  38 atoms, 37 bonds, 3 residues, 1 model selected
    9649 
    9650  > select up
    9651 
    9652  771 atoms, 792 bonds, 41 residues, 1 model selected
    9653 
    9654  > select clear
    9655 
    9656  > select clear
    9657 
    9658  > isolde stepto
    9659 
    9660  > isolde stepto
    9661 
    9662  > isolde stepto
    9663 
    9664  > isolde stepto
    9665 
    9666  > isolde stepto
    9667 
    9668  > isolde stepto
    9669 
    9670  > isolde stepto
    9671 
    9672  > isolde stepto
    9673 
    9674  > isolde stepto
    9675 
    9676  > isolde stepto
    9677 
    9678  > isolde stepto
    9679 
    9680  > isolde stepto
    9681 
    9682  > isolde stepto
    9683 
    9684  > isolde stepto
    9685 
    9686  > isolde stepto
    9687 
    9688  > isolde stepto
    9689 
    9690  > isolde stepto
    9691 
    9692  > isolde stepto
    9693 
    9694  > isolde stepto
    9695 
    9696  > isolde stepto
    9697 
    9698  > isolde stepto
    9699 
    9700  > isolde stepto
    9701 
    9702  > isolde stepto
    9703 
    9704  > isolde stepto
    9705 
    9706  > isolde stepto
    9707 
    9708  > isolde stepto
    9709 
    9710  > isolde stepto
    9711 
    9712  > isolde stepto
    9713 
    9714  > isolde stepto
    9715 
    9716  > isolde stepto
    9717 
    9718  > isolde stepto
    9719 
    9720  > isolde stepto
    9721 
    9722  > isolde stepto
    9723 
    9724  > isolde stepto
    9725 
    9726  > isolde stepto
    9727 
    9728  > isolde stepto
    9729 
    9730  > isolde stepto
    9731 
    9732  > isolde stepto
    9733 
    9734  > isolde stepto
    9735 
    9736  > select up
    9737 
    9738  7 atoms, 6 bonds, 1 residue, 1 model selected
    9739 
    9740  > select up
    9741 
    9742  38 atoms, 37 bonds, 3 residues, 1 model selected
    9743 
    9744  > select clear
    9745 
    9746  > isolde stepto
    9747 
    9748  > isolde stepto
    9749 
    9750  > isolde stepto
    9751 
    9752  > isolde stepto
    9753 
    9754  > isolde stepto
    9755 
    9756  > isolde stepto
    9757 
    9758  > isolde stepto
    9759 
    9760  > isolde stepto
    9761 
    9762  > isolde stepto
    9763 
    9764  > isolde stepto
    9765 
    9766  > isolde stepto
    9767 
    9768  > select up
    9769 
    9770  503 atoms, 512 bonds, 32 residues, 1 model selected
    9771 
    9772  > select up
    9773 
    9774  771 atoms, 792 bonds, 41 residues, 1 model selected
    9775 
    9776  > select down
    9777 
    9778  503 atoms, 512 bonds, 32 residues, 1 model selected
    9779 
    9780  > select up
    9781 
    9782  771 atoms, 792 bonds, 41 residues, 1 model selected
    9783 
    9784  > select clear
    9785 
    9786  > isolde stepto
    9787 
    9788  > isolde stepto
    9789 
    9790  > isolde stepto
    9791 
    9792  > isolde stepto
    9793 
    9794  > isolde stepto
    9795 
    9796  > isolde stepto
    9797 
    9798  > isolde stepto
    9799 
    9800  > isolde stepto
    9801 
    9802  > isolde stepto
    9803 
    9804  > isolde stepto
    9805 
    9806  > isolde stepto
    9807 
    9808  > isolde stepto
    9809 
    9810  > isolde stepto
    9811 
    9812  > isolde stepto
    9813 
    9814  > isolde stepto
    9815 
    9816  > isolde stepto
    9817 
    9818  > isolde stepto
    9819 
    9820  > isolde stepto
    9821 
    9822  > isolde stepto
    9823 
    9824  > isolde stepto
    9825 
    9826  > isolde stepto
    9827 
    9828  > isolde stepto
    9829 
    9830  > isolde stepto
    9831 
    9832  > isolde stepto
    9833 
    9834  > isolde stepto
    9835 
    9836  > isolde stepto
    9837 
    9838  > isolde stepto
    9839 
    9840  > isolde stepto
    9841 
    9842  > select up
    9843 
    9844  7 atoms, 6 bonds, 1 residue, 1 model selected
    9845 
    9846  > select up
    9847 
    9848  38 atoms, 37 bonds, 3 residues, 1 model selected
    9849 
    9850  > select up
    9851 
    9852  771 atoms, 792 bonds, 41 residues, 1 model selected
    9853 
    9854  > select clear
    9855 
    9856  > isolde stepto
    9857 
    9858  > isolde stepto
    9859 
    9860  > isolde stepto
    9861 
    9862  > isolde stepto
    9863 
    9864  > isolde stepto
    9865 
    9866  > isolde stepto
    9867 
    9868  > isolde stepto
    9869 
    9870  > isolde stepto
    9871 
    9872  > isolde stepto
    9873 
    9874  > isolde stepto
    9875 
    9876  > isolde stepto
    9877 
    9878  > isolde stepto
    9879 
    9880  > isolde stepto
    9881 
    9882  > isolde stepto
    9883 
    9884  > isolde stepto
    9885 
    9886  > isolde stepto
    9887 
    9888  > isolde stepto
    9889 
    9890  > isolde stepto
    9891 
    9892  > isolde stepto
    9893 
    9894  > isolde stepto
    9895 
    9896  > isolde stepto
    9897 
    9898  > isolde stepto
    9899 
    9900  > isolde stepto
    9901 
    9902  > isolde stepto
    9903 
    9904  > isolde stepto
    9905 
    9906  > isolde stepto
    9907 
    9908  > isolde stepto
    9909 
    9910  > isolde stepto
    9911 
    9912  > isolde stepto
    9913 
    9914  > isolde stepto
    9915 
    9916  > isolde stepto
    9917 
    9918  > isolde stepto
    9919 
    9920  > isolde stepto
    9921 
    9922  > isolde stepto
    9923 
    9924  > isolde stepto
    9925 
    9926  > isolde stepto
    9927 
    9928  > isolde stepto
    9929 
    9930  > isolde stepto
    9931 
    9932  > isolde stepto
    9933 
    9934  > select up
    9935 
    9936  7 atoms, 6 bonds, 1 residue, 1 model selected
    9937 
    9938  > select up
    9939 
    9940  38 atoms, 37 bonds, 3 residues, 1 model selected
    9941 
    9942  > select up
    9943 
    9944  771 atoms, 792 bonds, 41 residues, 1 model selected
    9945 
    9946  > select clear
    9947 
    9948  > isolde stepto
    9949 
    9950  > isolde stepto
    9951 
    9952  > isolde stepto
    9953 
    9954  > isolde stepto
    9955 
    9956  > isolde stepto
    9957 
    9958  > select up
    9959 
    9960  63 atoms, 60 bonds, 3 residues, 1 model selected
    9961 
    9962  > select up
    9963 
    9964  1073 atoms, 1092 bonds, 67 residues, 1 model selected
    9965 
    9966  > select clear
    9967 
    9968  > select clear
    9969 
    9970  > isolde stepto
    9971 
    9972  > isolde stepto
    9973 
    9974  > isolde stepto
    9975 
    9976  > isolde stepto
    9977 
    9978  > isolde stepto
    9979 
    9980  > isolde stepto
    9981 
    9982  > isolde stepto
    9983 
    9984  > isolde stepto
    9985 
    9986  > isolde stepto
    9987 
    9988  > isolde stepto
    9989 
    9990  > isolde stepto
    9991 
    9992  > isolde stepto
    9993 
    9994  > isolde stepto
    9995 
    9996  > isolde stepto
    9997 
    9998  > isolde stepto
    9999 
    10000  > isolde stepto
    10001 
    10002  > isolde stepto
    10003 
    10004  > isolde stepto
    10005 
    10006  > isolde stepto
    10007 
    10008  > isolde stepto
    10009 
    10010  > isolde stepto
    10011 
    10012  > isolde stepto
    10013 
    10014  > isolde stepto
    10015 
    10016  > isolde stepto
    10017 
    10018  > isolde stepto
    10019 
    10020  > isolde stepto
    10021 
    10022  > isolde stepto
    10023 
    10024  > isolde stepto
    10025 
    10026  > isolde stepto
    10027 
    10028  > isolde stepto
    10029 
    10030  > isolde stepto
    10031 
    10032  > isolde stepto
    10033 
    10034  > isolde stepto
    10035 
    10036  > isolde stepto
    10037 
    10038  > select up
    10039 
    10040  9 atoms, 8 bonds, 1 residue, 1 model selected
    10041 
    10042  > select up
    10043 
    10044  40 atoms, 39 bonds, 3 residues, 1 model selected
    10045 
    10046  > select up
    10047 
    10048  766 atoms, 787 bonds, 40 residues, 1 model selected
    10049 
    10050  > select clear
    10051 
    10052  > select clear
    10053 
    10054  > isolde stepto
    10055 
    10056  > isolde stepto
    10057 
    10058  > isolde stepto
    10059 
    10060  > isolde stepto
    10061 
    10062  > isolde stepto
    10063 
    10064  > isolde stepto
    10065 
    10066  > isolde stepto
    10067 
    10068  > isolde stepto
    10069 
    10070  > isolde stepto
    10071 
    10072  > isolde stepto
    10073 
    10074  > isolde stepto
    10075 
    10076  > isolde stepto
    10077 
    10078  > isolde stepto
    10079 
    10080  > isolde stepto
    10081 
    10082  > isolde stepto
    10083 
    10084  > isolde stepto
    10085 
    10086  > isolde stepto
    10087 
    10088  > isolde stepto
    10089 
    10090  > isolde stepto
    10091 
    10092  > isolde stepto
    10093 
    10094  > isolde stepto
    10095 
    10096  > isolde stepto
    10097 
    10098  > isolde stepto
    10099 
    10100  > isolde stepto
    10101 
    10102  > isolde stepto
    10103 
    10104  > isolde stepto
    10105 
    10106  > isolde stepto
    10107 
    10108  > isolde stepto
    10109 
    10110  > isolde stepto
    10111 
    10112  > isolde stepto
    10113 
    10114  > isolde stepto
    10115 
    10116  > isolde stepto
    10117 
    10118  > isolde stepto
    10119 
    10120  > isolde stepto
    10121 
    10122  > isolde stepto
    10123 
    10124  > isolde stepto
    10125 
    10126  > isolde stepto
    10127 
    10128  > isolde stepto
    10129 
    10130  > isolde stepto
    10131 
    10132  > select up
    10133 
    10134  9 atoms, 8 bonds, 1 residue, 1 model selected
    10135 
    10136  > select up
    10137 
    10138  47 atoms, 46 bonds, 4 residues, 1 model selected
    10139 
    10140  > select up
    10141 
    10142  773 atoms, 794 bonds, 41 residues, 1 model selected
    10143 
    10144  > select clear
    10145 
    10146  > isolde stepto
    10147 
    10148  > isolde stepto
    10149 
    10150  > isolde stepto
    10151 
    10152  > isolde stepto
    10153 
    10154  > isolde stepto
    10155 
    10156  > isolde stepto
    10157 
    10158  > isolde stepto
    10159 
    10160  > isolde stepto
    10161 
    10162  > isolde stepto
    10163 
    10164  > isolde stepto
    10165 
    10166  > isolde stepto
    10167 
    10168  > isolde stepto
    10169 
    10170  > isolde stepto
    10171 
    10172  > isolde stepto
    10173 
    10174  > isolde stepto
    10175 
    10176  > isolde stepto
    10177 
    10178  > isolde stepto
    10179 
    10180  > isolde stepto
    10181 
    10182  > isolde stepto
    10183 
    10184  > isolde stepto
    10185 
    10186  > isolde stepto
    10187 
    10188  > isolde stepto
    10189 
    10190  > isolde stepto
    10191 
    10192  > isolde stepto
    10193 
    10194  > isolde stepto
    10195 
    10196  > isolde stepto
    10197 
    10198  > isolde stepto
    10199 
    10200  > isolde stepto
    10201 
    10202  > isolde stepto
    10203 
    10204  > isolde stepto
    10205 
    10206  > isolde stepto
    10207 
    10208  > isolde stepto
    10209 
    10210  > isolde stepto
    10211 
    10212  > isolde stepto
    10213 
    10214  > isolde stepto
    10215 
    10216  > isolde stepto
    10217 
    10218  > isolde stepto
    10219 
    10220  > isolde stepto
    10221 
    10222  > isolde stepto
    10223 
    10224  > isolde stepto
    10225 
    10226  > select up
    10227 
    10228  17 atoms, 16 bonds, 1 residue, 1 model selected
    10229 
    10230  > select up
    10231 
    10232  47 atoms, 46 bonds, 4 residues, 1 model selected
    10233 
    10234  > select up
    10235 
    10236  773 atoms, 794 bonds, 41 residues, 1 model selected
    10237 
    10238  > select clear
    10239 
    10240  > select clear
    10241 
    10242  > select clear
    10243 
    10244  > isolde stepto
    10245 
    10246  > isolde stepto
    10247 
    10248  > isolde stepto
    10249 
    10250  > isolde stepto
    10251 
    10252  > isolde stepto
    10253 
    10254  > isolde stepto
    10255 
    10256  > isolde stepto
    10257 
    10258  > isolde stepto
    10259 
    10260  > isolde stepto
    10261 
    10262  > isolde stepto
    10263 
    10264  > isolde stepto
    10265 
    10266  > isolde stepto
    10267 
    10268  > isolde stepto
    10269 
    10270  > isolde stepto
    10271 
    10272  > isolde stepto
    10273 
    10274  > isolde stepto
    10275 
    10276  > isolde stepto
    10277 
    10278  > isolde stepto
    10279 
    10280  > isolde stepto
    10281 
    10282  > select clear
    10283 
    10284  > isolde stepto
    10285 
    10286  > isolde stepto
    10287 
    10288  > isolde stepto
    10289 
    10290  > isolde stepto
    10291 
    10292  > isolde stepto
    10293 
    10294  > isolde stepto
    10295 
    10296  > isolde stepto
    10297 
    10298  > isolde stepto
    10299 
    10300  > isolde stepto
    10301 
    10302  > isolde stepto
    10303 
    10304  > isolde stepto
    10305 
    10306  > isolde stepto
    10307 
    10308  > isolde stepto
    10309 
    10310  > isolde stepto
    10311 
    10312  > isolde stepto
    10313 
    10314  > isolde stepto
    10315 
    10316  > isolde stepto
    10317 
    10318  > isolde stepto
    10319 
    10320  > isolde stepto
    10321 
    10322  > isolde stepto
    10323 
    10324  > select clear
    10325 
    10326  > save working.cxs
    10327 
    10328  Taking snapshot of stepper: working_2.pdb
    10329 
    10330  > isolde stepto
    10331 
    10332  > select up
    10333 
    10334  9 atoms, 8 bonds, 1 residue, 1 model selected
    10335 
    10336  > select up
    10337 
    10338  40 atoms, 39 bonds, 3 residues, 1 model selected
    10339 
    10340  > select up
    10341 
    10342  766 atoms, 787 bonds, 40 residues, 1 model selected
    10343 
    10344  > select clear
    10345 
    10346  > isolde stepto
    10347 
    10348  > isolde stepto
    10349 
    10350  > isolde stepto
    10351 
    10352  > isolde stepto
    10353 
    10354  > isolde stepto
    10355 
    10356  > isolde stepto
    10357 
    10358  > isolde stepto
    10359 
    10360  > isolde stepto
    10361 
    10362  > isolde stepto
    10363 
    10364  > isolde stepto
    10365 
    10366  > isolde stepto
    10367 
    10368  > isolde stepto
    10369 
    10370  > isolde stepto
    10371 
    10372  > isolde stepto
    10373 
    10374  > isolde stepto
    10375 
    10376  > isolde stepto
    10377 
    10378  > isolde stepto
    10379 
    10380  > isolde stepto
    10381 
    10382  > isolde stepto
    10383 
    10384  > isolde stepto
    10385 
    10386  > isolde stepto
    10387 
    10388  > isolde stepto
    10389 
    10390  > isolde stepto
    10391 
    10392  > isolde stepto
    10393 
    10394  > isolde stepto
    10395 
    10396  > isolde stepto
    10397 
    10398  > isolde stepto
    10399 
    10400  > isolde stepto
    10401 
    10402  > isolde stepto
    10403 
    10404  > isolde stepto
    10405 
    10406  > isolde stepto
    10407 
    10408  > isolde stepto
    10409 
    10410  > isolde stepto
    10411 
    10412  > isolde stepto
    10413 
    10414  > isolde stepto
    10415 
    10416  > isolde stepto
    10417 
    10418  > isolde stepto
    10419 
    10420  > isolde stepto
    10421 
    10422  > isolde stepto
    10423 
    10424  > select clear
    10425 
    10426  > select clear
    10427 
    10428  > isolde stepto /aa
    10429 
    10430  Multiple residues selected! Going to the first...
    10431 
    10432  > select up
    10433 
    10434  24 atoms, 23 bonds, 1 residue, 1 model selected
    10435 
    10436  > select up
    10437 
    10438  86 atoms, 87 bonds, 4 residues, 1 model selected
    10439 
    10440  > select up
    10441 
    10442  1062 atoms, 1082 bonds, 60 residues, 1 model selected
    10443 
    10444  > select clear
    10445 
    10446  > isolde stepto
    10447 
    10448  > select clear
    10449 
    10450  > isolde stepto
    10451 
    10452  > isolde stepto
    10453 
    10454  > isolde stepto
    10455 
    10456  > isolde stepto
    10457 
    10458  > isolde stepto
    10459 
    10460  > isolde stepto
    10461 
    10462  > isolde stepto
    10463 
    10464  > isolde stepto
    10465 
    10466  > isolde stepto
    10467 
    10468  > isolde stepto
    10469 
    10470  > isolde stepto
    10471 
    10472  > isolde stepto
    10473 
    10474  > select clear
    10475 
    10476  > isolde stepto
    10477 
    10478  > isolde stepto
    10479 
    10480  > isolde stepto
    10481 
    10482  > isolde stepto
    10483 
    10484  > isolde stepto
    10485 
    10486  > isolde stepto
    10487 
    10488  > isolde stepto
    10489 
    10490  > isolde stepto
    10491 
    10492  > isolde stepto
    10493 
    10494  > isolde stepto
    10495 
    10496  > isolde stepto
    10497 
    10498  > isolde stepto
    10499 
    10500  > isolde stepto
    10501 
    10502  > isolde stepto
    10503 
    10504  > isolde stepto
    10505 
    10506  > isolde stepto
    10507 
    10508  > isolde stepto
    10509 
    10510  > isolde stepto
    10511 
    10512  > isolde stepto
    10513 
    10514  > isolde stepto
    10515 
    10516  > isolde stepto
    10517 
    10518  > isolde stepto
    10519 
    10520  > isolde stepto
    10521 
    10522  > isolde stepto
    10523 
    10524  > isolde stepto
    10525 
    10526  > isolde stepto
    10527 
    10528  > isolde stepto
    10529 
    10530  > isolde stepto
    10531 
    10532  > isolde stepto
    10533 
    10534  > isolde stepto
    10535 
    10536  > isolde stepto
    10537 
    10538  > isolde stepto
    10539 
    10540  > isolde stepto
    10541 
    10542  > isolde stepto
    10543 
    10544  > isolde stepto
    10545 
    10546  > isolde stepto
    10547 
    10548  > isolde stepto
    10549 
    10550  > isolde stepto
    10551 
    10552  > isolde stepto
    10553 
    10554  > isolde stepto
    10555 
    10556  > isolde stepto
    10557 
    10558  > isolde stepto
    10559 
    10560  > isolde stepto
    10561 
    10562  > isolde stepto
    10563 
    10564  > isolde stepto
    10565 
    10566  > isolde stepto
    10567 
    10568  > select up
    10569 
    10570  17 atoms, 17 bonds, 1 residue, 1 model selected
    10571 
    10572  > select up
    10573 
    10574  84 atoms, 86 bonds, 4 residues, 1 model selected
    10575 
    10576  > select up
    10577 
    10578  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10579 
    10580  > select up
    10581 
    10582  96659 atoms, 98767 bonds, 5198 residues, 1 model selected
    10583 
    10584  > select down
    10585 
    10586  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10587 
    10588  > select clear
    10589 
    10590  > select clear
    10591 
    10592  > isolde stepto
    10593 
    10594  > isolde stepto
    10595 
    10596  > isolde stepto
    10597 
    10598  > isolde stepto
    10599 
    10600  > isolde stepto
    10601 
    10602  > isolde stepto
    10603 
    10604  > isolde stepto
    10605 
    10606  > isolde stepto
    10607 
    10608  > isolde stepto
    10609 
    10610  > isolde stepto
    10611 
    10612  > isolde stepto
    10613 
    10614  > isolde stepto
    10615 
    10616  > isolde stepto
    10617 
    10618  > isolde stepto
    10619 
    10620  > isolde stepto
    10621 
    10622  > isolde stepto
    10623 
    10624  > isolde stepto
    10625 
    10626  > isolde stepto
    10627 
    10628  > isolde stepto
    10629 
    10630  > isolde stepto
    10631 
    10632  > isolde stepto
    10633 
    10634  > isolde stepto
    10635 
    10636  > isolde stepto
    10637 
    10638  > isolde stepto
    10639 
    10640  > isolde stepto
    10641 
    10642  > select clear
    10643 
    10644  > isolde stepto
    10645 
    10646  > isolde stepto
    10647 
    10648  > isolde stepto
    10649 
    10650  > isolde stepto
    10651 
    10652  > isolde stepto
    10653 
    10654  > isolde stepto
    10655 
    10656  > select clear
    10657 
    10658  > isolde stepto
    10659 
    10660  > isolde stepto
    10661 
    10662  > isolde stepto
    10663 
    10664  > isolde stepto
    10665 
    10666  > isolde stepto
    10667 
    10668  > isolde stepto
    10669 
    10670  > isolde stepto
    10671 
    10672  > isolde stepto
    10673 
    10674  > isolde stepto
    10675 
    10676  > isolde stepto
    10677 
    10678  > isolde stepto
    10679 
    10680  > isolde stepto
    10681 
    10682  > isolde stepto
    10683 
    10684  > isolde stepto
    10685 
    10686  > isolde stepto
    10687 
    10688  > isolde stepto
    10689 
    10690  > isolde stepto
    10691 
    10692  > isolde stepto
    10693 
    10694  > isolde stepto
    10695 
    10696  > isolde stepto
    10697 
    10698  > isolde stepto
    10699 
    10700  > isolde stepto
    10701 
    10702  > isolde stepto
    10703 
    10704  > isolde stepto
    10705 
    10706  > select clear
    10707 
    10708  > isolde stepto
    10709 
    10710  > isolde stepto
    10711 
    10712  > isolde stepto
    10713 
    10714  > isolde stepto
    10715 
    10716  > isolde stepto
    10717 
    10718  > view /ab:2
    10719 
    10720  > select clear
    10721 
    10722  > isolde stepto
    10723 
    10724  > view /ab:2
    10725 
    10726  > select clear
    10727 
    10728  > select clear
    10729 
    10730  > isolde stepto
    10731 
    10732  > select up
    10733 
    10734  19 atoms, 18 bonds, 1 residue, 1 model selected
    10735 
    10736  > select up
    10737 
    10738  84 atoms, 86 bonds, 4 residues, 1 model selected
    10739 
    10740  > select up
    10741 
    10742  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10743 
    10744  > select clear
    10745 
    10746  > isolde stepto
    10747 
    10748  > isolde stepto
    10749 
    10750  > isolde stepto
    10751 
    10752  > isolde stepto
    10753 
    10754  > select clear
    10755 
    10756  > isolde stepto
    10757 
    10758  > isolde stepto
    10759 
    10760  > isolde stepto
    10761 
    10762  > isolde stepto
    10763 
    10764  > select clear
    10765 
    10766  > isolde stepto
    10767 
    10768  > isolde stepto
    10769 
    10770  > isolde stepto
    10771 
    10772  > isolde stepto
    10773 
    10774  > isolde stepto
    10775 
    10776  > isolde stepto
    10777 
    10778  > isolde stepto
    10779 
    10780  > isolde stepto
    10781 
    10782  > isolde stepto
    10783 
    10784  > isolde stepto
    10785 
    10786  > isolde stepto
    10787 
    10788  > isolde stepto
    10789 
    10790  > isolde stepto
    10791 
    10792  > isolde stepto
    10793 
    10794  > isolde stepto
    10795 
    10796  > isolde stepto
    10797 
    10798  > isolde stepto
    10799 
    10800  > isolde stepto
    10801 
    10802  > isolde stepto
    10803 
    10804  > select clear
    10805 
    10806  > isolde stepto
    10807 
    10808  > isolde stepto
    10809 
    10810  > isolde stepto
    10811 
    10812  > isolde stepto
    10813 
    10814  > isolde stepto
    10815 
    10816  > isolde stepto
    10817 
    10818  > isolde stepto
    10819 
    10820  > isolde stepto
    10821 
    10822  > isolde stepto
    10823 
    10824  > isolde stepto
    10825 
    10826  > isolde stepto
    10827 
    10828  > isolde stepto
    10829 
    10830  > isolde stepto
    10831 
    10832  > isolde stepto
    10833 
    10834  > isolde stepto
    10835 
    10836  > isolde stepto
    10837 
    10838  > isolde stepto
    10839 
    10840  > isolde stepto
    10841 
    10842  > isolde stepto
    10843 
    10844  > isolde stepto
    10845 
    10846  > isolde stepto
    10847 
    10848  > isolde stepto
    10849 
    10850  > isolde stepto
    10851 
    10852  > isolde stepto
    10853 
    10854  > select clear
    10855 
    10856  > delete sel
    10857 
    10858  > select clear
    10859 
    10860  > isolde stepto
    10861 
    10862  > isolde stepto
    10863 
    10864  > isolde stepto
    10865 
    10866  > select up
    10867 
    10868  19 atoms, 18 bonds, 1 residue, 1 model selected
    10869 
    10870  > select up
    10871 
    10872  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10873 
    10874  > save working.cxs
    10875 
    10876  Taking snapshot of stepper: working_2.pdb
    10877 
    10878  > select clear
    10879 
    10880  > select up
    10881 
    10882  19 atoms, 18 bonds, 1 residue, 1 model selected
    10883 
    10884  > select up
    10885 
    10886  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10887 
    10888  > select up
    10889 
    10890  96615 atoms, 98722 bonds, 5194 residues, 1 model selected
    10891 
    10892  > select down
    10893 
    10894  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10895 
    10896  > select clear
    10897 
    10898  > select clear
    10899 
    10900  > save working.cxs
    10901 
    10902  Taking snapshot of stepper: working_2.pdb
    10903 
    10904  > select up
    10905 
    10906  19 atoms, 18 bonds, 1 residue, 1 model selected
    10907 
    10908  > select up
    10909 
    10910  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    10911 
    10912  > select clear
    10913 
    10914  > isolde stepto
    10915 
    10916  > isolde stepto
    10917 
    10918  > isolde stepto
    10919 
    10920  > isolde stepto
    10921 
    10922  > isolde stepto
    10923 
    10924  > isolde stepto
    10925 
    10926  > isolde stepto
    10927 
    10928  > isolde stepto
    10929 
    10930  > isolde stepto
    10931 
    10932  > isolde stepto
    10933 
    10934  > isolde stepto
    10935 
    10936  > isolde add ligand CDL
    10937 
    10938  place_ligand() was called with use_md_template=True, but no suitable
    10939  template
    10940  was found. This command has been ignored.
    10941 
    10942  > select up
    10943 
    10944  256 atoms, 255 bonds, 1 residue, 1 model selected
    10945 
    10946  > isolde ignore ~sel
    10947 
    10948  ISOLDE: currently ignoring 5194 residues in model 8.2
    10949 
    10950  > select up
    10951 
    10952  256 atoms, 255 bonds, 1 residue, 1 model selected
    10953 
    10954  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10955  bonded heavy atom.
    10956 
    10957  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10958  bonded heavy atom.
    10959 
    10960  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10961  bonded heavy atom.
    10962 
    10963  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10964  bonded heavy atom.
    10965 
    10966  > isolde ~ignore
    10967 
    10968  > select up
    10969 
    10970  256 atoms, 255 bonds, 1 residue, 1 model selected
    10971 
    10972  > select up
    10973 
    10974  140 atoms, 148 bonds, 1 residue, 1 model selected
    10975 
    10976  > isolde ignore sel
    10977 
    10978  ISOLDE: currently ignoring 1 residues in model 8.2
    10979 
    10980  > select up
    10981 
    10982  256 atoms, 255 bonds, 1 residue, 1 model selected
    10983 
    10984  > select down
    10985 
    10986  2 atoms, 1 bond, 1 residue, 1 model selected
    10987 
    10988  > isolde ~ignore
    10989 
    10990  > select up
    10991 
    10992  256 atoms, 255 bonds, 1 residue, 1 model selected
    10993 
    10994  > isolde ignore sel
    10995 
    10996  ISOLDE: currently ignoring 1 residues in model 8.2
    10997 
    10998  > isolde ~ignore
    10999 
    11000  Chain ak, residue 67 specifies more than one residue! The simulation can
    11001  still
    11002  run, but this will probably cause problems later if not rectified by
    11003  renumbering.
    11004 
    11005  > select clear
    11006 
    11007  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11008  bonded heavy atom.
    11009 
    11010  > select up
    11011 
    11012  256 atoms, 255 bonds, 1 residue, 1 model selected
    11013 
    11014  > clipper isolate sel contextDistance 0 maskRadius 3
    11015 
    11016  > select clear
    11017 
    11018  > ~cartoon
    11019 
    11020  > hide HC
    11021 
    11022  > hide #!8.1.1.2 models
    11023 
    11024  > show #!8.1.1.2 models
    11025 
    11026  > select clear
    11027 
    11028  > save resolved_cdl.jpg
    11029 
    11030  > cartoon
    11031 
    11032  > select /ae:CDL
    11033 
    11034  256 atoms, 255 bonds, 1 residue, 1 model selected
    11035 
    11036  > select /ae:11-30@CA
    11037 
    11038  20 atoms, 20 residues, 1 model selected
    11039 
    11040  > select /af:11-30@CA
    11041 
    11042  20 atoms, 20 residues, 1 model selected
    11043 
    11044  > save working_cdl.cxs
    11045 
    11046  Taking snapshot of stepper: working_2.pdb
    11047 
    11048  > select up
    11049 
    11050  256 atoms, 255 bonds, 1 residue, 1 model selected
    11051 
    11052  > isolde ignore ~sel
    11053 
    11054  ISOLDE: currently ignoring 5195 residues in model 8.2
    11055 
    11056  > select up
    11057 
    11058  256 atoms, 255 bonds, 1 residue, 1 model selected
    11059 
    11060  > isolde ignore sel
    11061 
    11062  ISOLDE: currently ignoring 5196 residues in model 8.2
    11063  Traceback (most recent call last):
    11064  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11065  packages/chimerax/isolde/isolde.py", line 2707, in
    11066  _start_sim_or_toggle_pause
    11067  self.start_sim()
    11068  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11069  packages/chimerax/isolde/isolde.py", line 2727, in start_sim
    11070  self.params, self.sim_params, excluded_residues = self.ignored_residues)
    11071  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11072  packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in
    11073  __init__
    11074  self._prepare_mdff_managers()
    11075  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11076  packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    11077  _prepare_mdff_managers
    11078  focus = False)
    11079  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11080  packages/chimerax/clipper/symmetry.py", line 982, in
    11081  isolate_and_cover_selection
    11082  extra_padding=extra_padding)
    11083  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11084  packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms
    11085  zm.set_symmetry_map(atoms, transforms, transform_indices)
    11086  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11087  packages/chimerax/clipper/maps/mask_handler.py", line 119, in
    11088  set_symmetry_map
    11089  self.structure = self._unique_structure(atoms)
    11090  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11091  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    11092  _unique_structure
    11093  raise TypeError('All atoms for zone mask must be from a single model!')
    11094  TypeError: All atoms for zone mask must be from a single model!
    11095 
    11096  TypeError: All atoms for zone mask must be from a single model!
    11097 
    11098  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    11099  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    11100  _unique_structure
    11101  raise TypeError('All atoms for zone mask must be from a single model!')
    11102 
    11103  See log for complete Python traceback.
    11104 
    11105 
    11106  > isolde ~ignore
    11107 
    11108  > color bychain
    11109 
    11110  > color byhetero
    11111 
    11112  > select up
    11113 
    11114  256 atoms, 255 bonds, 1 residue, 1 model selected
    11115 
    11116  > isolde ignore sel
    11117 
    11118  ISOLDE: currently ignoring 1 residues in model 8.2
    11119 
    11120  > select up
    11121 
    11122  256 atoms, 255 bonds, 1 residue, 1 model selected
    11123 
    11124  > isolde ~ignore
    11125 
    11126  > isolde ignore ~sel
    11127 
    11128  ISOLDE: currently ignoring 5195 residues in model 8.2
    11129 
    11130  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11131  bonded heavy atom.
    11132 
    11133  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11134  bonded heavy atom.
    11135 
    11136  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11137  bonded heavy atom.
    11138 
    11139  > select up
    11140 
    11141  256 atoms, 255 bonds, 1 residue, 1 model selected
    11142 
    11143  > isolde ~ignore
    11144 
    11145  > select clear
    11146 
    11147  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11148  bonded heavy atom.
    11149 
    11150  > select /ag:11-30@CA
    11151 
    11152  20 atoms, 20 residues, 1 model selected
    11153 
    11154  > select up
    11155 
    11156  256 atoms, 255 bonds, 1 residue, 1 model selected
    11157 
    11158  > isolde ignore ~sel
    11159 
    11160  ISOLDE: currently ignoring 5196 residues in model 8.2
    11161 
    11162  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11163  bonded heavy atom.
    11164 
    11165  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11166  bonded heavy atom.
    11167 
    11168  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11169  bonded heavy atom.
    11170 
    11171  > select up
    11172 
    11173  256 atoms, 255 bonds, 1 residue, 1 model selected
    11174 
    11175  > isolde ~ignore
    11176 
    11177  > select up
    11178 
    11179  256 atoms, 255 bonds, 1 residue, 1 model selected
    11180 
    11181  > isolde ignore sel
    11182 
    11183  ISOLDE: currently ignoring 1 residues in model 8.2
    11184 
    11185  > select clear
    11186 
    11187  > isolde ~ignore
    11188 
    11189  > select clear
    11190 
    11191  > save working_cdl.cxs
    11192 
    11193  Taking snapshot of stepper: working_2.pdb
    11194 
    11195  > select /ah:11-30@CA
    11196 
    11197  20 atoms, 20 residues, 1 model selected
    11198 
    11199  > select /AH
    11200 
    11201  1018 atoms, 1040 bonds, 51 residues, 1 model selected
    11202 
    11203  > cartoon
    11204 
    11205  > select :CDL
    11206 
    11207  768 atoms, 765 bonds, 3 residues, 1 model selected
    11208 
    11209  > select /ae, af, ag
    11210 
    11211  4005 atoms, 4062 bonds, 186 residues, 1 model selected
    11212 
    11213  > select /ae, af, ag,ah
    11214 
    11215  5084 atoms, 5161 bonds, 247 residues, 1 model selected
    11216 
    11217  > select clear
    11218 
    11219  > select /ah:11-30@CA
    11220 
    11221  20 atoms, 20 residues, 1 model selected
    11222 
    11223  > select up
    11224 
    11225  256 atoms, 255 bonds, 1 residue, 1 model selected
    11226 
    11227  > delete sel
    11228 
    11229  > select /ad
    11230 
    11231  1079 atoms, 1099 bonds, 61 residues, 1 model selected
    11232 
    11233  > select /ad,ae
    11234 
    11235  2414 atoms, 2453 bonds, 123 residues, 1 model selected
    11236 
    11237  > select /ad:11-30@CA
    11238 
    11239  20 atoms, 20 residues, 1 model selected
    11240 
    11241  > select up
    11242 
    11243  256 atoms, 255 bonds, 1 residue, 1 model selected
    11244 
    11245  > delete sel
    11246 
    11247  > select clear
    11248 
    11249  > isolde stepto
    11250 
    11251  > select clear
    11252 
    11253  > select up
    11254 
    11255  24 atoms, 23 bonds, 1 residue, 1 model selected
    11256 
    11257  > select up
    11258 
    11259  84 atoms, 86 bonds, 4 residues, 1 model selected
    11260 
    11261  > select up
    11262 
    11263  184 atoms, 185 bonds, 5 residues, 1 model selected
    11264 
    11265  > select up
    11266 
    11267  2037 atoms, 2081 bonds, 102 residues, 1 model selected
    11268 
    11269  > select down
    11270 
    11271  184 atoms, 185 bonds, 5 residues, 1 model selected
    11272 
    11273  > select up
    11274 
    11275  2037 atoms, 2081 bonds, 102 residues, 1 model selected
    11276 
    11277  > select down
    11278 
    11279  184 atoms, 185 bonds, 5 residues, 1 model selected
    11280 
    11281  > select up
    11282 
    11283  2037 atoms, 2081 bonds, 102 residues, 1 model selected
    11284 
    11285  > select clear
    11286 
    11287  > isolde stepto
    11288 
    11289  > isolde stepto
    11290 
    11291  > isolde stepto
    11292 
    11293  > isolde stepto
    11294 
    11295  > isolde stepto
    11296 
    11297  > isolde stepto
    11298 
    11299  > isolde stepto
    11300 
    11301  > isolde stepto
    11302 
    11303  > isolde stepto
    11304 
    11305  > isolde stepto
    11306 
    11307  > isolde stepto
    11308 
    11309  > isolde stepto
    11310 
    11311  > select clear
    11312 
    11313  > isolde stepto
    11314 
    11315  > isolde stepto
    11316 
    11317  > isolde stepto
    11318 
    11319  > isolde stepto
    11320 
    11321  > isolde stepto
    11322 
    11323  > isolde stepto
    11324 
    11325  > isolde stepto
    11326 
    11327  > isolde stepto
    11328 
    11329  > isolde stepto
    11330 
    11331  > isolde stepto
    11332 
    11333  > isolde stepto
    11334 
    11335  > isolde stepto
    11336 
    11337  > isolde stepto
    11338 
    11339  > isolde stepto
    11340 
    11341  > isolde stepto
    11342 
    11343  > isolde stepto
    11344 
    11345  > isolde stepto
    11346 
    11347  > isolde stepto
    11348 
    11349  > isolde stepto
    11350 
    11351  > isolde stepto
    11352 
    11353  > isolde stepto
    11354 
    11355  > isolde stepto
    11356 
    11357  > isolde stepto
    11358 
    11359  > isolde stepto
    11360 
    11361  > isolde stepto
    11362 
    11363  > isolde stepto
    11364 
    11365  > isolde stepto
    11366 
    11367  > isolde stepto
    11368 
    11369  > isolde stepto
    11370 
    11371  > isolde stepto
    11372 
    11373  > select clear
    11374 
    11375  > isolde stepto
    11376 
    11377  > isolde stepto
    11378 
    11379  > isolde stepto
    11380 
    11381  > isolde stepto
    11382 
    11383  > isolde stepto
    11384 
    11385  > isolde stepto
    11386 
    11387  > isolde stepto
    11388 
    11389  > select up
    11390 
    11391  17 atoms, 17 bonds, 1 residue, 1 model selected
    11392 
    11393  > select up
    11394 
    11395  1018 atoms, 1040 bonds, 51 residues, 1 model selected
    11396 
    11397  > select clear
    11398 
    11399  > select clear
    11400 
    11401  > select clear
    11402 
    11403  > isolde stepto
    11404 
    11405  > isolde stepto
    11406 
    11407  > isolde stepto
    11408 
    11409  > isolde stepto
    11410 
    11411  > isolde stepto
    11412 
    11413  > isolde stepto
    11414 
    11415  > isolde stepto
    11416 
    11417  > isolde stepto
    11418 
    11419  > isolde stepto
    11420 
    11421  > isolde stepto
    11422 
    11423  > isolde stepto
    11424 
    11425  > isolde stepto
    11426 
    11427  > isolde stepto
    11428 
    11429  > isolde stepto
    11430 
    11431  > isolde stepto
    11432 
    11433  > isolde stepto
    11434 
    11435  > isolde stepto
    11436 
    11437  > isolde stepto
    11438 
    11439  > isolde stepto
    11440 
    11441  > isolde stepto
    11442 
    11443  > isolde stepto
    11444 
    11445  > isolde stepto
    11446 
    11447  > isolde stepto
    11448 
    11449  > isolde stepto
    11450 
    11451  > isolde stepto
    11452 
    11453  > isolde stepto
    11454 
    11455  > isolde stepto
    11456 
    11457  > isolde stepto
    11458 
    11459  > isolde stepto
    11460 
    11461  > isolde stepto
    11462 
    11463  > isolde stepto
    11464 
    11465  > isolde stepto
    11466 
    11467  > isolde stepto
    11468 
    11469  > isolde stepto
    11470 
    11471  > isolde stepto
    11472 
    11473  > isolde stepto
    11474 
    11475  > isolde stepto
    11476 
    11477  > isolde stepto
    11478 
    11479  > isolde stepto
    11480 
    11481  > isolde stepto
    11482 
    11483  > isolde stepto
    11484 
    11485  > isolde stepto
    11486 
    11487  > isolde stepto
    11488 
    11489  > isolde stepto
    11490 
    11491  > isolde stepto
    11492 
    11493  > isolde stepto
    11494 
    11495  > isolde stepto
    11496 
    11497  > isolde stepto
    11498 
    11499  > isolde stepto
    11500 
    11501  > select up
    11502 
    11503  17 atoms, 16 bonds, 1 residue, 1 model selected
    11504 
    11505  > select up
    11506 
    11507  1004 atoms, 1025 bonds, 50 residues, 1 model selected
    11508 
    11509  > select clear
    11510 
    11511  > isolde stepto
    11512 
    11513  > isolde stepto
    11514 
    11515  > isolde stepto
    11516 
    11517  > isolde stepto
    11518 
    11519  > isolde stepto
    11520 
    11521  > isolde stepto
    11522 
    11523  > isolde stepto
    11524 
    11525  > isolde stepto
    11526 
    11527  > isolde stepto
    11528 
    11529  > isolde stepto
    11530 
    11531  > isolde stepto
    11532 
    11533  > isolde stepto
    11534 
    11535  > isolde stepto
    11536 
    11537  > isolde stepto
    11538 
    11539  > isolde stepto
    11540 
    11541  > isolde stepto
    11542 
    11543  > isolde stepto
    11544 
    11545  > isolde stepto
    11546 
    11547  > isolde stepto
    11548 
    11549  > isolde stepto
    11550 
    11551  > isolde stepto
    11552 
    11553  > isolde stepto
    11554 
    11555  > isolde stepto
    11556 
    11557  > isolde stepto
    11558 
    11559  > isolde stepto
    11560 
    11561  > isolde stepto
    11562 
    11563  > isolde stepto
    11564 
    11565  > isolde stepto
    11566 
    11567  > isolde stepto
    11568 
    11569  > isolde stepto
    11570 
    11571  > isolde stepto
    11572 
    11573  > isolde stepto
    11574 
    11575  > isolde stepto
    11576 
    11577  > isolde stepto
    11578 
    11579  > isolde stepto
    11580 
    11581  > isolde stepto
    11582 
    11583  > isolde stepto
    11584 
    11585  > isolde stepto
    11586 
    11587  > isolde stepto
    11588 
    11589  > isolde stepto
    11590 
    11591  > isolde stepto
    11592 
    11593  > isolde stepto
    11594 
    11595  > select clear
    11596 
    11597  > isolde stepto
    11598 
    11599  > isolde stepto
    11600 
    11601  > isolde stepto
    11602 
    11603  > isolde stepto
    11604 
    11605  > isolde stepto
    11606 
    11607  > select clear
    11608 
    11609  > isolde stepto
    11610 
    11611  > select up
    11612 
    11613  17 atoms, 16 bonds, 1 residue, 1 model selected
    11614 
    11615  > select up
    11616 
    11617  1004 atoms, 1025 bonds, 50 residues, 1 model selected
    11618 
    11619  > select clear
    11620 
    11621  > usage isolde jupm
    11622 
    11623  Subcommands are:
    11624 
    11625    * isolde add ligand
    11626    * isolde add water
    11627    * isolde adjust distances
    11628    * isolde adjust torsions
    11629    * isolde cisflip
    11630    * isolde demo
    11631    * isolde ignore
    11632    * isolde ~ignore
    11633    * isolde jumpto
    11634    * isolde pepflip
    11635    * isolde release distances
    11636    * isolde release torsions
    11637    * isolde remote rest info
    11638    * isolde remote rest start
    11639    * isolde remote rest stop
    11640    * isolde remote xmlrpc
    11641    * isolde replace ligand
    11642    * isolde report
    11643    * isolde reset forcefield
    11644    * isolde restrain distances
    11645    * isolde restrain ligands
    11646    * isolde restrain single distance
    11647    * isolde restrain torsions
    11648    * isolde set
    11649    * isolde sim
    11650    * isolde start
    11651    * isolde stepto
    11652    * isolde tutorial
    11653 
    11654 
    11655 
    11656  > usage isolde jump
    11657 
    11658  isolde jumpto [direction]
    11659  — Jump the view to the first residue of the next chain or the last residue
    11660  of
    11661  the previous chain.
    11662  direction: one of next or prev
    11663 
    11664  > isolde jumpto prev
    11665 
    11666  > isolde jumpto prev
    11667 
    11668  > isolde jumpto prev
    11669 
    11670  > isolde jumpto prev
    11671 
    11672  > save working.cxs
    11673 
    11674  Taking snapshot of stepper: working_2.pdb
    11675  Restoring stepper: working_2.pdb
    11676  opened ChimeraX session
    11677 
    11678  > usage volume mask
    11679 
    11680  volume mask volumes surfaces a surfaces specifier [pad a number] [extend
    11681  an
    11682  integer] [fullMap true or false] [slab slab] [invertMask true or false]
    11683  [axis
    11684  an axis vector] [sandwich true or false] [fillOverlap true or false]
    11685  [modelId
    11686  modelId]
    11687  — Mask a map to a surface
    11688  slab: a number or some numbers
    11689  modelId: a model id
    11690 
    11691  > usage volume zone
    11692 
    11693  volume zone volumes nearAtoms an atoms specifier [range a number]
    11694  [bondPointSpacing a number] [minimalBounds true or false] [newMap true or
    11695  false] [invert true or false] [subregion map region] [step map step]
    11696  [modelId
    11697  modelId]
    11698  — Zero map values beyond a distance range from atoms
    11699  modelId: a model id
    11700 
    11701  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11702 
    11703  > close #1
    11704 
    11705  > select #1
    11706 
    11707  Nothing selected
    11708 
    11709  > select #8
    11710 
    11711  97383 atoms, 99487 bonds, 14 pseudobonds, 5197 residues, 21 models
    11712  selected
    11713 
    11714  > select clear
    11715 
    11716  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11717 
    11718  > usage volume subtr
    11719 
    11720  volume subtract volumes [onGrid a density maps specifier] [boundingGrid
    11721  true
    11722  or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
    11723  floats] [valueType numeric value type] [hideMaps true or false] [subregion
    11724  map
    11725  region] [step map step] [modelId modelId] [inPlace true or false]
    11726  [scaleFactors scaleFactors] [minRms true or false]
    11727  — Subtract maps pointwise
    11728  modelId: a model id
    11729  scaleFactors: some numbers
    11730 
    11731  > volume subtract #8.1.1.1 #1 inPlace false
    11732 
    11733  > close #1
    11734 
    11735  > volume #2 level 0.03352
    11736 
    11737  > volume #2 level 0.03748
    11738 
    11739  > select :CDL
    11740 
    11741  768 atoms, 765 bonds, 3 residues, 1 model selected
    11742 
    11743  > select /C1
    11744 
    11745  1472 atoms, 1487 bonds, 92 residues, 1 model selected
    11746 
    11747  > select clear
    11748 
    11749  > delete sel
    11750 
    11751  > select up
    11752 
    11753  12 atoms, 11 bonds, 1 residue, 1 model selected
    11754 
    11755  > select up
    11756 
    11757  125 atoms, 128 bonds, 9 residues, 1 model selected
    11758 
    11759  > hide #!2 models
    11760 
    11761  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11762  bonded heavy atom.
    11763 
    11764  > show #!2 models
    11765 
    11766  > select clear
    11767 
    11768  > hide #!2 models
    11769 
    11770  > show #!2 models
    11771 
    11772  > hide #!2 models
    11773 
    11774  > ui tool show "Build Structure"
    11775 
    11776  > build start peptide "custom built" AAAAAAAAAAAAAA -139.0,135.0
    11777  -139.0,135.0
    11778  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11779  > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11780  > -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    11781 
    11782  Chain information for custom built #1
    11783  ---
    11784  Chain | Description
    11785  A | No description available
    11786 
    11787 
    11788  > select #1
    11789 
    11790  71 atoms, 70 bonds, 14 residues, 1 model selected
    11791 
    11792  > ui mousemode right "translate selected models"
    11793 
    11794  > ui mousemode right "rotate selected models"
    11795 
    11796  > ui mousemode right "translate selected models"
    11797 
    11798  > delete /C1:1-14
    11799 
    11800  > addh #1
    11801 
    11802  Summary of feedback from adding hydrogens to custom built #1
    11803  ---
    11804  notes | No usable SEQRES records for custom built (#1) chain A; guessing
    11805  termini instead
    11806  Chain-initial residues that are actual N termini: custom built #1/A ALA 1
    11807  Chain-initial residues that are not actual N termini:
    11808  Chain-final residues that are actual C termini: custom built #1/A ALA 14
    11809  Chain-final residues that are not actual C termini:
    11810  0 hydrogen bonds
    11811  72 hydrogens added
    11812 
    11813 
    11814  > hide #1 models
    11815 
    11816  > select /C1:1-14
    11817 
    11818  143 atoms, 142 bonds, 14 residues, 1 model selected
    11819 
    11820  > select /C1:1-14
    11821 
    11822  143 atoms, 142 bonds, 14 residues, 1 model selected
    11823 
    11824  > swapaa mousemode sel PRO
    11825 
    11826  > select clear
    11827 
    11828  > swapaa mousemode sel PRO
    11829 
    11830  > swapaa mousemode sel GLN
    11831 
    11832  > swapaa mousemode sel THR
    11833 
    11834  > swapaa mousemode sel GLY
    11835 
    11836  > open
    11837  >
    11838  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1a_24A.mrc
    11839 
    11840  Opened class1a_24A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11841  0.0212, step 2, values float32
    11842 
    11843  > ui tool show "Volume Viewer"
    11844 
    11845  > volume #3 step 1
    11846 
    11847  > volume #3 level 0.04119
    11848 
    11849  > volume #3 level 0.03163
    11850 
    11851  > open
    11852  >
    11853  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc
    11854 
    11855  Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11856  0.0249, step 2, values float32
    11857 
    11858  > volume #4 step 1
    11859 
    11860  > volume #4 level 0.05455
    11861 
    11862  > fitmap #4 inMap #8.1.1.1
    11863 
    11864  Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points
    11865  correlation = 0.0582, correlation about mean = 0.003368, overlap = 2.152
    11866  steps = 964, shift = 6.3, angle = 5.34 degrees
    11867 
    11868  Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11869  coordinates:
    11870  Matrix rotation and translation
    11871  0.99577666 -0.02365016 -0.08871027 25.10161578
    11872  0.02499610 0.99958822 0.01409207 -14.07791580
    11873  0.08834046 -0.01624996 0.99595778 -13.06451755
    11874  Axis -0.16303956 -0.95136249 0.26139533
    11875  Axis point 178.35759174 0.00000000 285.28764281
    11876  Rotation angle (degrees) 5.33916146
    11877  Shift along axis 5.88564083
    11878 
    11879 
    11880  > fitmap #4 inMap #8.1.1.1
    11881 
    11882  Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points
    11883  correlation = 0.1152, correlation about mean = 0.06419, overlap = 9.627
    11884  steps = 672, shift = 6.89, angle = 21.3 degrees
    11885 
    11886  Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11887  coordinates:
    11888  Matrix rotation and translation
    11889  0.92701975 -0.37501178 0.00074524 89.89128138
    11890  0.37500543 0.92701261 0.00430577 -61.35976247
    11891  -0.00230557 -0.00371206 0.99999045 1.56396515
    11892  Axis -0.01068950 0.00406739 0.99993459
    11893  Axis point 202.60869093 200.28337525 0.00000000
    11894  Rotation angle (degrees) 22.02636092
    11895  Shift along axis 0.35339585
    11896 
    11897 
    11898  > select /C1:1-14
    11899 
    11900  159 atoms, 160 bonds, 14 residues, 1 model selected
    11901 
    11902  > select /C1
    11903 
    11904  1784 atoms, 1805 bonds, 117 residues, 1 model selected
    11905 
    11906  > volume #4 level 0.04206
    11907 
    11908  > swapaa mousemode sel GLN
    11909 
    11910  > select up
    11911 
    11912  17 atoms, 16 bonds, 1 residue, 1 model selected
    11913 
    11914  > select up
    11915 
    11916  166 atoms, 167 bonds, 14 residues, 1 model selected
    11917 
    11918  > swapaa mousemode sel ASSP
    11919 
    11920  Missing or invalid "restype" argument: Should be one of 'ALA', 'ARG',
    11921  'ASN',
    11922  'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET',
    11923  'PHE',
    11924  'PRO', 'SER', 'THR', 'TRP', 'TYR', or 'VAL'
    11925 
    11926  > swapaa mousemode sel ASP
    11927 
    11928  > swapaa mousemode sel ARG
    11929 
    11930  > swapaa mousemode sel GLY
    11931 
    11932  > swapaa mousemode sel VAL
    11933 
    11934  > swapaa mousemode sel PRO
    11935 
    11936  > select up
    11937 
    11938  16 atoms, 15 bonds, 1 residue, 1 model selected
    11939 
    11940  > select up
    11941 
    11942  190 atoms, 193 bonds, 14 residues, 1 model selected
    11943 
    11944  > select clear
    11945 
    11946  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11947  bonded heavy atom.
    11948 
    11949  Unable to flip peptide bond after 50 rounds. Giving up.
    11950 
    11951  > select /C1:1-14
    11952 
    11953  190 atoms, 193 bonds, 14 residues, 1 model selected
    11954 
    11955  > select clear
    11956 
    11957  > save working.cxs
    11958 
    11959  Taking snapshot of stepper: working_2.pdb
    11960 
    11961  > select /C1
    11962 
    11963  1815 atoms, 1838 bonds, 117 residues, 1 model selected
    11964 
    11965  > select clear
    11966 
    11967  > select /ak
    11968 
    11969  1234 atoms, 1257 bonds, 72 residues, 1 model selected
    11970 
    11971  > isolde stepto /c
    11972 
    11973  Selection contains no residues!
    11974 
    11975  > isolde stepto /ac
    11976 
    11977  Multiple residues selected! Going to the first...
    11978 
    11979  > select up
    11980 
    11981  17 atoms, 17 bonds, 1 residue, 1 model selected
    11982 
    11983  > select up
    11984 
    11985  84 atoms, 86 bonds, 4 residues, 1 model selected
    11986 
    11987  > select up
    11988 
    11989  1035 atoms, 1054 bonds, 57 residues, 1 model selected
    11990 
    11991  > select clear
    11992 
    11993  > isolde stepto
    11994 
    11995  > isolde stepto
    11996 
    11997  > isolde stepto
    11998 
    11999  > isolde stepto
    12000 
    12001  > isolde stepto
    12002 
    12003  > isolde stepto
    12004 
    12005  > isolde stepto
    12006 
    12007  > isolde stepto
    12008 
    12009  > isolde stepto
    12010 
    12011  > isolde stepto
    12012 
    12013  > isolde stepto
    12014 
    12015  > isolde stepto
    12016 
    12017  > isolde stepto
    12018 
    12019  > isolde stepto
    12020 
    12021  > isolde stepto
    12022 
    12023  > isolde stepto
    12024 
    12025  > isolde stepto
    12026 
    12027  > isolde stepto
    12028 
    12029  > isolde stepto
    12030 
    12031  > isolde stepto
    12032 
    12033  > isolde stepto
    12034 
    12035  > isolde stepto
    12036 
    12037  > isolde stepto
    12038 
    12039  > isolde stepto
    12040 
    12041  > isolde stepto
    12042 
    12043  > isolde stepto
    12044 
    12045  > isolde stepto
    12046 
    12047  > isolde stepto
    12048 
    12049  > isolde stepto
    12050 
    12051  > isolde stepto
    12052 
    12053  > isolde stepto
    12054 
    12055  > isolde stepto
    12056 
    12057  > isolde stepto
    12058 
    12059  > isolde stepto
    12060 
    12061  > isolde stepto
    12062 
    12063  > isolde stepto
    12064 
    12065  > isolde stepto
    12066 
    12067  > isolde stepto
    12068 
    12069  > isolde stepto
    12070 
    12071  > isolde stepto
    12072 
    12073  > isolde stepto
    12074 
    12075  > isolde stepto
    12076 
    12077  > isolde stepto
    12078 
    12079  > isolde stepto
    12080 
    12081  > isolde stepto
    12082 
    12083  > isolde stepto
    12084 
    12085  > isolde stepto
    12086 
    12087  > isolde stepto
    12088 
    12089  > isolde stepto
    12090 
    12091  > isolde stepto
    12092 
    12093  > close #1
    12094 
    12095  > show #!2 models
    12096 
    12097  > select :CDL
    12098 
    12099  768 atoms, 765 bonds, 3 residues, 1 model selected
    12100 
    12101  > hide #!2 models
    12102 
    12103  > clipper set contourSensitivity o.25
    12104 
    12105  Missing or invalid "sensitivity" argument: Expected a number
    12106 
    12107  > clipper set contourSensitivity 0.25
    12108 
    12109  > show #!2 models
    12110 
    12111  > select :BCL
    12112 
    12113  11760 atoms, 12432 bonds, 84 residues, 1 model selected
    12114 
    12115  > hide #!2 models
    12116 
    12117  > show #!2 models
    12118 
    12119  > select clear
    12120 
    12121  > hide #!2 models
    12122 
    12123  > select /af
    12124 
    12125  1335 atoms, 1354 bonds, 62 residues, 1 model selected
    12126 
    12127  > select /ag
    12128 
    12129  1335 atoms, 1354 bonds, 62 residues, 1 model selected
    12130 
    12131  > select /ae
    12132 
    12133  1335 atoms, 1354 bonds, 62 residues, 1 model selected
    12134 
    12135  > select down
    12136 
    12137  2 atoms, 1 bond, 1 residue, 1 model selected
    12138 
    12139  > select up
    12140 
    12141  256 atoms, 255 bonds, 1 residue, 1 model selected
    12142 
    12143  > save working.cxs
    12144 
    12145  Taking snapshot of stepper: working_2.pdb
    12146 
    12147  > isolde add ligand CDL
    12148 
    12149  place_ligand() was called with use_md_template=True, but no suitable
    12150  template
    12151  was found. This command has been ignored.
    12152 
    12153  > show #!2 models
    12154 
    12155  > hide #!2 models
    12156 
    12157  > select up
    12158 
    12159  256 atoms, 255 bonds, 1 residue, 1 model selected
    12160 
    12161  > hide ~sel
    12162 
    12163  > isolde ignore ~sel
    12164 
    12165  ISOLDE: currently ignoring 5222 residues in model 8.2
    12166 
    12167  > show #!2 models
    12168 
    12169  > show ~HC
    12170 
    12171  > hide protein&~@CA
    12172 
    12173  > select up
    12174 
    12175  256 atoms, 255 bonds, 1 residue, 1 model selected
    12176 
    12177  > select up
    12178 
    12179  1282 atoms, 1300 bonds, 63 residues, 1 model selected
    12180 
    12181  > select down
    12182 
    12183  256 atoms, 255 bonds, 1 residue, 1 model selected
    12184 
    12185  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12186  bonded heavy atom.
    12187 
    12188  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12189  bonded heavy atom.
    12190 
    12191  > select clear
    12192 
    12193  > select clear
    12194 
    12195  > isolde ~ignore
    12196 
    12197  > select up
    12198 
    12199  256 atoms, 255 bonds, 1 residue, 1 model selected
    12200 
    12201  > show ~HC
    12202 
    12203  > isolde ignore sel
    12204 
    12205  ISOLDE: currently ignoring 1 residues in model 8.2
    12206 
    12207  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12208  bonded heavy atom.
    12209 
    12210  > select up
    12211 
    12212  256 atoms, 255 bonds, 1 residue, 1 model selected
    12213 
    12214  > isolde ~ignore
    12215 
    12216  > select clear
    12217 
    12218  > save working.cxs
    12219 
    12220  Taking snapshot of stepper: working_2.pdb
    12221 
    12222  > hide
    12223 
    12224  > hide #!8 models
    12225 
    12226  > volume #2 level 0.03016
    12227 
    12228  > volume #2 level 0.03131
    12229 
    12230  > show #!8 models
    12231 
    12232  > show ~HC
    12233 
    12234  > hide #!8 models
    12235 
    12236  > show #!8 models
    12237 
    12238  > select :CDL
    12239 
    12240  1024 atoms, 1020 bonds, 4 residues, 1 model selected
    12241 
    12242  > hide #!2 models
    12243 
    12244  > show #!2 models
    12245 
    12246  > hide #!2 models
    12247 
    12248  > select clear
    12249 
    12250  > select :CDL
    12251 
    12252  1024 atoms, 1020 bonds, 4 residues, 1 model selected
    12253 
    12254  > select up
    12255 
    12256  256 atoms, 255 bonds, 1 residue, 1 model selected
    12257 
    12258  > save cdl_ref.pdb #8 selectedOnly true
    12259 
    12260  > open cdl_ref.pdb
    12261 
    12262  Summary of feedback from opening cdl_ref.pdb
    12263  ---
    12264  warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A
    12265  2
    12266  TRP A 5 1 4
    12267  Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A
    12268  35 1
    12269  26
    12270  Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A
    12271  45 1
    12272  6
    12273  Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5
    12274  1 3
    12275  Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A
    12276  36 1
    12277  27
    12278  267 messages similar to the above omitted
    12279  Cannot find LINK/SSBOND residue CYS (95 )
    12280  Cannot find LINK/SSBOND residue CYS (98 )
    12281  Cannot find LINK/SSBOND residue THR (108 )
    12282  Cannot find LINK/SSBOND residue CYS (146 )
    12283  Cannot find LINK/SSBOND residue CYS (149 )
    12284  25 messages similar to the above omitted
    12285 
    12286 
    12287  > select #1
    12288 
    12289  256 atoms, 255 bonds, 1 residue, 1 model selected
    12290 
    12291  > ui mousemode right "translate selected models"
    12292 
    12293  > hide #1 models
    12294 
    12295  > select up
    12296 
    12297  256 atoms, 255 bonds, 1 residue, 1 model selected
    12298 
    12299  > isolde ~ignore
    12300 
    12301  > isolde ignore ~sel
    12302 
    12303  ISOLDE: currently ignoring 5223 residues in model 8.2
    12304  ISOLDE: currently ignoring 1 residues in model 1
    12305 
    12306  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12307  bonded heavy atom.
    12308 
    12309  > isolde ~ignore
    12310 
    12311  > save working.cxs
    12312 
    12313  Taking snapshot of stepper: working_2.pdb
    12314 
    12315  > show #!2 models
    12316 
    12317  > close #2
    12318 
    12319  > select #8
    12320 
    12321  98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models
    12322  selected
    12323 
    12324  > select clear
    12325 
    12326  > volume zone #8.1.1.1 nearAtoms #8 dist 1.5 newMap true
    12327 
    12328  Expected a keyword
    12329 
    12330  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12331 
    12332  > volume subtract #8.1.1.1 #2 inPlace false
    12333 
    12334  > close #2
    12335 
    12336  > volume #5 level 0.03153
    12337 
    12338  > volume #5 color #73d216
    12339 
    12340  > select clear
    12341 
    12342  > hide #!5 models
    12343 
    12344  > show #!5 models
    12345 
    12346  > volume #5 level 0.03261
    12347 
    12348  > select :CDL
    12349 
    12350  1536 atoms, 1530 bonds, 6 residues, 2 models selected
    12351 
    12352  > volume #3 level 0.03461
    12353 
    12354  > volume #5 level 0.03526
    12355 
    12356  > volume #5 level 0.0345
    12357 
    12358  > hide #!5 models
    12359 
    12360  > select :MAN
    12361 
    12362  40 atoms, 40 bonds, 2 residues, 1 model selected
    12363 
    12364  > show #!5 models
    12365 
    12366  > select ~CDL
    12367 
    12368  Expected an objects specifier or a keyword
    12369 
    12370  > select :CDL
    12371 
    12372  1536 atoms, 1530 bonds, 6 residues, 2 models selected
    12373 
    12374  > hide #!5 models
    12375 
    12376  > select :GPC
    12377 
    12378  4000 atoms, 3960 bonds, 40 residues, 1 model selected
    12379 
    12380  > select clear
    12381 
    12382  > select ~protein
    12383 
    12384  18265 atoms, 18944 bonds, 14 pseudobonds, 147 residues, 35 models selected
    12385 
    12386  > select clear
    12387 
    12388  > select clear
    12389 
    12390  > select up
    12391 
    12392  140 atoms, 148 bonds, 1 residue, 1 model selected
    12393 
    12394  > show sel
    12395 
    12396  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12397  bonded heavy atom.
    12398 
    12399  > select clear
    12400 
    12401  > select clear
    12402 
    12403  > select clear
    12404 
    12405  > show sel
    12406 
    12407  > show sel
    12408 
    12409  > select clear
    12410 
    12411  > select clear
    12412 
    12413  > select clear
    12414 
    12415  > select clear
    12416 
    12417  > select clear
    12418 
    12419  > select clear
    12420 
    12421  > select clear
    12422 
    12423  > select clear
    12424 
    12425  > select clear
    12426 
    12427  > select clear
    12428 
    12429  > select clear
    12430 
    12431  > select clear
    12432 
    12433  > select clear
    12434 
    12435  > select clear
    12436 
    12437  > select clear
    12438 
    12439  > select clear
    12440 
    12441  > show sel
    12442 
    12443  > select clear
    12444 
    12445  > select up
    12446 
    12447  140 atoms, 148 bonds, 1 residue, 1 model selected
    12448 
    12449  > select clear
    12450 
    12451  > select clear
    12452 
    12453  > select clear
    12454 
    12455  > select clear
    12456 
    12457  > show sel
    12458 
    12459  > select clear
    12460 
    12461  > select clear
    12462 
    12463  > select clear
    12464 
    12465  > select clear
    12466 
    12467  > select clear
    12468 
    12469  > select clear
    12470 
    12471  > select clear
    12472 
    12473  > select clear
    12474 
    12475  > select clear
    12476 
    12477  > select clear
    12478 
    12479  > select clear
    12480 
    12481  > select clear
    12482 
    12483  > select clear
    12484 
    12485  > select clear
    12486 
    12487  > select clear
    12488 
    12489  > select clear
    12490 
    12491  > select clear
    12492 
    12493  > select clear
    12494 
    12495  > select clear
    12496 
    12497  > select clear
    12498 
    12499  > select clear
    12500 
    12501  > select clear
    12502 
    12503  > select clear
    12504 
    12505  > select clear
    12506 
    12507  > select clear
    12508 
    12509  > select clear
    12510 
    12511  > select clear
    12512 
    12513  > select clear
    12514 
    12515  > select clear
    12516 
    12517  > select clear
    12518 
    12519  > select clear
    12520 
    12521  > select up
    12522 
    12523  140 atoms, 148 bonds, 1 residue, 1 model selected
    12524 
    12525  > select clear
    12526 
    12527  > select clear
    12528 
    12529  > select clear
    12530 
    12531  > save working.cxs
    12532 
    12533  Taking snapshot of stepper: working_2.pdb
    12534 
    12535  > select clear
    12536 
    12537  > select clear
    12538 
    12539  > select clear
    12540 
    12541  > select clear
    12542 
    12543  > select clear
    12544 
    12545  > select clear
    12546 
    12547  > select clear
    12548 
    12549  > select clear
    12550 
    12551  > select clear
    12552 
    12553  > select clear
    12554 
    12555  > select clear
    12556 
    12557  > select clear
    12558 
    12559  Chain L, residue 68 specifies more than one residue! The simulation can
    12560  still
    12561  run, but this will probably cause problems later if not rectified by
    12562  renumbering.
    12563 
    12564  > select clear
    12565 
    12566  > select clear
    12567 
    12568  > select clear
    12569 
    12570  > select clear
    12571 
    12572  > select clear
    12573 
    12574  > select up
    12575 
    12576  138 atoms, 139 bonds, 1 residue, 1 model selected
    12577 
    12578  > show sel
    12579 
    12580  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12581  bonded heavy atom.
    12582 
    12583  Chain ak, residue 67 specifies more than one residue! The simulation can
    12584  still
    12585  run, but this will probably cause problems later if not rectified by
    12586  renumbering.
    12587 
    12588  > select clear
    12589 
    12590  > isolde ignore ~sel
    12591 
    12592  ISOLDE: currently ignoring 5223 residues in model 8.2
    12593  ISOLDE: currently ignoring 1 residues in model 1
    12594 
    12595  > isolde ~ignore
    12596 
    12597  > select clear
    12598 
    12599  > isolde ~ignore
    12600 
    12601  > select clear
    12602 
    12603  > select clear
    12604 
    12605  > select clear
    12606 
    12607  > select clear
    12608 
    12609  > select clear
    12610 
    12611  > select clear
    12612 
    12613  > select clear
    12614 
    12615  > select clear
    12616 
    12617  > view /C:234
    12618 
    12619  > swapaa mousemode sel GLN
    12620 
    12621  Traceback (most recent call last):
    12622  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12623  packages/chimerax/isolde/isolde.py", line 2707, in
    12624  _start_sim_or_toggle_pause
    12625  self.start_sim()
    12626  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12627  packages/chimerax/isolde/isolde.py", line 2724, in start_sim
    12628  main_sel = self._last_main_sel = self._get_main_sim_selection()
    12629  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12630  packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
    12631  raise TypeError('You must select at least one atom from the current '
    12632  TypeError: You must select at least one atom from the current working
    12633  model
    12634  prior to starting a simulation!
    12635 
    12636  TypeError: You must select at least one atom from the current working
    12637  model
    12638  prior to starting a simulation!
    12639 
    12640  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12641  packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection
    12642  raise TypeError('You must select at least one atom from the current '
    12643 
    12644  See log for complete Python traceback.
    12645 
    12646 
    12647  > swapaa mousemode sel ALA
    12648 
    12649  > select clear
    12650 
    12651  > select clear
    12652 
    12653  > select clear
    12654 
    12655  > select clear
    12656 
    12657  > select clear
    12658 
    12659  > select clear
    12660 
    12661  > select clear
    12662 
    12663  > select clear
    12664 
    12665  > select clear
    12666 
    12667  > select clear
    12668 
    12669  > select clear
    12670 
    12671  > select clear
    12672 
    12673  > select clear
    12674 
    12675  > select clear
    12676 
    12677  > select clear
    12678 
    12679  > select clear
    12680 
    12681  > select clear
    12682 
    12683  > select clear
    12684 
    12685  > select clear
    12686 
    12687  > select clear
    12688 
    12689  > select clear
    12690 
    12691  > select up
    12692 
    12693  100 atoms, 99 bonds, 1 residue, 1 model selected
    12694 
    12695  > select clear
    12696 
    12697  > select clear
    12698 
    12699  > select clear
    12700 
    12701  > select clear
    12702 
    12703  > select clear
    12704 
    12705  > select clear
    12706 
    12707  > select clear
    12708 
    12709  > select clear
    12710 
    12711  > select clear
    12712 
    12713  > select up
    12714 
    12715  98238 atoms, 100348 bonds, 5224 residues, 1 model selected
    12716 
    12717  > select clear
    12718 
    12719  > select clear
    12720 
    12721  > select clear
    12722 
    12723  > select clear
    12724 
    12725  > select clear
    12726 
    12727  > select clear
    12728 
    12729  > select clear
    12730 
    12731  > select clear
    12732 
    12733  > select clear
    12734 
    12735  > select clear
    12736 
    12737  > select clear
    12738 
    12739  > select clear
    12740 
    12741  > select clear
    12742 
    12743  > select clear
    12744 
    12745  > select clear
    12746 
    12747  > save working.cxs
    12748 
    12749  Taking snapshot of stepper: working_2.pdb
    12750 
    12751  > close #5
    12752 
    12753  > select #8
    12754 
    12755  98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models
    12756  selected
    12757 
    12758  > select clear
    12759 
    12760  > volume zone #8.1.1.1.1 nearAtoms #8 range 1.5 newMap true
    12761 
    12762  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12763 
    12764  > volume subtract #8.1.1.1 #2 inPlace false
    12765 
    12766  > close #2
    12767 
    12768  > volume #5 level 0.04033
    12769 
    12770  > volume #5 level 0.03573
    12771 
    12772  > isolde add ligand LMT
    12773 
    12774  place_ligand() was called with use_md_template=True, but no suitable
    12775  template
    12776  was found. This command has been ignored.
    12777 
    12778  > select up
    12779 
    12780  81 atoms, 82 bonds, 1 residue, 1 model selected
    12781 
    12782  > ui mousemode right "translate selected atoms"
    12783 
    12784  > isolde ignore ~sel
    12785 
    12786  ISOLDE: currently ignoring 5224 residues in model 8.2
    12787  ISOLDE: currently ignoring 1 residues in model 1
    12788 
    12789  Chain L, residue 68 specifies more than one residue! The simulation can
    12790  still
    12791  run, but this will probably cause problems later if not rectified by
    12792  renumbering.
    12793 
    12794  Chain ak, residue 67 specifies more than one residue! The simulation can
    12795  still
    12796  run, but this will probably cause problems later if not rectified by
    12797  renumbering.
    12798 
    12799  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12800  bonded heavy atom.
    12801 
    12802  > isolde ~ignore
    12803 
    12804  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12805  bonded heavy atom.
    12806 
    12807  > select /AG:10-30@CA
    12808 
    12809  21 atoms, 21 residues, 1 model selected
    12810 
    12811  > select /AH:10-30@CA
    12812 
    12813  21 atoms, 21 residues, 1 model selected
    12814 
    12815  > select up
    12816 
    12817  81 atoms, 82 bonds, 1 residue, 1 model selected
    12818 
    12819  > delete sel
    12820 
    12821  > show #!5 models
    12822 
    12823  > select /AG,AH,AI,AJ
    12824 
    12825  4153 atoms, 4242 bonds, 205 residues, 1 model selected
    12826 
    12827  > select /AI:10-30@CA
    12828 
    12829  21 atoms, 21 residues, 1 model selected
    12830 
    12831  > select clear
    12832 
    12833  > select up
    12834 
    12835  81 atoms, 82 bonds, 1 residue, 1 model selected
    12836 
    12837  > ui mousemode right "translate selected atoms"
    12838 
    12839  > hide #!5 models
    12840 
    12841  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12842  bonded heavy atom.
    12843 
    12844  > select /AG,AI:LMT
    12845 
    12846  162 atoms, 164 bonds, 2 residues, 1 model selected
    12847 
    12848  > show #!5 models
    12849 
    12850  > select /AG,AJ
    12851 
    12852  2117 atoms, 2162 bonds, 103 residues, 1 model selected
    12853 
    12854  > select /AJ:10-30@CA
    12855 
    12856  21 atoms, 21 residues, 1 model selected
    12857 
    12858  > select /AG:LMT
    12859 
    12860  81 atoms, 82 bonds, 1 residue, 1 model selected
    12861 
    12862  > select /AI:LMT
    12863 
    12864  81 atoms, 82 bonds, 1 residue, 1 model selected
    12865 
    12866  > select /AJ:10-30@CA
    12867 
    12868  21 atoms, 21 residues, 1 model selected
    12869 
    12870  > hide #!5 models
    12871 
    12872  > select up
    12873 
    12874  81 atoms, 82 bonds, 1 residue, 1 model selected
    12875 
    12876  > select clear
    12877 
    12878  > view /AL:LMT
    12879 
    12880  > select clear
    12881 
    12882  > select /AM:10-30@CA
    12883 
    12884  21 atoms, 21 residues, 1 model selected
    12885 
    12886  > select up
    12887 
    12888  81 atoms, 82 bonds, 1 residue, 1 model selected
    12889 
    12890  > select /AM:10-30@CA
    12891 
    12892  21 atoms, 21 residues, 1 model selected
    12893 
    12894  > view /AM:LMT
    12895 
    12896  > select up
    12897 
    12898  81 atoms, 82 bonds, 1 residue, 1 model selected
    12899 
    12900  > view /AO:LMT
    12901 
    12902  > select /AP:10-30@CA
    12903 
    12904  21 atoms, 21 residues, 1 model selected
    12905 
    12906  > select up
    12907 
    12908  81 atoms, 82 bonds, 1 residue, 1 model selected
    12909 
    12910  > view /AP:LMT
    12911 
    12912  > select up
    12913 
    12914  81 atoms, 82 bonds, 1 residue, 1 model selected
    12915 
    12916  > view /AR:LMT
    12917 
    12918  > select clear
    12919 
    12920  > select /AS:10-30@CA
    12921 
    12922  21 atoms, 21 residues, 1 model selected
    12923 
    12924  > select up
    12925 
    12926  81 atoms, 82 bonds, 1 residue, 1 model selected
    12927 
    12928  > view /AS:LMT
    12929 
    12930  > select up
    12931 
    12932  81 atoms, 82 bonds, 1 residue, 1 model selected
    12933 
    12934  > view /AU:LMT
    12935 
    12936  > select /AV:10-30@CA
    12937 
    12938  21 atoms, 21 residues, 1 model selected
    12939 
    12940  > select up
    12941 
    12942  81 atoms, 82 bonds, 1 residue, 1 model selected
    12943 
    12944  > view /AV:LMT
    12945 
    12946  > view /AV:LMT
    12947 
    12948  > select up
    12949 
    12950  81 atoms, 82 bonds, 1 residue, 1 model selected
    12951 
    12952  > select clear
    12953 
    12954  > view /AX:LMT
    12955 
    12956  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12957  bonded heavy atom.
    12958 
    12959  > select up
    12960 
    12961  81 atoms, 82 bonds, 1 residue, 1 model selected
    12962 
    12963  > select /AA:10-30@CA
    12964 
    12965  21 atoms, 21 residues, 1 model selected
    12966 
    12967  > view /AA:LMT
    12968 
    12969  > select clear
    12970 
    12971  > select up
    12972 
    12973  81 atoms, 82 bonds, 1 residue, 1 model selected
    12974 
    12975  > view /AC:LMT
    12976 
    12977  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12978  bonded heavy atom.
    12979 
    12980  > select up
    12981 
    12982  81 atoms, 82 bonds, 1 residue, 1 model selected
    12983 
    12984  > select /AD:10-30@CA
    12985 
    12986  21 atoms, 21 residues, 1 model selected
    12987 
    12988  > select up
    12989 
    12990  81 atoms, 82 bonds, 1 residue, 1 model selected
    12991 
    12992  > view /AD:LMT
    12993 
    12994  > select up
    12995 
    12996  81 atoms, 82 bonds, 1 residue, 1 model selected
    12997 
    12998  > view /AF:LMT
    12999 
    13000  > save working.cxs
    13001 
    13002  Taking snapshot of stepper: working_2.pdb
    13003  opened ChimeraX session
    13004 
    13005  > open
    13006  >
    13007  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    13008 
    13009  Summary of feedback from opening
    13010  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    13011  ---
    13012  warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A
    13013  2
    13014  TRP A 5 1 4
    13015  Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A
    13016  35 1
    13017  26
    13018  Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A
    13019  45 1
    13020  6
    13021  Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5
    13022  1 3
    13023  Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A
    13024  36 1
    13025  27
    13026  264 messages similar to the above omitted
    13027  Cannot find LINK/SSBOND residue CYS (95 )
    13028  Cannot find LINK/SSBOND residue CYS (98 )
    13029  Cannot find LINK/SSBOND residue THR (108 )
    13030  Cannot find LINK/SSBOND residue CYS (146 )
    13031  Cannot find LINK/SSBOND residue CYS (149 )
    13032  25 messages similar to the above omitted
    13033 
    13034 
    13035  > view #2
    13036 
    13037  > select #2/AJ:61@C5'
    13038 
    13039  1 atom, 1 residue, 1 model selected
    13040 
    13041  > select #2:61
    13042 
    13043  162 atoms, 164 bonds, 2 residues, 1 model selected
    13044 
    13045  > delete sel
    13046 
    13047  > close #2
    13048 
    13049  > open
    13050  >
    13051  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    13052 
    13053  Summary of feedback from opening
    13054  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    13055  ---
    13056  warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A
    13057  2
    13058  TRP A 5 1 4
    13059  Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A
    13060  35 1
    13061  26
    13062  Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A
    13063  45 1
    13064  6
    13065  Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5
    13066  1 3
    13067  Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A
    13068  36 1
    13069  27
    13070  264 messages similar to the above omitted
    13071  Cannot find LINK/SSBOND residue CYS (95 )
    13072  Cannot find LINK/SSBOND residue CYS (98 )
    13073  Cannot find LINK/SSBOND residue THR (108 )
    13074  Cannot find LINK/SSBOND residue CYS (146 )
    13075  Cannot find LINK/SSBOND residue CYS (149 )
    13076  25 messages similar to the above omitted
    13077 
    13078 
    13079  > delete #2/AJ:61
    13080 
    13081  > isolde start
    13082 
    13083  > set selectionWidth 4
    13084 
    13085  Done loading forcefield
    13086 
    13087  > ui tool show Shell
    13088 
    13089  /opt/UCSF/ChimeraX/lib/python3.7/site-
    13090  packages/IPython/core/history.py:226:
    13091  UserWarning: IPython History requires SQLite, your history will not be
    13092  saved
    13093  warn("IPython History requires SQLite, your history will not be saved")
    13094 
    13095  > select #2
    13096 
    13097  194 atoms, 194 bonds, 2 residues, 1 model selected
    13098 
    13099  > hide #2 models
    13100 
    13101  > hide #!1 models
    13102 
    13103  > select clear
    13104 
    13105  > select clear
    13106 
    13107  > select /AK
    13108 
    13109  1406 atoms, 1428 bonds, 55 residues, 2 models selected
    13110 
    13111  > select /AK:10-30@CA
    13112 
    13113  21 atoms, 21 residues, 1 model selected
    13114 
    13115  > view /AA:PEX
    13116 
    13117  > select /AA:PEX
    13118 
    13119  113 atoms, 112 bonds, 1 residue, 1 model selected
    13120 
    13121  > select up
    13122 
    13123  194 atoms, 194 bonds, 2 residues, 1 model selected
    13124 
    13125  > delete sel
    13126 
    13127  > view /AC:PEX
    13128 
    13129  > select up
    13130 
    13131  113 atoms, 112 bonds, 1 residue, 1 model selected
    13132 
    13133  > select up
    13134 
    13135  194 atoms, 194 bonds, 2 residues, 1 model selected
    13136 
    13137  > delete sel
    13138 
    13139  > view /AE:PEX
    13140 
    13141  > select /AA, AC, AE,
    13142 
    13143  Expected an objects specifier or a keyword
    13144 
    13145  > select /AA, AC, AE
    13146 
    13147  3397 atoms, 3464 bonds, 156 residues, 1 model selected
    13148 
    13149  > select clear
    13150 
    13151  > view /AG:PEX
    13152 
    13153  > select /AG:PEX
    13154 
    13155  113 atoms, 112 bonds, 1 residue, 1 model selected
    13156 
    13157  > delete /AA,AC,AE,AG,AI,AM,AO,AQ,AS,AU,AW:61,62
    13158 
    13159  > view /AB:PEX
    13160 
    13161  > view /AE:PEX
    13162 
    13163  > view /AH:PEX
    13164 
    13165  > view /AB:PEX
    13166 
    13167  > select /AB:PEX,LMT
    13168 
    13169  194 atoms, 194 bonds, 2 residues, 1 model selected
    13170 
    13171  > select clear
    13172 
    13173  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13174  bonded heavy atom.
    13175 
    13176  > select /AE:PEX,LMT
    13177 
    13178  194 atoms, 194 bonds, 2 residues, 1 model selected
    13179 
    13180  > view sel
    13181 
    13182  > select clear
    13183 
    13184  > select /AH:PEX,LMT
    13185 
    13186  194 atoms, 194 bonds, 2 residues, 1 model selected
    13187 
    13188  > view sel
    13189 
    13190  > select clear
    13191 
    13192  > isolde add ligand LMT
    13193 
    13194  > ui mousemode right "translate selected atoms"
    13195 
    13196  > isolde add ligand BCL
    13197 
    13198  > ui mousemode right "translate selected atoms"
    13199 
    13200  > isolde ignore ~sel
    13201 
    13202  ISOLDE: currently ignoring 2 residues in model 2
    13203  ISOLDE: currently ignoring 5249 residues in model 8.2
    13204  ISOLDE: currently ignoring 1 residues in model 1.2
    13205 
    13206  > select up
    13207 
    13208  140 atoms, 148 bonds, 1 residue, 1 model selected
    13209 
    13210  > delete sel
    13211 
    13212  > isolde add ligand BPH
    13213 
    13214  > ui mousemode right "translate selected atoms"
    13215 
    13216  > isolde add ligand BCL
    13217 
    13218  > ui mousemode right "translate selected atoms"
    13219 
    13220  > select up
    13221 
    13222  141 atoms, 146 bonds, 1 residue, 1 model selected
    13223 
    13224  > delete sel
    13225 
    13226  > select up
    13227 
    13228  140 atoms, 148 bonds, 1 residue, 1 model selected
    13229 
    13230  > isolde ~ignore
    13231 
    13232  > select clear
    13233 
    13234  > select up
    13235 
    13236  140 atoms, 148 bonds, 1 residue, 1 model selected
    13237 
    13238  > save extra_bcl.pdb #1 selectedOnly true
    13239 
    13240  > select /AN:PEX,LMT
    13241 
    13242  194 atoms, 194 bonds, 2 residues, 1 model selected
    13243 
    13244  > view sel
    13245 
    13246  > select clear
    13247 
    13248  > isolde add ligand LMT
    13249 
    13250  > ui mousemode right "translate selected atoms"
    13251 
    13252  > isolde ignore ~sel
    13253 
    13254  ISOLDE: currently ignoring 2 residues in model 2
    13255  ISOLDE: currently ignoring 5250 residues in model 8.2
    13256  ISOLDE: currently ignoring 1 residues in model 1.2
    13257 
    13258  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13259  bonded heavy atom.
    13260 
    13261  > isolde ~ignore
    13262 
    13263  > select up
    13264 
    13265  19 atoms, 18 bonds, 1 residue, 1 model selected
    13266 
    13267  > isolde ignore sel
    13268 
    13269  ISOLDE: currently ignoring 1 residues in model 8.2
    13270 
    13271  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13272  bonded heavy atom.
    13273 
    13274  > isolde ~ignore
    13275 
    13276  > select clear
    13277 
    13278  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13279  bonded heavy atom.
    13280 
    13281  > select /AQ:PEX,LMT
    13282 
    13283  194 atoms, 194 bonds, 2 residues, 1 model selected
    13284 
    13285  > view sel
    13286 
    13287  > select clear
    13288 
    13289  > select /AT:PEX,LMT
    13290 
    13291  194 atoms, 194 bonds, 2 residues, 1 model selected
    13292 
    13293  > view sel
    13294 
    13295  > select clear
    13296 
    13297  > isolde add ligand LMT
    13298 
    13299  > ui mousemode right "translate selected atoms"
    13300 
    13301  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13302  bonded heavy atom.
    13303 
    13304  > select clear
    13305 
    13306  > select /AW:PEX,LMT
    13307 
    13308  194 atoms, 194 bonds, 2 residues, 1 model selected
    13309 
    13310  > view sel
    13311 
    13312  > select clear
    13313 
    13314  > select clear
    13315 
    13316  > save working.cxs
    13317 
    13318  Taking snapshot of stepper: working_2.pdb
    13319 
    13320  > close #5
    13321 
    13322  > select #8
    13323 
    13324  100821 atoms, 102950 bonds, 14 pseudobonds, 5252 residues, 22 models
    13325  selected
    13326 
    13327  > select clear
    13328 
    13329  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13330 
    13331  > volume diff #8.1.1.1 #5 inpl f
    13332 
    13333  Expected a density maps specifier or a keyword
    13334 
    13335  > volume subtract #8.1.1.1 #5 inPlace false
    13336 
    13337  > close #5
    13338 
    13339  > show #2 models
    13340 
    13341  > select #2
    13342 
    13343  194 atoms, 194 bonds, 2 residues, 1 model selected
    13344 
    13345  > select clear
    13346 
    13347  > select #2
    13348 
    13349  194 atoms, 194 bonds, 2 residues, 1 model selected
    13350 
    13351  > hide #!6 models
    13352 
    13353  > show #!6 models
    13354 
    13355  > ui mousemode right "translate selected models"
    13356 
    13357  > select #2:PEX
    13358 
    13359  113 atoms, 112 bonds, 1 residue, 1 model selected
    13360 
    13361  > select clear
    13362 
    13363  > volume #6 level 0.0417
    13364 
    13365  > hide #2 models
    13366 
    13367  > hide #!6 models
    13368 
    13369  > select up
    13370 
    13371  113 atoms, 112 bonds, 1 residue, 1 model selected
    13372 
    13373  > isolde ignore ~sel
    13374 
    13375  ISOLDE: currently ignoring 2 residues in model 2
    13376  ISOLDE: currently ignoring 5252 residues in model 8.2
    13377  ISOLDE: currently ignoring 1 residues in model 1.2
    13378 
    13379  > select clear
    13380 
    13381  > select clear
    13382 
    13383  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13384  bonded heavy atom.
    13385 
    13386  > isolde ~ignore
    13387 
    13388  > isolde add ligand LMT
    13389 
    13390  > ui mousemode right "translate selected atoms"
    13391 
    13392  > select up
    13393 
    13394  194 atoms, 194 bonds, 2 residues, 1 model selected
    13395 
    13396  > select /AX:10-30@CA
    13397 
    13398  21 atoms, 21 residues, 1 model selected
    13399 
    13400  > select /AC:PEX,LMT
    13401 
    13402  194 atoms, 194 bonds, 2 residues, 1 model selected
    13403 
    13404  > view sel
    13405 
    13406  > select up
    13407 
    13408  81 atoms, 82 bonds, 1 residue, 1 model selected
    13409 
    13410  > ui mousemode right "translate selected atoms"
    13411 
    13412  > select /AF:PEX,LMT
    13413 
    13414  275 atoms, 276 bonds, 3 residues, 1 model selected
    13415 
    13416  > view sel
    13417 
    13418  > select up
    13419 
    13420  81 atoms, 82 bonds, 1 residue, 1 model selected
    13421 
    13422  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13423  bonded heavy atom.
    13424 
    13425  > select /AI:PEX,LMT
    13426 
    13427  194 atoms, 194 bonds, 2 residues, 1 model selected
    13428 
    13429  > view sel
    13430 
    13431  > isolde add ligand LMT
    13432 
    13433  > ui mousemode right "translate selected atoms"
    13434 
    13435  > select up
    13436 
    13437  140 atoms, 148 bonds, 1 residue, 1 model selected
    13438 
    13439  > isolde ignore sel
    13440 
    13441  ISOLDE: currently ignoring 1 residues in model 8.2
    13442 
    13443  > select up
    13444 
    13445  81 atoms, 82 bonds, 1 residue, 1 model selected
    13446 
    13447  > isolde ~ignore
    13448 
    13449  > select /AL:PEX,LMT
    13450 
    13451  275 atoms, 276 bonds, 3 residues, 1 model selected
    13452 
    13453  > view sel
    13454 
    13455  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13456  bonded heavy atom.
    13457 
    13458  > select /AO:PEX,LMT
    13459 
    13460  194 atoms, 194 bonds, 2 residues, 1 model selected
    13461 
    13462  > view sel
    13463 
    13464  > isolde add ligand LMT
    13465 
    13466  > ui mousemode right "translate selected atoms"
    13467 
    13468  > select up
    13469 
    13470  81 atoms, 82 bonds, 1 residue, 1 model selected
    13471 
    13472  > delete sel
    13473 
    13474  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13475  bonded heavy atom.
    13476 
    13477  > select /AR:PEX,LMT
    13478 
    13479  275 atoms, 276 bonds, 3 residues, 1 model selected
    13480 
    13481  > view sel
    13482 
    13483  > select up
    13484 
    13485  81 atoms, 82 bonds, 1 residue, 1 model selected
    13486 
    13487  > delete sel
    13488 
    13489  > select /AU:PEX,LMT
    13490 
    13491  194 atoms, 194 bonds, 2 residues, 1 model selected
    13492 
    13493  > view sel
    13494 
    13495  > isolde add ligand LMT
    13496 
    13497  > ui mousemode right "translate selected atoms"
    13498 
    13499  > select clear
    13500 
    13501  > save working.cxs
    13502 
    13503  Taking snapshot of stepper: working_2.pdb
    13504 
    13505  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13506  bonded heavy atom.
    13507 
    13508  > select clear
    13509 
    13510  > close #6
    13511 
    13512  > select #8
    13513 
    13514  102454 atoms, 104584 bonds, 14 pseudobonds, 5269 residues, 22 models
    13515  selected
    13516 
    13517  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13518 
    13519  > volume subtract #8.1.1.1 #5 inPlace false
    13520 
    13521  > close #5
    13522 
    13523  > select clear
    13524 
    13525  > select :LMT
    13526 
    13527  2349 atoms, 2378 bonds, 29 residues, 2 models selected
    13528 
    13529  > isolde add ligand LMT
    13530 
    13531  > ui mousemode right "translate selected atoms"
    13532 
    13533  > delete sel
    13534 
    13535  > isolde add ligand LMT
    13536 
    13537  > ui mousemode right "translate selected atoms"
    13538 
    13539  > isolde add ligand LMT
    13540 
    13541  > ui mousemode right "translate selected atoms"
    13542 
    13543  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13544  bonded heavy atom.
    13545 
    13546  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13547  bonded heavy atom.
    13548 
    13549  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13550  bonded heavy atom.
    13551 
    13552  > isolde add ligand LMT
    13553 
    13554  > ui mousemode right "translate selected atoms"
    13555 
    13556  > save working.cxs
    13557 
    13558  Taking snapshot of stepper: working_2.pdb
    13559  opened ChimeraX session
    13560 
    13561  > isolde start
    13562 
    13563  > set selectionWidth 4
    13564 
    13565  Done loading forcefield
    13566 
    13567  > select up
    13568 
    13569  162 atoms, 164 bonds, 2 residues, 1 model selected
    13570 
    13571  > ui tool show Shell
    13572 
    13573  /opt/UCSF/ChimeraX/lib/python3.7/site-
    13574  packages/IPython/core/history.py:226:
    13575  UserWarning: IPython History requires SQLite, your history will not be
    13576  saved
    13577  warn("IPython History requires SQLite, your history will not be saved")
    13578 
    13579  > select /BH:10-30@CA
    13580 
    13581  21 atoms, 21 residues, 1 model selected
    13582 
    13583  > select /BH:10-40@CA
    13584 
    13585  31 atoms, 31 residues, 1 model selected
    13586 
    13587  > select up
    13588 
    13589  81 atoms, 82 bonds, 1 residue, 1 model selected
    13590 
    13591  > select /BG:10-40@CA
    13592 
    13593  31 atoms, 31 residues, 1 model selected
    13594  Loading residue template for PEX from internal database
    13595 
    13596  Chain BH, residue 60 specifies more than one residue! The simulation can
    13597  still
    13598  run, but this will probably cause problems later if not rectified by
    13599  renumbering.
    13600 
    13601  Chain BI, residue 60 specifies more than one residue! The simulation can
    13602  still
    13603  run, but this will probably cause problems later if not rectified by
    13604  renumbering.
    13605 
    13606  Chain BA, residue 60 specifies more than one residue! The simulation can
    13607  still
    13608  run, but this will probably cause problems later if not rectified by
    13609  renumbering.
    13610 
    13611  Chain BB, residue 60 specifies more than one residue! The simulation can
    13612  still
    13613  run, but this will probably cause problems later if not rectified by
    13614  renumbering.
    13615 
    13616  Chain BC, residue 60 specifies more than one residue! The simulation can
    13617  still
    13618  run, but this will probably cause problems later if not rectified by
    13619  renumbering.
    13620 
    13621  Chain BD, residue 60 specifies more than one residue! The simulation can
    13622  still
    13623  run, but this will probably cause problems later if not rectified by
    13624  renumbering.
    13625 
    13626  Chain BE, residue 60 specifies more than one residue! The simulation can
    13627  still
    13628  run, but this will probably cause problems later if not rectified by
    13629  renumbering.
    13630 
    13631  Chain BF, residue 60 specifies more than one residue! The simulation can
    13632  still
    13633  run, but this will probably cause problems later if not rectified by
    13634  renumbering.
    13635 
    13636  Chain BG, residue 60 specifies more than one residue! The simulation can
    13637  still
    13638  run, but this will probably cause problems later if not rectified by
    13639  renumbering.
    13640 
    13641  Chain BH, residue 60 specifies more than one residue! The simulation can
    13642  still
    13643  run, but this will probably cause problems later if not rectified by
    13644  renumbering.
    13645 
    13646  Chain BI, residue 60 specifies more than one residue! The simulation can
    13647  still
    13648  run, but this will probably cause problems later if not rectified by
    13649  renumbering.
    13650 
    13651  Chain BJ, residue 60 specifies more than one residue! The simulation can
    13652  still
    13653  run, but this will probably cause problems later if not rectified by
    13654  renumbering.
    13655 
    13656  Chain BK, residue 60 specifies more than one residue! The simulation can
    13657  still
    13658  run, but this will probably cause problems later if not rectified by
    13659  renumbering.
    13660 
    13661  Chain BL, residue 60 specifies more than one residue! The simulation can
    13662  still
    13663  run, but this will probably cause problems later if not rectified by
    13664  renumbering.
    13665 
    13666  Chain BM, residue 60 specifies more than one residue! The simulation can
    13667  still
    13668  run, but this will probably cause problems later if not rectified by
    13669  renumbering.
    13670 
    13671  Chain BN, residue 60 specifies more than one residue! The simulation can
    13672  still
    13673  run, but this will probably cause problems later if not rectified by
    13674  renumbering.
    13675 
    13676  Chain BO, residue 60 specifies more than one residue! The simulation can
    13677  still
    13678  run, but this will probably cause problems later if not rectified by
    13679  renumbering.
    13680 
    13681  Chain BP, residue 60 specifies more than one residue! The simulation can
    13682  still
    13683  run, but this will probably cause problems later if not rectified by
    13684  renumbering.
    13685 
    13686  Chain BQ, residue 60 specifies more than one residue! The simulation can
    13687  still
    13688  run, but this will probably cause problems later if not rectified by
    13689  renumbering.
    13690 
    13691  Chain BR, residue 60 specifies more than one residue! The simulation can
    13692  still
    13693  run, but this will probably cause problems later if not rectified by
    13694  renumbering.
    13695 
    13696  Chain BS, residue 60 specifies more than one residue! The simulation can
    13697  still
    13698  run, but this will probably cause problems later if not rectified by
    13699  renumbering.
    13700 
    13701  Chain BT, residue 60 specifies more than one residue! The simulation can
    13702  still
    13703  run, but this will probably cause problems later if not rectified by
    13704  renumbering.
    13705 
    13706  Chain BU, residue 60 specifies more than one residue! The simulation can
    13707  still
    13708  run, but this will probably cause problems later if not rectified by
    13709  renumbering.
    13710 
    13711  Chain BV, residue 60 specifies more than one residue! The simulation can
    13712  still
    13713  run, but this will probably cause problems later if not rectified by
    13714  renumbering.
    13715 
    13716  Chain BW, residue 60 specifies more than one residue! The simulation can
    13717  still
    13718  run, but this will probably cause problems later if not rectified by
    13719  renumbering.
    13720 
    13721  Chain BX, residue 60 specifies more than one residue! The simulation can
    13722  still
    13723  run, but this will probably cause problems later if not rectified by
    13724  renumbering.
    13725 
    13726  Chain L, residue 68 specifies more than one residue! The simulation can
    13727  still
    13728  run, but this will probably cause problems later if not rectified by
    13729  renumbering.
    13730 
    13731  Chain ak, residue 67 specifies more than one residue! The simulation can
    13732  still
    13733  run, but this will probably cause problems later if not rectified by
    13734  renumbering.
    13735 
    13736  Chain BH, residue 60 specifies more than one residue! The simulation can
    13737  still
    13738  run, but this will probably cause problems later if not rectified by
    13739  renumbering.
    13740 
    13741  Chain BI, residue 60 specifies more than one residue! The simulation can
    13742  still
    13743  run, but this will probably cause problems later if not rectified by
    13744  renumbering.
    13745 
    13746  Chain BI, residue 60 specifies more than one residue! The simulation can
    13747  still
    13748  run, but this will probably cause problems later if not rectified by
    13749  renumbering.
    13750 
    13751  Chain BJ, residue 60 specifies more than one residue! The simulation can
    13752  still
    13753  run, but this will probably cause problems later if not rectified by
    13754  renumbering.
    13755 
    13756  Chain BJ, residue 60 specifies more than one residue! The simulation can
    13757  still
    13758  run, but this will probably cause problems later if not rectified by
    13759  renumbering.
    13760 
    13761  Chain BK, residue 60 specifies more than one residue! The simulation can
    13762  still
    13763  run, but this will probably cause problems later if not rectified by
    13764  renumbering.
    13765 
    13766  Chain BK, residue 60 specifies more than one residue! The simulation can
    13767  still
    13768  run, but this will probably cause problems later if not rectified by
    13769  renumbering.
    13770 
    13771  Chain BL, residue 60 specifies more than one residue! The simulation can
    13772  still
    13773  run, but this will probably cause problems later if not rectified by
    13774  renumbering.
    13775 
    13776  > select ~protein
    13777 
    13778  28426 atoms, 29196 bonds, 14 pseudobonds, 265 residues, 39 models selected
    13779 
    13780  > select clear
    13781 
    13782  Chain BL, residue 60 specifies more than one residue! The simulation can
    13783  still
    13784  run, but this will probably cause problems later if not rectified by
    13785  renumbering.
    13786 
    13787  Chain BM, residue 60 specifies more than one residue! The simulation can
    13788  still
    13789  run, but this will probably cause problems later if not rectified by
    13790  renumbering.
    13791 
    13792  > select clear
    13793 
    13794  Chain BM, residue 60 specifies more than one residue! The simulation can
    13795  still
    13796  run, but this will probably cause problems later if not rectified by
    13797  renumbering.
    13798 
    13799  Chain BN, residue 60 specifies more than one residue! The simulation can
    13800  still
    13801  run, but this will probably cause problems later if not rectified by
    13802  renumbering.
    13803 
    13804  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13805  bonded heavy atom.
    13806 
    13807  Chain BN, residue 60 specifies more than one residue! The simulation can
    13808  still
    13809  run, but this will probably cause problems later if not rectified by
    13810  renumbering.
    13811 
    13812  Chain BO, residue 60 specifies more than one residue! The simulation can
    13813  still
    13814  run, but this will probably cause problems later if not rectified by
    13815  renumbering.
    13816 
    13817  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13818  bonded heavy atom.
    13819 
    13820  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13821  bonded heavy atom.
    13822 
    13823  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13824  bonded heavy atom.
    13825 
    13826  Chain BO, residue 60 specifies more than one residue! The simulation can
    13827  still
    13828  run, but this will probably cause problems later if not rectified by
    13829  renumbering.
    13830 
    13831  Chain BP, residue 60 specifies more than one residue! The simulation can
    13832  still
    13833  run, but this will probably cause problems later if not rectified by
    13834  renumbering.
    13835 
    13836  > select clear
    13837 
    13838  Chain BP, residue 60 specifies more than one residue! The simulation can
    13839  still
    13840  run, but this will probably cause problems later if not rectified by
    13841  renumbering.
    13842 
    13843  Chain BQ, residue 60 specifies more than one residue! The simulation can
    13844  still
    13845  run, but this will probably cause problems later if not rectified by
    13846  renumbering.
    13847 
    13848  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13849  bonded heavy atom.
    13850 
    13851  Chain BQ, residue 60 specifies more than one residue! The simulation can
    13852  still
    13853  run, but this will probably cause problems later if not rectified by
    13854  renumbering.
    13855 
    13856  Chain BR, residue 60 specifies more than one residue! The simulation can
    13857  still
    13858  run, but this will probably cause problems later if not rectified by
    13859  renumbering.
    13860 
    13861  > select clear
    13862 
    13863  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13864  bonded heavy atom.
    13865 
    13866  > hide #!6 models
    13867 
    13868  Chain BR, residue 60 specifies more than one residue! The simulation can
    13869  still
    13870  run, but this will probably cause problems later if not rectified by
    13871  renumbering.
    13872 
    13873  Chain BS, residue 60 specifies more than one residue! The simulation can
    13874  still
    13875  run, but this will probably cause problems later if not rectified by
    13876  renumbering.
    13877 
    13878  > select clear
    13879 
    13880  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13881  bonded heavy atom.
    13882 
    13883  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13884  bonded heavy atom.
    13885 
    13886  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13887  bonded heavy atom.
    13888 
    13889  Chain BS, residue 60 specifies more than one residue! The simulation can
    13890  still
    13891  run, but this will probably cause problems later if not rectified by
    13892  renumbering.
    13893 
    13894  Chain BT, residue 60 specifies more than one residue! The simulation can
    13895  still
    13896  run, but this will probably cause problems later if not rectified by
    13897  renumbering.
    13898 
    13899  Chain BT, residue 60 specifies more than one residue! The simulation can
    13900  still
    13901  run, but this will probably cause problems later if not rectified by
    13902  renumbering.
    13903 
    13904  Chain BU, residue 60 specifies more than one residue! The simulation can
    13905  still
    13906  run, but this will probably cause problems later if not rectified by
    13907  renumbering.
    13908 
    13909  > select clear
    13910 
    13911  Chain BU, residue 60 specifies more than one residue! The simulation can
    13912  still
    13913  run, but this will probably cause problems later if not rectified by
    13914  renumbering.
    13915 
    13916  Chain BV, residue 60 specifies more than one residue! The simulation can
    13917  still
    13918  run, but this will probably cause problems later if not rectified by
    13919  renumbering.
    13920 
    13921  Chain BV, residue 60 specifies more than one residue! The simulation can
    13922  still
    13923  run, but this will probably cause problems later if not rectified by
    13924  renumbering.
    13925 
    13926  Chain BW, residue 60 specifies more than one residue! The simulation can
    13927  still
    13928  run, but this will probably cause problems later if not rectified by
    13929  renumbering.
    13930 
    13931  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13932  bonded heavy atom.
    13933 
    13934  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13935  bonded heavy atom.
    13936 
    13937  Chain BW, residue 60 specifies more than one residue! The simulation can
    13938  still
    13939  run, but this will probably cause problems later if not rectified by
    13940  renumbering.
    13941 
    13942  Chain BX, residue 60 specifies more than one residue! The simulation can
    13943  still
    13944  run, but this will probably cause problems later if not rectified by
    13945  renumbering.
    13946 
    13947  Chain BA, residue 60 specifies more than one residue! The simulation can
    13948  still
    13949  run, but this will probably cause problems later if not rectified by
    13950  renumbering.
    13951 
    13952  Chain BX, residue 60 specifies more than one residue! The simulation can
    13953  still
    13954  run, but this will probably cause problems later if not rectified by
    13955  renumbering.
    13956 
    13957  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13958  bonded heavy atom.
    13959 
    13960  Chain BA, residue 60 specifies more than one residue! The simulation can
    13961  still
    13962  run, but this will probably cause problems later if not rectified by
    13963  renumbering.
    13964 
    13965  Chain BB, residue 60 specifies more than one residue! The simulation can
    13966  still
    13967  run, but this will probably cause problems later if not rectified by
    13968  renumbering.
    13969 
    13970  Chain BB, residue 60 specifies more than one residue! The simulation can
    13971  still
    13972  run, but this will probably cause problems later if not rectified by
    13973  renumbering.
    13974 
    13975  Chain BC, residue 60 specifies more than one residue! The simulation can
    13976  still
    13977  run, but this will probably cause problems later if not rectified by
    13978  renumbering.
    13979 
    13980  Chain BC, residue 60 specifies more than one residue! The simulation can
    13981  still
    13982  run, but this will probably cause problems later if not rectified by
    13983  renumbering.
    13984 
    13985  Chain BD, residue 60 specifies more than one residue! The simulation can
    13986  still
    13987  run, but this will probably cause problems later if not rectified by
    13988  renumbering.
    13989 
    13990  Chain BD, residue 60 specifies more than one residue! The simulation can
    13991  still
    13992  run, but this will probably cause problems later if not rectified by
    13993  renumbering.
    13994 
    13995  Chain BE, residue 60 specifies more than one residue! The simulation can
    13996  still
    13997  run, but this will probably cause problems later if not rectified by
    13998  renumbering.
    13999 
    14000  > select clear
    14001 
    14002  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14003  bonded heavy atom.
    14004 
    14005  Chain BE, residue 60 specifies more than one residue! The simulation can
    14006  still
    14007  run, but this will probably cause problems later if not rectified by
    14008  renumbering.
    14009 
    14010  Chain BF, residue 60 specifies more than one residue! The simulation can
    14011  still
    14012  run, but this will probably cause problems later if not rectified by
    14013  renumbering.
    14014 
    14015  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14016  bonded heavy atom.
    14017 
    14018  Chain BE, residue 60 specifies more than one residue! The simulation can
    14019  still
    14020  run, but this will probably cause problems later if not rectified by
    14021  renumbering.
    14022 
    14023  Chain BF, residue 60 specifies more than one residue! The simulation can
    14024  still
    14025  run, but this will probably cause problems later if not rectified by
    14026  renumbering.
    14027 
    14028  Chain BF, residue 60 specifies more than one residue! The simulation can
    14029  still
    14030  run, but this will probably cause problems later if not rectified by
    14031  renumbering.
    14032 
    14033  Chain BG, residue 60 specifies more than one residue! The simulation can
    14034  still
    14035  run, but this will probably cause problems later if not rectified by
    14036  renumbering.
    14037 
    14038  Chain BG, residue 60 specifies more than one residue! The simulation can
    14039  still
    14040  run, but this will probably cause problems later if not rectified by
    14041  renumbering.
    14042 
    14043  Chain BH, residue 60 specifies more than one residue! The simulation can
    14044  still
    14045  run, but this will probably cause problems later if not rectified by
    14046  renumbering.
    14047 
    14048  Chain BH, residue 60 specifies more than one residue! The simulation can
    14049  still
    14050  run, but this will probably cause problems later if not rectified by
    14051  renumbering.
    14052 
    14053  Chain BI, residue 60 specifies more than one residue! The simulation can
    14054  still
    14055  run, but this will probably cause problems later if not rectified by
    14056  renumbering.
    14057 
    14058  Chain BI, residue 60 specifies more than one residue! The simulation can
    14059  still
    14060  run, but this will probably cause problems later if not rectified by
    14061  renumbering.
    14062 
    14063  Chain BJ, residue 60 specifies more than one residue! The simulation can
    14064  still
    14065  run, but this will probably cause problems later if not rectified by
    14066  renumbering.
    14067 
    14068  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14069  bonded heavy atom.
    14070 
    14071  Chain BJ, residue 60 specifies more than one residue! The simulation can
    14072  still
    14073  run, but this will probably cause problems later if not rectified by
    14074  renumbering.
    14075 
    14076  Chain BK, residue 60 specifies more than one residue! The simulation can
    14077  still
    14078  run, but this will probably cause problems later if not rectified by
    14079  renumbering.
    14080 
    14081  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14082  bonded heavy atom.
    14083 
    14084  Chain BK, residue 60 specifies more than one residue! The simulation can
    14085  still
    14086  run, but this will probably cause problems later if not rectified by
    14087  renumbering.
    14088 
    14089  Chain BL, residue 60 specifies more than one residue! The simulation can
    14090  still
    14091  run, but this will probably cause problems later if not rectified by
    14092  renumbering.
    14093 
    14094  > select clear
    14095 
    14096  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14097  bonded heavy atom.
    14098 
    14099  Chain BL, residue 60 specifies more than one residue! The simulation can
    14100  still
    14101  run, but this will probably cause problems later if not rectified by
    14102  renumbering.
    14103 
    14104  Chain BM, residue 60 specifies more than one residue! The simulation can
    14105  still
    14106  run, but this will probably cause problems later if not rectified by
    14107  renumbering.
    14108 
    14109  Chain BM, residue 60 specifies more than one residue! The simulation can
    14110  still
    14111  run, but this will probably cause problems later if not rectified by
    14112  renumbering.
    14113 
    14114  Chain BN, residue 60 specifies more than one residue! The simulation can
    14115  still
    14116  run, but this will probably cause problems later if not rectified by
    14117  renumbering.
    14118 
    14119  > save working.cxs
    14120 
    14121  Taking snapshot of stepper: working_2.pdb
    14122 
    14123  > close #6
    14124 
    14125  > select #8
    14126 
    14127  108286 atoms, 110488 bonds, 14 pseudobonds, 5341 residues, 22 models
    14128  selected
    14129 
    14130  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14131 
    14132  > volume subtract #8.1.1.1 #5 inPlace false
    14133 
    14134  > close #5
    14135 
    14136  > select clear
    14137 
    14138  > hide #!6 models
    14139 
    14140  > show #!6 models
    14141 
    14142  > isolde add ligand PC1
    14143 
    14144  > ui mousemode right "translate selected atoms"
    14145 
    14146  > isolde ignore ~sel
    14147 
    14148  ISOLDE: currently ignoring 5341 residues in model 8.2
    14149  ISOLDE: currently ignoring 1 residues in model 2
    14150  ISOLDE: currently ignoring 1 residues in model 1.2
    14151 
    14152  > volume #6 level 0.04625
    14153 
    14154  > hide #!6 models
    14155 
    14156  > isolde ~ignore
    14157 
    14158  > select up
    14159 
    14160  142 atoms, 141 bonds, 1 residue, 1 model selected
    14161 
    14162  > isolde ignore sel
    14163 
    14164  ISOLDE: currently ignoring 1 residues in model 8.2
    14165 
    14166  > isolde ~ignore
    14167 
    14168  > select up
    14169 
    14170  256 atoms, 255 bonds, 1 residue, 1 model selected
    14171 
    14172  > select clear
    14173 
    14174  Chain L, residue 68 specifies more than one residue! The simulation can
    14175  still
    14176  run, but this will probably cause problems later if not rectified by
    14177  renumbering.
    14178 
    14179  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14180  bonded heavy atom.
    14181 
    14182  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14183  bonded heavy atom.
    14184 
    14185  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14186  bonded heavy atom.
    14187 
    14188  > select up
    14189 
    14190  142 atoms, 141 bonds, 1 residue, 1 model selected
    14191 
    14192  > isolde replace ligand sel P5S
    14193 
    14194  Deleted the following atoms from residue PC1 H11001: H143, H151, H122,
    14195  C14,
    14196  C15, H152, H131, H142, H141, H153, H132, C13, H133
    14197 
    14198  126 atoms were automatically renamed to match the template: C12->CA,
    14199  C11->CB,
    14200  O13->OG, P->P12, H111->HB, H112->HBA, H121->HA, O11->O16, C1->C3, C3->C1,
    14201  O21->O37, C21->C38, C22->C39, C23->C40, C24->C41, C25->C42, C26->C43,
    14202  C27->C44, C28->C45, C29->C46, C2A->C48, C2B->C49, C2C->C50, C2D->C51,
    14203  C2E->C52, C2F->C53, C2G->C54, C2H->C55, C2I->C56, O31->O19, C31->C17,
    14204  C32->C20, C33->C21, C34->C22, C35->C23, C36->C24, C37->C25, C38->C26,
    14205  C39->C27, C3A->C28, C3B->C29, C3C->C30, C3D->C31, C3E->C32, C3F->C33,
    14206  C3G->C34, C3H->C35, C3I->C36, O22->O47, O32->O18, H11->H3, H12->H3A,
    14207  H221->H39, H222->H39A, H231->H40, H232->H40A, H241->H41, H242->H41A,
    14208  H251->H42, H252->H42A, H261->H43, H262->H43A, H271->H44, H272->H44A,
    14209  H281->H45, H282->H45A, H291->H46, H292->H46A, H2A1->H48, H2A2->H48A,
    14210  H2B1->H49, H2B2->H49A, H2C1->H50, H2C2->H50A, H2D1->H51, H2D2->H51A,
    14211  H2E1->H52, H2E2->H52A, H2F1->H53, H2F2->H53A, H2G1->H54, H2G2->H54A,
    14212  H2H1->H55, H2H2->H55A, H31->H1, H32->H1A, H321->H20, H322->H20A,
    14213  H331->H21,
    14214  H332->H21A, H341->H22, H342->H22A, H351->H23, H352->H23A, H361->H24,
    14215  H362->H24A, H371->H25, H372->H25A, H381->H26, H382->H26A, H391->H27,
    14216  H392->H27A, H3A1->H28, H3A2->H28A, H3B1->H29, H3B2->H29A, H3C1->H30,
    14217  H3C2->H30A, H3D1->H31, H3D2->H31A, H3E1->H32, H3E2->H32A, H3F1->H33,
    14218  H3F2->H33A, H3G1->H34, H3G2->H34A, H3H1->H35, H3H2->H35A, O12->O15,
    14219  O14->O13,
    14220  H2I1->H56, H2I2->H56A, H2I3->H56B, H3I1->H36, H3I2->H36A, H3I3->H36B
    14221 
    14222  Rebuilt ligand P5S has chiral centres at atoms CA,C2 (highlighted). Since
    14223  the
    14224  current algorithm used to match topologies is not chirality aware, you
    14225  should
    14226  check these sites carefully to ensure they are sensible. If in doubt, it
    14227  is
    14228  best to delete with "del #8.2/H1:1001" and replace with "isolde add ligand
    14229  P5S".
    14230 
    14231  > isolde replace ligand sel P5S
    14232 
    14233  Deleted the following atoms from residue P5S H11001: HXT, HO15
    14234  Traceback (most recent call last):
    14235  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    14236  packages/chimerax/cmd_line/tool.py", line 275, in execute
    14237  cmd.run(cmd_text)
    14238  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    14239  packages/chimerax/core/commands/cli.py", line 2805, in run
    14240  result = ci.function(session, **kw_args)
    14241  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14242  packages/chimerax/isolde/atomic/building/cmd.py", line 44, in
    14243  replace_residue
    14244  chiral_centers = Atoms([a for a in residue.atoms if
    14245  residue.ideal_chirality(a.name) != 'N'])
    14246  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14247  packages/chimerax/isolde/atomic/building/cmd.py", line 44, in <listcomp>
    14248  chiral_centers = Atoms([a for a in residue.atoms if
    14249  residue.ideal_chirality(a.name) != 'N'])
    14250  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    14251  packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality
    14252  return f(self.name.encode('utf-8'), atom_name.encode('utf-8'))
    14253  KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S'
    14254 
    14255  KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S'
    14256 
    14257  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    14258  packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality
    14259  return f(self.name.encode('utf-8'), atom_name.encode('utf-8'))
    14260 
    14261  See log for complete Python traceback.
    14262 
    14263 
    14264  Chain L, residue 68 specifies more than one residue! The simulation can
    14265  still
    14266  run, but this will probably cause problems later if not rectified by
    14267  renumbering.
    14268 
    14269  > select clear
    14270 
    14271  > isolde add ligand P5S
    14272 
    14273  Deleted the following atoms from residue P5S H11002: HO15, HXT
    14274 
    14275  > ui mousemode right "translate selected atoms"
    14276 
    14277  > delete sel
    14278 
    14279  Chain L, residue 68 specifies more than one residue! The simulation can
    14280  still
    14281  run, but this will probably cause problems later if not rectified by
    14282  renumbering.
    14283 
    14284  > show #!6 models
    14285 
    14286  running convert_amber_files
    14287 
    14288  > isolde add ligand 2Y5
    14289 
    14290  Fetching CCD 2Y5 from http://ligand-expo.rcsb.org/reports/2/2Y5/2Y5.cif
    14291  Deleted the following atoms from residue 2Y5 L607: H81, H18, H78
    14292 
    14293  > ui mousemode right "translate selected atoms"
    14294 
    14295  > isolde ignore ~sel
    14296 
    14297  ISOLDE: currently ignoring 5342 residues in model 8.2
    14298  ISOLDE: currently ignoring 1 residues in model 2
    14299  ISOLDE: currently ignoring 1 residues in model 1.2
    14300 
    14301  > hide #!6 models
    14302 
    14303  > delete sel
    14304 
    14305  > isolde add ligand LMG
    14306 
    14307  Fetching CCD LMG from http://ligand-expo.rcsb.org/reports/L/LMG/LMG.cif
    14308 
    14309  > ui mousemode right "translate selected atoms"
    14310 
    14311  > isolde ignore ~sel
    14312 
    14313  ISOLDE: currently ignoring 5342 residues in model 8.2
    14314  ISOLDE: currently ignoring 1 residues in model 2
    14315  ISOLDE: currently ignoring 1 residues in model 1.2
    14316 
    14317  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14318  bonded heavy atom.
    14319 
    14320  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14321  bonded heavy atom.
    14322 
    14323  > select clear
    14324 
    14325  > delete sel
    14326 
    14327  > select up
    14328 
    14329  129 atoms, 129 bonds, 1 residue, 1 model selected
    14330 
    14331  > save LMX.pdb #8 selectedOnly true
    14332 
    14333  running convert_amber_files
    14334 
    14335  > isolde ~ignore
    14336 
    14337  > select clear
    14338 
    14339  Failed to add
    14340  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/PEE.xml:
    14341  Residue template USER_PEE with the same override level 0 already exists.
    14342 
    14343  > isolde add ligand PEE
    14344 
    14345  Deleted the following atoms from residue PEE L608: H83
    14346 
    14347  > ui mousemode right "translate selected atoms"
    14348 
    14349  > isolde ignore ~sel
    14350 
    14351  ISOLDE: currently ignoring 5343 residues in model 8.2
    14352  ISOLDE: currently ignoring 1 residues in model 2
    14353  ISOLDE: currently ignoring 1 residues in model 1.2
    14354 
    14355  > isolde ~ignore
    14356 
    14357  > select up
    14358 
    14359  133 atoms, 132 bonds, 1 residue, 1 model selected
    14360 
    14361  > isolde ignore sel
    14362 
    14363  ISOLDE: currently ignoring 1 residues in model 8.2
    14364 
    14365  > select clear
    14366 
    14367  > select up
    14368 
    14369  256 atoms, 255 bonds, 1 residue, 1 model selected
    14370 
    14371  > isolde ~ignore
    14372 
    14373  > select clear
    14374 
    14375  > select :PEE@H35
    14376 
    14377  1 atom, 1 residue, 1 model selected
    14378 
    14379  > select up
    14380 
    14381  133 atoms, 132 bonds, 1 residue, 1 model selected
    14382 
    14383  > isolde ignore sel
    14384 
    14385  ISOLDE: currently ignoring 1 residues in model 8.2
    14386 
    14387  > isolde ~ignore
    14388 
    14389  > select clear
    14390 
    14391  > select clear
    14392 
    14393  > isolde add ligand LMT
    14394 
    14395  > ui mousemode right "translate selected atoms"
    14396 
    14397  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14398  bonded heavy atom.
    14399 
    14400  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14401  bonded heavy atom.
    14402 
    14403  > select clear
    14404 
    14405  > save working.cxs
    14406 
    14407  Taking snapshot of stepper: working_2.pdb
    14408 
    14409  > isolde add ligand LMT
    14410 
    14411  > ui mousemode right "translate selected atoms"
    14412 
    14413  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14414  bonded heavy atom.
    14415 
    14416  > isolde add ligand LMG
    14417 
    14418  > ui mousemode right "translate selected atoms"
    14419 
    14420  > isolde ignore sel
    14421 
    14422  ISOLDE: currently ignoring 1 residues in model 8.2
    14423 
    14424  > isolde ~ignore
    14425 
    14426  > isolde ignore ~sel
    14427 
    14428  ISOLDE: currently ignoring 5346 residues in model 8.2
    14429  ISOLDE: currently ignoring 1 residues in model 2
    14430  ISOLDE: currently ignoring 1 residues in model 1.2
    14431 
    14432  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14433  bonded heavy atom.
    14434 
    14435  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14436  bonded heavy atom.
    14437 
    14438  > isolde ~ignore
    14439 
    14440  > select clear
    14441 
    14442  > isolde add ligand PEE
    14443 
    14444  Deleted the following atoms from residue PEE H11002: H83
    14445 
    14446  > ui mousemode right "translate selected atoms"
    14447 
    14448  > isolde ignore ~sel
    14449 
    14450  ISOLDE: currently ignoring 5347 residues in model 8.2
    14451  ISOLDE: currently ignoring 1 residues in model 2
    14452  ISOLDE: currently ignoring 1 residues in model 1.2
    14453 
    14454  > isolde ~ignore
    14455 
    14456  > select up
    14457 
    14458  133 atoms, 132 bonds, 1 residue, 1 model selected
    14459 
    14460  > select clear
    14461 
    14462  > show #!6 models
    14463 
    14464  > hide #!6 models
    14465 
    14466  > isolde add ligand PEE
    14467 
    14468  Deleted the following atoms from residue PEE M704: H83
    14469 
    14470  > ui mousemode right "translate selected atoms"
    14471 
    14472  > isolde ignore ~sel
    14473 
    14474  ISOLDE: currently ignoring 5348 residues in model 8.2
    14475  ISOLDE: currently ignoring 1 residues in model 2
    14476  ISOLDE: currently ignoring 1 residues in model 1.2
    14477 
    14478  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14479  bonded heavy atom.
    14480 
    14481  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14482  bonded heavy atom.
    14483 
    14484  > isolde ~ignore
    14485 
    14486  Chain ak, residue 67 specifies more than one residue! The simulation can
    14487  still
    14488  run, but this will probably cause problems later if not rectified by
    14489  renumbering.
    14490 
    14491  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14492  bonded heavy atom.
    14493 
    14494  > select #8
    14495 
    14496  109253 atoms, 111453 bonds, 14 pseudobonds, 5349 residues, 22 models
    14497  selected
    14498 
    14499  > close #6
    14500 
    14501  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14502 
    14503  > volume subtract #8.1.1.1 #5 new t
    14504 
    14505  Expected a keyword
    14506 
    14507  > volume subtract #8.1.1.1 #5 inPlace true
    14508 
    14509  Can't modify volume in place: class1b_26A.mrc
    14510 
    14511  > volume subtract #8.1.1.1 #5 inPlace false
    14512 
    14513  > close #5
    14514 
    14515  > select clear
    14516 
    14517  > save working.cxs
    14518 
    14519  Taking snapshot of stepper: working_2.pdb
    14520 
    14521  > isolde add ligand LMT
    14522 
    14523  > hide #!6 models
    14524 
    14525  > ui mousemode right "translate selected atoms"
    14526 
    14527  > isolde add ligand LMT
    14528 
    14529  > ui mousemode right "rotate selected models"
    14530 
    14531  > ui mousemode right "translate selected atoms"
    14532 
    14533  > isolde add ligand LMT
    14534 
    14535  > ui mousemode right "translate selected atoms"
    14536 
    14537  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14538  bonded heavy atom.
    14539 
    14540  > isolde add ligand LMT
    14541 
    14542  > ui mousemode right "translate selected atoms"
    14543 
    14544  > ui mousemode right "translate selected atoms"
    14545 
    14546  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14547  bonded heavy atom.
    14548 
    14549  > show #!6 models
    14550 
    14551  > isolde add ligand LMT
    14552 
    14553  > ui mousemode right "translate selected atoms"
    14554 
    14555  > hide #!6 models
    14556 
    14557  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14558  bonded heavy atom.
    14559 
    14560  > select clear
    14561 
    14562  > show #!6 models
    14563 
    14564  > isolde add ligand LMT
    14565 
    14566  > ui mousemode right "translate selected atoms"
    14567 
    14568  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14569  bonded heavy atom.
    14570 
    14571  > close #6
    14572 
    14573  > select #8
    14574 
    14575  109739 atoms, 111945 bonds, 14 pseudobonds, 5355 residues, 22 models
    14576  selected
    14577 
    14578  > select clear
    14579 
    14580  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14581 
    14582  > volume subtract #8.1.1.1 #5 inPlace false
    14583 
    14584  > close #5
    14585 
    14586  > select ~BCL
    14587 
    14588  Expected an objects specifier or a keyword
    14589 
    14590  > select :BCL
    14591 
    14592  11900 atoms, 12580 bonds, 85 residues, 1 model selected
    14593 
    14594  > select down
    14595 
    14596  2 atoms, 1 bond, 1 residue, 1 model selected
    14597 
    14598  > select up
    14599 
    14600  140 atoms, 148 bonds, 1 residue, 1 model selected
    14601 
    14602  > select /AG:10-40@CA
    14603 
    14604  31 atoms, 31 residues, 1 model selected
    14605 
    14606  > select /AH:10-40@CA
    14607 
    14608  31 atoms, 31 residues, 1 model selected
    14609 
    14610  Chain AH, residue 62 specifies more than one residue! The simulation can
    14611  still
    14612  run, but this will probably cause problems later if not rectified by
    14613  renumbering.
    14614 
    14615  Chain BG, residue 60 specifies more than one residue! The simulation can
    14616  still
    14617  run, but this will probably cause problems later if not rectified by
    14618  renumbering.
    14619 
    14620  Chain BH, residue 60 specifies more than one residue! The simulation can
    14621  still
    14622  run, but this will probably cause problems later if not rectified by
    14623  renumbering.
    14624 
    14625  > isolde add ligand LMT
    14626 
    14627  > ui mousemode right "translate selected atoms"
    14628 
    14629  Chain AH, residue 62 specifies more than one residue! The simulation can
    14630  still
    14631  run, but this will probably cause problems later if not rectified by
    14632  renumbering.
    14633 
    14634  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14635  bonded heavy atom.
    14636 
    14637  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14638  bonded heavy atom.
    14639 
    14640  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14641  bonded heavy atom.
    14642 
    14643  > ui mousemode right "translate selected atoms"
    14644 
    14645  Chain AH, residue 62 specifies more than one residue! The simulation can
    14646  still
    14647  run, but this will probably cause problems later if not rectified by
    14648  renumbering.
    14649 
    14650  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14651  bonded heavy atom.
    14652 
    14653  > select /AJ:10-40@CA
    14654 
    14655  31 atoms, 31 residues, 1 model selected
    14656 
    14657  Chain BI, residue 60 specifies more than one residue! The simulation can
    14658  still
    14659  run, but this will probably cause problems later if not rectified by
    14660  renumbering.
    14661 
    14662  Chain BJ, residue 60 specifies more than one residue! The simulation can
    14663  still
    14664  run, but this will probably cause problems later if not rectified by
    14665  renumbering.
    14666 
    14667  > select /AK:10-40@CA
    14668 
    14669  31 atoms, 31 residues, 1 model selected
    14670 
    14671  Chain AK, residue 62 specifies more than one residue! The simulation can
    14672  still
    14673  run, but this will probably cause problems later if not rectified by
    14674  renumbering.
    14675 
    14676  Chain BJ, residue 60 specifies more than one residue! The simulation can
    14677  still
    14678  run, but this will probably cause problems later if not rectified by
    14679  renumbering.
    14680 
    14681  Chain BK, residue 60 specifies more than one residue! The simulation can
    14682  still
    14683  run, but this will probably cause problems later if not rectified by
    14684  renumbering.
    14685 
    14686  > select /AM:10-40@CA
    14687 
    14688  31 atoms, 31 residues, 1 model selected
    14689 
    14690  Chain BL, residue 60 specifies more than one residue! The simulation can
    14691  still
    14692  run, but this will probably cause problems later if not rectified by
    14693  renumbering.
    14694 
    14695  Chain BM, residue 60 specifies more than one residue! The simulation can
    14696  still
    14697  run, but this will probably cause problems later if not rectified by
    14698  renumbering.
    14699 
    14700  Chain BN, residue 60 specifies more than one residue! The simulation can
    14701  still
    14702  run, but this will probably cause problems later if not rectified by
    14703  renumbering.
    14704 
    14705  > select clear
    14706 
    14707  > select /AN:10-40@CA
    14708 
    14709  31 atoms, 31 residues, 1 model selected
    14710 
    14711  Chain AN, residue 62 specifies more than one residue! The simulation can
    14712  still
    14713  run, but this will probably cause problems later if not rectified by
    14714  renumbering.
    14715 
    14716  Chain BM, residue 60 specifies more than one residue! The simulation can
    14717  still
    14718  run, but this will probably cause problems later if not rectified by
    14719  renumbering.
    14720 
    14721  Chain BN, residue 60 specifies more than one residue! The simulation can
    14722  still
    14723  run, but this will probably cause problems later if not rectified by
    14724  renumbering.
    14725 
    14726  > select /AP:10-40@CA
    14727 
    14728  31 atoms, 31 residues, 1 model selected
    14729 
    14730  Chain BO, residue 60 specifies more than one residue! The simulation can
    14731  still
    14732  run, but this will probably cause problems later if not rectified by
    14733  renumbering.
    14734 
    14735  Chain BP, residue 60 specifies more than one residue! The simulation can
    14736  still
    14737  run, but this will probably cause problems later if not rectified by
    14738  renumbering.
    14739 
    14740  > select /AQ:10-40@CA
    14741 
    14742  31 atoms, 31 residues, 1 model selected
    14743 
    14744  > select up
    14745 
    14746  140 atoms, 148 bonds, 1 residue, 1 model selected
    14747 
    14748  Chain AQ, residue 62 specifies more than one residue! The simulation can
    14749  still
    14750  run, but this will probably cause problems later if not rectified by
    14751  renumbering.
    14752 
    14753  Chain BQ, residue 60 specifies more than one residue! The simulation can
    14754  still
    14755  run, but this will probably cause problems later if not rectified by
    14756  renumbering.
    14757 
    14758  > select clear
    14759 
    14760  > select /AS:10-40@CA
    14761 
    14762  31 atoms, 31 residues, 1 model selected
    14763 
    14764  > select up
    14765 
    14766  140 atoms, 148 bonds, 1 residue, 1 model selected
    14767 
    14768  Chain BS, residue 60 specifies more than one residue! The simulation can
    14769  still
    14770  run, but this will probably cause problems later if not rectified by
    14771  renumbering.
    14772 
    14773  > select clear
    14774 
    14775  > select /AT:10-40@CA
    14776 
    14777  31 atoms, 31 residues, 1 model selected
    14778 
    14779  > select up
    14780 
    14781  140 atoms, 148 bonds, 1 residue, 1 model selected
    14782 
    14783  Chain AT, residue 62 specifies more than one residue! The simulation can
    14784  still
    14785  run, but this will probably cause problems later if not rectified by
    14786  renumbering.
    14787 
    14788  Chain BS, residue 60 specifies more than one residue! The simulation can
    14789  still
    14790  run, but this will probably cause problems later if not rectified by
    14791  renumbering.
    14792 
    14793  Chain BT, residue 60 specifies more than one residue! The simulation can
    14794  still
    14795  run, but this will probably cause problems later if not rectified by
    14796  renumbering.
    14797 
    14798  > select clear
    14799 
    14800  > select /AV:10-40@CA
    14801 
    14802  31 atoms, 31 residues, 1 model selected
    14803 
    14804  > hide #!6 models
    14805 
    14806  Chain BU, residue 60 specifies more than one residue! The simulation can
    14807  still
    14808  run, but this will probably cause problems later if not rectified by
    14809  renumbering.
    14810 
    14811  Chain BV, residue 60 specifies more than one residue! The simulation can
    14812  still
    14813  run, but this will probably cause problems later if not rectified by
    14814  renumbering.
    14815 
    14816  > select clear
    14817 
    14818  > show #!6 models
    14819 
    14820  Chain BV, residue 60 specifies more than one residue! The simulation can
    14821  still
    14822  run, but this will probably cause problems later if not rectified by
    14823  renumbering.
    14824 
    14825  Chain BW, residue 60 specifies more than one residue! The simulation can
    14826  still
    14827  run, but this will probably cause problems later if not rectified by
    14828  renumbering.
    14829 
    14830  > select /AW:10-40@CA
    14831 
    14832  31 atoms, 31 residues, 1 model selected
    14833 
    14834  > select ~protein
    14835 
    14836  31499 atoms, 32362 bonds, 14 pseudobonds, 291 residues, 39 models selected
    14837 
    14838  > select clear
    14839 
    14840  > select up
    14841 
    14842  140 atoms, 148 bonds, 1 residue, 1 model selected
    14843 
    14844  Chain AW, residue 62 specifies more than one residue! The simulation can
    14845  still
    14846  run, but this will probably cause problems later if not rectified by
    14847  renumbering.
    14848 
    14849  Chain BV, residue 60 specifies more than one residue! The simulation can
    14850  still
    14851  run, but this will probably cause problems later if not rectified by
    14852  renumbering.
    14853 
    14854  Chain BW, residue 60 specifies more than one residue! The simulation can
    14855  still
    14856  run, but this will probably cause problems later if not rectified by
    14857  renumbering.
    14858 
    14859  > select clear
    14860 
    14861  > select /AA:10-40@CA
    14862 
    14863  31 atoms, 31 residues, 1 model selected
    14864 
    14865  Chain BA, residue 60 specifies more than one residue! The simulation can
    14866  still
    14867  run, but this will probably cause problems later if not rectified by
    14868  renumbering.
    14869 
    14870  Chain BB, residue 60 specifies more than one residue! The simulation can
    14871  still
    14872  run, but this will probably cause problems later if not rectified by
    14873  renumbering.
    14874 
    14875  Chain BX, residue 60 specifies more than one residue! The simulation can
    14876  still
    14877  run, but this will probably cause problems later if not rectified by
    14878  renumbering.
    14879 
    14880  > select /AD:10-40@CA
    14881 
    14882  31 atoms, 31 residues, 1 model selected
    14883 
    14884  Chain BC, residue 60 specifies more than one residue! The simulation can
    14885  still
    14886  run, but this will probably cause problems later if not rectified by
    14887  renumbering.
    14888 
    14889  Chain BD, residue 60 specifies more than one residue! The simulation can
    14890  still
    14891  run, but this will probably cause problems later if not rectified by
    14892  renumbering.
    14893 
    14894  > select /AE:10-40@CA
    14895 
    14896  31 atoms, 31 residues, 1 model selected
    14897 
    14898  Chain AE, residue 62 specifies more than one residue! The simulation can
    14899  still
    14900  run, but this will probably cause problems later if not rectified by
    14901  renumbering.
    14902 
    14903  Chain BE, residue 60 specifies more than one residue! The simulation can
    14904  still
    14905  run, but this will probably cause problems later if not rectified by
    14906  renumbering.
    14907 
    14908  > isolde add ligand LMT
    14909 
    14910  > ui mousemode right "translate selected atoms"
    14911 
    14912  Chain AE, residue 62 specifies more than one residue! The simulation can
    14913  still
    14914  run, but this will probably cause problems later if not rectified by
    14915  renumbering.
    14916 
    14917  > isolde ignore ~se;
    14918 
    14919  Expected a residues specifier or a keyword
    14920 
    14921  Chain AE, residue 62 specifies more than one residue! The simulation can
    14922  still
    14923  run, but this will probably cause problems later if not rectified by
    14924  renumbering.
    14925 
    14926  > isolde ignore ~sel
    14927 
    14928  ISOLDE: currently ignoring 5370 residues in model 8.2
    14929  ISOLDE: currently ignoring 1 residues in model 2
    14930  ISOLDE: currently ignoring 1 residues in model 1.2
    14931 
    14932  > isolde ~ignore
    14933 
    14934  Chain AE, residue 62 specifies more than one residue! The simulation can
    14935  still
    14936  run, but this will probably cause problems later if not rectified by
    14937  renumbering.
    14938 
    14939  Chain AH, residue 62 specifies more than one residue! The simulation can
    14940  still
    14941  run, but this will probably cause problems later if not rectified by
    14942  renumbering.
    14943 
    14944  Chain BG, residue 60 specifies more than one residue! The simulation can
    14945  still
    14946  run, but this will probably cause problems later if not rectified by
    14947  renumbering.
    14948 
    14949  > select clear
    14950 
    14951  > select clear
    14952 
    14953  Chain AH, residue 62 specifies more than one residue! The simulation can
    14954  still
    14955  run, but this will probably cause problems later if not rectified by
    14956  renumbering.
    14957 
    14958  Chain BG, residue 60 specifies more than one residue! The simulation can
    14959  still
    14960  run, but this will probably cause problems later if not rectified by
    14961  renumbering.
    14962 
    14963  > save working.cxs
    14964 
    14965  Taking snapshot of stepper: working_2.pdb
    14966 
    14967  > select ~protein
    14968 
    14969  32000 atoms, 32888 bonds, 14 pseudobonds, 295 residues, 39 models selected
    14970 
    14971  > select clear
    14972 
    14973  > hide #!6 models
    14974 
    14975  > hide #!8.1 models
    14976 
    14977  > hide protein
    14978 
    14979  > ~cartoon
    14980 
    14981  > show ~HC
    14982 
    14983  > show #!8.1 models
    14984 
    14985  > cartoon
    14986 
    14987  > select clear
    14988 
    14989  > close #6
    14990 
    14991  > select #8
    14992 
    14993  111861 atoms, 114181 bonds, 14 pseudobonds, 5371 residues, 22 models
    14994  selected
    14995 
    14996  > select clear
    14997 
    14998  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14999 
    15000  > volume subtract #8.1.1.1 #5 inPlace false
    15001 
    15002  > close #5
    15003 
    15004  > select clear
    15005 
    15006  > select clear
    15007 
    15008  Chain AW, residue 62 specifies more than one residue! The simulation can
    15009  still
    15010  run, but this will probably cause problems later if not rectified by
    15011  renumbering.
    15012 
    15013  Chain BV, residue 60 specifies more than one residue! The simulation can
    15014  still
    15015  run, but this will probably cause problems later if not rectified by
    15016  renumbering.
    15017 
    15018  > isolde add ligand LMT
    15019 
    15020  > ui mousemode right "translate selected atoms"
    15021 
    15022  > isolde ignore ~sel
    15023 
    15024  ISOLDE: currently ignoring 5371 residues in model 8.2
    15025  ISOLDE: currently ignoring 1 residues in model 2
    15026  ISOLDE: currently ignoring 1 residues in model 1.2
    15027  Traceback (most recent call last):
    15028  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15029  packages/chimerax/isolde/isolde.py", line 2707, in
    15030  _start_sim_or_toggle_pause
    15031  self.start_sim()
    15032  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15033  packages/chimerax/isolde/isolde.py", line 2727, in start_sim
    15034  self.params, self.sim_params, excluded_residues = self.ignored_residues)
    15035  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15036  packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in
    15037  __init__
    15038  self._prepare_mdff_managers()
    15039  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15040  packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    15041  _prepare_mdff_managers
    15042  focus = False)
    15043  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15044  packages/chimerax/clipper/symmetry.py", line 982, in
    15045  isolate_and_cover_selection
    15046  extra_padding=extra_padding)
    15047  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15048  packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms
    15049  zm.set_symmetry_map(atoms, transforms, transform_indices)
    15050  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15051  packages/chimerax/clipper/maps/mask_handler.py", line 119, in
    15052  set_symmetry_map
    15053  self.structure = self._unique_structure(atoms)
    15054  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15055  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15056  _unique_structure
    15057  raise TypeError('All atoms for zone mask must be from a single model!')
    15058  TypeError: All atoms for zone mask must be from a single model!
    15059 
    15060  TypeError: All atoms for zone mask must be from a single model!
    15061 
    15062  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15063  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15064  _unique_structure
    15065  raise TypeError('All atoms for zone mask must be from a single model!')
    15066 
    15067  See log for complete Python traceback.
    15068 
    15069 
    15070  > isolde ~ignore
    15071 
    15072  > show ~HC
    15073 
    15074  > color bychain
    15075 
    15076  > color byhetero
    15077 
    15078  > cartoon
    15079 
    15080  Chain AW, residue 62 specifies more than one residue! The simulation can
    15081  still
    15082  run, but this will probably cause problems later if not rectified by
    15083  renumbering.
    15084 
    15085  Chain BV, residue 60 specifies more than one residue! The simulation can
    15086  still
    15087  run, but this will probably cause problems later if not rectified by
    15088  renumbering.
    15089 
    15090  Chain BW, residue 60 specifies more than one residue! The simulation can
    15091  still
    15092  run, but this will probably cause problems later if not rectified by
    15093  renumbering.
    15094 
    15095  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15096  bonded heavy atom.
    15097 
    15098  > isolde add ligand LMT
    15099 
    15100  > ui mousemode right "translate selected atoms"
    15101 
    15102  > isolde ignore ~sel
    15103 
    15104  ISOLDE: currently ignoring 5372 residues in model 8.2
    15105  ISOLDE: currently ignoring 1 residues in model 2
    15106  ISOLDE: currently ignoring 1 residues in model 1.2
    15107 
    15108  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15109  bonded heavy atom.
    15110 
    15111  > isolde ~ignore
    15112 
    15113  Chain AW, residue 62 specifies more than one residue! The simulation can
    15114  still
    15115  run, but this will probably cause problems later if not rectified by
    15116  renumbering.
    15117 
    15118  Chain BW, residue 60 specifies more than one residue! The simulation can
    15119  still
    15120  run, but this will probably cause problems later if not rectified by
    15121  renumbering.
    15122 
    15123  > isolde ignore sel
    15124 
    15125  ISOLDE: currently ignoring 1 residues in model 8.2
    15126 
    15127  Chain AW, residue 62 specifies more than one residue! The simulation can
    15128  still
    15129  run, but this will probably cause problems later if not rectified by
    15130  renumbering.
    15131 
    15132  Chain BV, residue 60 specifies more than one residue! The simulation can
    15133  still
    15134  run, but this will probably cause problems later if not rectified by
    15135  renumbering.
    15136 
    15137  Chain BW, residue 60 specifies more than one residue! The simulation can
    15138  still
    15139  run, but this will probably cause problems later if not rectified by
    15140  renumbering.
    15141 
    15142  > isolde ~ignore
    15143 
    15144  Chain AW, residue 62 specifies more than one residue! The simulation can
    15145  still
    15146  run, but this will probably cause problems later if not rectified by
    15147  renumbering.
    15148 
    15149  Chain BV, residue 60 specifies more than one residue! The simulation can
    15150  still
    15151  run, but this will probably cause problems later if not rectified by
    15152  renumbering.
    15153 
    15154  Chain BW, residue 60 specifies more than one residue! The simulation can
    15155  still
    15156  run, but this will probably cause problems later if not rectified by
    15157  renumbering.
    15158 
    15159  > select :LMT
    15160 
    15161  9072 atoms, 9184 bonds, 112 residues, 1 model selected
    15162 
    15163  > isolde add ligand LMT
    15164 
    15165  > ui mousemode right "translate selected atoms"
    15166 
    15167  > isolde ignore ~sel
    15168 
    15169  ISOLDE: currently ignoring 5373 residues in model 8.2
    15170  ISOLDE: currently ignoring 1 residues in model 2
    15171  ISOLDE: currently ignoring 1 residues in model 1.2
    15172 
    15173  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15174  bonded heavy atom.
    15175 
    15176  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15177  bonded heavy atom.
    15178 
    15179  > isolde ~ignore
    15180 
    15181  > isolde ignore sel
    15182 
    15183  ISOLDE: currently ignoring 1 residues in model 8.2
    15184 
    15185  Chain AT, residue 62 specifies more than one residue! The simulation can
    15186  still
    15187  run, but this will probably cause problems later if not rectified by
    15188  renumbering.
    15189 
    15190  Chain BT, residue 60 specifies more than one residue! The simulation can
    15191  still
    15192  run, but this will probably cause problems later if not rectified by
    15193  renumbering.
    15194 
    15195  > isolde ~ignore
    15196 
    15197  Chain AT, residue 62 specifies more than one residue! The simulation can
    15198  still
    15199  run, but this will probably cause problems later if not rectified by
    15200  renumbering.
    15201 
    15202  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15203  bonded heavy atom.
    15204 
    15205  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15206  bonded heavy atom.
    15207 
    15208  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15209  bonded heavy atom.
    15210 
    15211  > isolde add ligand LMT
    15212 
    15213  > ui mousemode right "translate selected atoms"
    15214 
    15215  > isolde ~ignore
    15216 
    15217  > isolde ignore ~sel
    15218 
    15219  ISOLDE: currently ignoring 5374 residues in model 8.2
    15220  ISOLDE: currently ignoring 1 residues in model 2
    15221  ISOLDE: currently ignoring 1 residues in model 1.2
    15222 
    15223  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15224  bonded heavy atom.
    15225 
    15226  > isolde ~ignore
    15227 
    15228  Chain AT, residue 62 specifies more than one residue! The simulation can
    15229  still
    15230  run, but this will probably cause problems later if not rectified by
    15231  renumbering.
    15232 
    15233  > select ~protein
    15234 
    15235  32324 atoms, 33216 bonds, 14 pseudobonds, 299 residues, 39 models selected
    15236 
    15237  > select clear
    15238 
    15239  > isolde add ligand LMT
    15240 
    15241  > ui mousemode right "translate selected atoms"
    15242 
    15243  > isolde ignore ~sel
    15244 
    15245  ISOLDE: currently ignoring 5375 residues in model 8.2
    15246  ISOLDE: currently ignoring 1 residues in model 2
    15247  ISOLDE: currently ignoring 1 residues in model 1.2
    15248 
    15249  > isolde ~ignore
    15250 
    15251  Chain AQ, residue 62 specifies more than one residue! The simulation can
    15252  still
    15253  run, but this will probably cause problems later if not rectified by
    15254  renumbering.
    15255 
    15256  > select clear
    15257 
    15258  Chain AN, residue 62 specifies more than one residue! The simulation can
    15259  still
    15260  run, but this will probably cause problems later if not rectified by
    15261  renumbering.
    15262 
    15263  Chain BM, residue 60 specifies more than one residue! The simulation can
    15264  still
    15265  run, but this will probably cause problems later if not rectified by
    15266  renumbering.
    15267 
    15268  Chain BN, residue 60 specifies more than one residue! The simulation can
    15269  still
    15270  run, but this will probably cause problems later if not rectified by
    15271  renumbering.
    15272 
    15273  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15274  bonded heavy atom.
    15275 
    15276  > isolde add ligand LMT
    15277 
    15278  > ui mousemode right "translate selected atoms"
    15279 
    15280  > isolde ignore ~sel
    15281 
    15282  ISOLDE: currently ignoring 5376 residues in model 8.2
    15283  ISOLDE: currently ignoring 1 residues in model 2
    15284  ISOLDE: currently ignoring 1 residues in model 1.2
    15285 
    15286  > isolde ~ignore
    15287 
    15288  Chain AN, residue 62 specifies more than one residue! The simulation can
    15289  still
    15290  run, but this will probably cause problems later if not rectified by
    15291  renumbering.
    15292 
    15293  Chain BN, residue 60 specifies more than one residue! The simulation can
    15294  still
    15295  run, but this will probably cause problems later if not rectified by
    15296  renumbering.
    15297 
    15298  Chain AN, residue 62 specifies more than one residue! The simulation can
    15299  still
    15300  run, but this will probably cause problems later if not rectified by
    15301  renumbering.
    15302 
    15303  Chain BL, residue 60 specifies more than one residue! The simulation can
    15304  still
    15305  run, but this will probably cause problems later if not rectified by
    15306  renumbering.
    15307 
    15308  Chain BM, residue 60 specifies more than one residue! The simulation can
    15309  still
    15310  run, but this will probably cause problems later if not rectified by
    15311  renumbering.
    15312 
    15313  > isolde add ligand LMT
    15314 
    15315  > ui mousemode right "translate selected atoms"
    15316 
    15317  > isolde ignore ~sel
    15318 
    15319  ISOLDE: currently ignoring 5377 residues in model 8.2
    15320  ISOLDE: currently ignoring 1 residues in model 2
    15321  ISOLDE: currently ignoring 1 residues in model 1.2
    15322 
    15323  > isolde ~ignore
    15324 
    15325  Chain AN, residue 62 specifies more than one residue! The simulation can
    15326  still
    15327  run, but this will probably cause problems later if not rectified by
    15328  renumbering.
    15329 
    15330  Chain BM, residue 60 specifies more than one residue! The simulation can
    15331  still
    15332  run, but this will probably cause problems later if not rectified by
    15333  renumbering.
    15334 
    15335  > isolde add ligand LMT
    15336 
    15337  > ui mousemode right "translate selected atoms"
    15338 
    15339  > isolde ignore ~sel
    15340 
    15341  ISOLDE: currently ignoring 5378 residues in model 8.2
    15342  ISOLDE: currently ignoring 1 residues in model 2
    15343  ISOLDE: currently ignoring 1 residues in model 1.2
    15344 
    15345  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15346  bonded heavy atom.
    15347 
    15348  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15349  bonded heavy atom.
    15350 
    15351  > isolde ~ignore
    15352 
    15353  > select up
    15354 
    15355  81 atoms, 82 bonds, 1 residue, 1 model selected
    15356 
    15357  > isolde ignore sel
    15358 
    15359  ISOLDE: currently ignoring 1 residues in model 8.2
    15360 
    15361  Chain AK, residue 62 specifies more than one residue! The simulation can
    15362  still
    15363  run, but this will probably cause problems later if not rectified by
    15364  renumbering.
    15365 
    15366  > isolde ~ignore
    15367 
    15368  Chain AK, residue 62 specifies more than one residue! The simulation can
    15369  still
    15370  run, but this will probably cause problems later if not rectified by
    15371  renumbering.
    15372 
    15373  Chain BK, residue 60 specifies more than one residue! The simulation can
    15374  still
    15375  run, but this will probably cause problems later if not rectified by
    15376  renumbering.
    15377 
    15378  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15379  bonded heavy atom.
    15380 
    15381  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15382  bonded heavy atom.
    15383 
    15384  > isolde ~ignore
    15385 
    15386  > select up
    15387 
    15388  140 atoms, 148 bonds, 1 residue, 1 model selected
    15389 
    15390  > isolde ignore ~sel
    15391 
    15392  ISOLDE: currently ignoring 5378 residues in model 8.2
    15393  ISOLDE: currently ignoring 1 residues in model 2
    15394  ISOLDE: currently ignoring 1 residues in model 1.2
    15395 
    15396  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15397  bonded heavy atom.
    15398 
    15399  > isolde ~ignore
    15400 
    15401  Chain AK, residue 62 specifies more than one residue! The simulation can
    15402  still
    15403  run, but this will probably cause problems later if not rectified by
    15404  renumbering.
    15405 
    15406  Chain BI, residue 60 specifies more than one residue! The simulation can
    15407  still
    15408  run, but this will probably cause problems later if not rectified by
    15409  renumbering.
    15410 
    15411  Chain BJ, residue 60 specifies more than one residue! The simulation can
    15412  still
    15413  run, but this will probably cause problems later if not rectified by
    15414  renumbering.
    15415 
    15416  > select clear
    15417 
    15418  > isolde add ligand LMT
    15419 
    15420  > ui mousemode right "translate selected atoms"
    15421 
    15422  > isolde ignore ~sel
    15423 
    15424  ISOLDE: currently ignoring 5379 residues in model 8.2
    15425  ISOLDE: currently ignoring 1 residues in model 2
    15426  ISOLDE: currently ignoring 1 residues in model 1.2
    15427 
    15428  > isolde ~ignore
    15429 
    15430  Chain AK, residue 62 specifies more than one residue! The simulation can
    15431  still
    15432  run, but this will probably cause problems later if not rectified by
    15433  renumbering.
    15434 
    15435  Chain BJ, residue 60 specifies more than one residue! The simulation can
    15436  still
    15437  run, but this will probably cause problems later if not rectified by
    15438  renumbering.
    15439 
    15440  > save working.cxs
    15441 
    15442  Taking snapshot of stepper: working_2.pdb
    15443 
    15444  > isolde add ligand LMT
    15445 
    15446  > ui mousemode right "translate selected atoms"
    15447 
    15448  > isolde ignore ~sel
    15449 
    15450  ISOLDE: currently ignoring 5380 residues in model 8.2
    15451  ISOLDE: currently ignoring 1 residues in model 2
    15452  ISOLDE: currently ignoring 1 residues in model 1.2
    15453 
    15454  > isolde ~ignore
    15455 
    15456  > isolde ignore sel
    15457 
    15458  ISOLDE: currently ignoring 1 residues in model 8.2
    15459 
    15460  Chain AH, residue 62 specifies more than one residue! The simulation can
    15461  still
    15462  run, but this will probably cause problems later if not rectified by
    15463  renumbering.
    15464 
    15465  Chain BH, residue 60 specifies more than one residue! The simulation can
    15466  still
    15467  run, but this will probably cause problems later if not rectified by
    15468  renumbering.
    15469 
    15470  Chain BI, residue 60 specifies more than one residue! The simulation can
    15471  still
    15472  run, but this will probably cause problems later if not rectified by
    15473  renumbering.
    15474 
    15475  > isolde ~ignore
    15476 
    15477  Chain BH, residue 60 specifies more than one residue! The simulation can
    15478  still
    15479  run, but this will probably cause problems later if not rectified by
    15480  renumbering.
    15481 
    15482  Chain BI, residue 60 specifies more than one residue! The simulation can
    15483  still
    15484  run, but this will probably cause problems later if not rectified by
    15485  renumbering.
    15486 
    15487  > isolde add ligand LMT
    15488 
    15489  > ui mousemode right "translate selected atoms"
    15490 
    15491  > isolde ignore ~sel
    15492 
    15493  ISOLDE: currently ignoring 5381 residues in model 8.2
    15494  ISOLDE: currently ignoring 1 residues in model 2
    15495  ISOLDE: currently ignoring 1 residues in model 1.2
    15496 
    15497  > isolde ~ignore
    15498 
    15499  Chain AH, residue 62 specifies more than one residue! The simulation can
    15500  still
    15501  run, but this will probably cause problems later if not rectified by
    15502  renumbering.
    15503 
    15504  Chain AH, residue 62 specifies more than one residue! The simulation can
    15505  still
    15506  run, but this will probably cause problems later if not rectified by
    15507  renumbering.
    15508 
    15509  > isolde add ligand LMT
    15510 
    15511  > ui mousemode right "rotate selected models"
    15512 
    15513  > ui mousemode right "translate selected atoms"
    15514 
    15515  > isolde ignore ~sel
    15516 
    15517  ISOLDE: currently ignoring 5382 residues in model 8.2
    15518  ISOLDE: currently ignoring 1 residues in model 2
    15519  ISOLDE: currently ignoring 1 residues in model 1.2
    15520 
    15521  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15522  bonded heavy atom.
    15523 
    15524  > isolde ~ignore
    15525 
    15526  Chain AE, residue 62 specifies more than one residue! The simulation can
    15527  still
    15528  run, but this will probably cause problems later if not rectified by
    15529  renumbering.
    15530 
    15531  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15532  bonded heavy atom.
    15533 
    15534  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15535  bonded heavy atom.
    15536 
    15537  > select up
    15538 
    15539  140 atoms, 148 bonds, 1 residue, 1 model selected
    15540 
    15541  > isolde ignore ~sel
    15542 
    15543  ISOLDE: currently ignoring 5382 residues in model 8.2
    15544  ISOLDE: currently ignoring 1 residues in model 2
    15545  ISOLDE: currently ignoring 1 residues in model 1.2
    15546 
    15547  > isolde ignore ~sel
    15548 
    15549  ISOLDE: currently ignoring 5382 residues in model 8.2
    15550  ISOLDE: currently ignoring 1 residues in model 2
    15551  ISOLDE: currently ignoring 1 residues in model 1.2
    15552 
    15553  > isolde add ligand LMT
    15554 
    15555  > ui mousemode right "translate selected atoms"
    15556 
    15557  > isolde ignore ~sel
    15558 
    15559  ISOLDE: currently ignoring 5383 residues in model 8.2
    15560  ISOLDE: currently ignoring 1 residues in model 2
    15561  ISOLDE: currently ignoring 1 residues in model 1.2
    15562 
    15563  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15564  bonded heavy atom.
    15565 
    15566  > isolde ~ignore
    15567 
    15568  Chain AE, residue 62 specifies more than one residue! The simulation can
    15569  still
    15570  run, but this will probably cause problems later if not rectified by
    15571  renumbering.
    15572 
    15573  Chain BC, residue 60 specifies more than one residue! The simulation can
    15574  still
    15575  run, but this will probably cause problems later if not rectified by
    15576  renumbering.
    15577 
    15578  Chain BD, residue 60 specifies more than one residue! The simulation can
    15579  still
    15580  run, but this will probably cause problems later if not rectified by
    15581  renumbering.
    15582 
    15583  Chain AE, residue 62 specifies more than one residue! The simulation can
    15584  still
    15585  run, but this will probably cause problems later if not rectified by
    15586  renumbering.
    15587 
    15588  Chain BC, residue 60 specifies more than one residue! The simulation can
    15589  still
    15590  run, but this will probably cause problems later if not rectified by
    15591  renumbering.
    15592 
    15593  Chain BD, residue 60 specifies more than one residue! The simulation can
    15594  still
    15595  run, but this will probably cause problems later if not rectified by
    15596  renumbering.
    15597 
    15598  > setattr #8 bonds radius 0.05
    15599 
    15600  Assigning radius attribute to 115247 items
    15601 
    15602  > setattr #8 bonds radius 0.2
    15603 
    15604  Assigning radius attribute to 115247 items
    15605 
    15606  > save working.cxs
    15607 
    15608  Taking snapshot of stepper: working_2.pdb
    15609 
    15610  > close #6
    15611 
    15612  > select #8
    15613 
    15614  112914 atoms, 115247 bonds, 14 pseudobonds, 5384 residues, 22 models
    15615  selected
    15616 
    15617  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    15618 
    15619  > volume subtract #8.1.1.1 #5
    15620 
    15621  > close #5
    15622 
    15623  > select clear
    15624 
    15625  Chain AQ, residue 62 specifies more than one residue! The simulation can
    15626  still
    15627  run, but this will probably cause problems later if not rectified by
    15628  renumbering.
    15629 
    15630  > isolde add ligand LMT
    15631 
    15632  > ui mousemode right "translate selected atoms"
    15633 
    15634  > isolde ignore ~sel
    15635 
    15636  ISOLDE: currently ignoring 5384 residues in model 8.2
    15637  ISOLDE: currently ignoring 1 residues in model 2
    15638  ISOLDE: currently ignoring 1 residues in model 1.2
    15639 
    15640  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15641  bonded heavy atom.
    15642 
    15643  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15644  bonded heavy atom.
    15645 
    15646  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15647  bonded heavy atom.
    15648 
    15649  > isolde ~ignore
    15650 
    15651  Chain AQ, residue 62 specifies more than one residue! The simulation can
    15652  still
    15653  run, but this will probably cause problems later if not rectified by
    15654  renumbering.
    15655 
    15656  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15657  bonded heavy atom.
    15658 
    15659  > select up
    15660 
    15661  81 atoms, 82 bonds, 1 residue, 1 model selected
    15662 
    15663  > delete sel
    15664 
    15665  Chain AQ, residue 62 specifies more than one residue! The simulation can
    15666  still
    15667  run, but this will probably cause problems later if not rectified by
    15668  renumbering.
    15669 
    15670  Chain BQ, residue 60 specifies more than one residue! The simulation can
    15671  still
    15672  run, but this will probably cause problems later if not rectified by
    15673  renumbering.
    15674 
    15675  > isolde add ligand PEE
    15676 
    15677  Deleted the following atoms from residue PEE AQ63: H83
    15678 
    15679  > ui mousemode right "translate selected atoms"
    15680 
    15681  > isolde ignore ~sel
    15682 
    15683  ISOLDE: currently ignoring 5384 residues in model 8.2
    15684  ISOLDE: currently ignoring 1 residues in model 2
    15685  ISOLDE: currently ignoring 1 residues in model 1.2
    15686 
    15687  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15688  bonded heavy atom.
    15689 
    15690  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15691  bonded heavy atom.
    15692 
    15693  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15694  bonded heavy atom.
    15695 
    15696  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15697  bonded heavy atom.
    15698 
    15699  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15700  bonded heavy atom.
    15701 
    15702  > isolde ~ignore
    15703 
    15704  Chain AQ, residue 62 specifies more than one residue! The simulation can
    15705  still
    15706  run, but this will probably cause problems later if not rectified by
    15707  renumbering.
    15708 
    15709  > save working.cxs
    15710 
    15711  Taking snapshot of stepper: working_2.pdb
    15712 
    15713  > isolde add ligand LMT
    15714 
    15715  > ui mousemode right "translate selected atoms"
    15716 
    15717  > select ~protein
    15718 
    15719  33267 atoms, 34168 bonds, 14 pseudobonds, 310 residues, 39 models selected
    15720 
    15721  > select clear
    15722 
    15723  > isolde add ligand P5S
    15724 
    15725  Deleted the following atoms from residue P5S M705: HXT, HO15
    15726 
    15727  > ui mousemode right "translate selected atoms"
    15728 
    15729  > isolde ignore ~sel
    15730 
    15731  ISOLDE: currently ignoring 5386 residues in model 8.2
    15732  ISOLDE: currently ignoring 1 residues in model 2
    15733  ISOLDE: currently ignoring 1 residues in model 1.2
    15734 
    15735  > hide #!6 models
    15736 
    15737  > select up
    15738 
    15739  135 atoms, 134 bonds, 1 residue, 1 model selected
    15740 
    15741  > delete sel
    15742 
    15743  > isolde add ligand PSF
    15744 
    15745  Fetching CCD PSF from http://ligand-expo.rcsb.org/reports/P/PSF/PSF.cif
    15746  Deleted the following atoms from residue PSF M705: HO3, HXT
    15747 
    15748  > ui mousemode right "translate selected atoms"
    15749 
    15750  > isolde ignore ~sel
    15751 
    15752  ISOLDE: currently ignoring 5386 residues in model 8.2
    15753  ISOLDE: currently ignoring 1 residues in model 2
    15754  ISOLDE: currently ignoring 1 residues in model 1.2
    15755 
    15756  > isolde add ligand PSF
    15757 
    15758  Deleted the following atoms from residue PSF ai68: HO3, HXT
    15759 
    15760  > isolde ignore ~sel
    15761 
    15762  ISOLDE: currently ignoring 5387 residues in model 8.2
    15763  ISOLDE: currently ignoring 1 residues in model 2
    15764  ISOLDE: currently ignoring 1 residues in model 1.2
    15765 
    15766  > ui mousemode right "translate selected atoms"
    15767 
    15768  > isolde ~ignore
    15769 
    15770  Chain AN, residue 62 specifies more than one residue! The simulation can
    15771  still
    15772  run, but this will probably cause problems later if not rectified by
    15773  renumbering.
    15774 
    15775  > select up
    15776 
    15777  62 atoms, 61 bonds, 1 residue, 1 model selected
    15778 
    15779  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15780  bonded heavy atom.
    15781 
    15782  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15783  bonded heavy atom.
    15784 
    15785  > show #!6 models
    15786 
    15787  Chain AH, residue 62 specifies more than one residue! The simulation can
    15788  still
    15789  run, but this will probably cause problems later if not rectified by
    15790  renumbering.
    15791 
    15792  Chain AK, residue 62 specifies more than one residue! The simulation can
    15793  still
    15794  run, but this will probably cause problems later if not rectified by
    15795  renumbering.
    15796 
    15797  Chain BJ, residue 60 specifies more than one residue! The simulation can
    15798  still
    15799  run, but this will probably cause problems later if not rectified by
    15800  renumbering.
    15801 
    15802  > select up
    15803 
    15804  140 atoms, 148 bonds, 1 residue, 1 model selected
    15805 
    15806  > isolde ignore ~sel
    15807 
    15808  ISOLDE: currently ignoring 5387 residues in model 8.2
    15809  ISOLDE: currently ignoring 1 residues in model 2
    15810  ISOLDE: currently ignoring 1 residues in model 1.2
    15811 
    15812  > isolde ~ignore
    15813 
    15814  > isolde ignore se
    15815 
    15816  Expected a residues specifier or a keyword
    15817 
    15818  Chain AH, residue 62 specifies more than one residue! The simulation can
    15819  still
    15820  run, but this will probably cause problems later if not rectified by
    15821  renumbering.
    15822 
    15823  Chain AK, residue 62 specifies more than one residue! The simulation can
    15824  still
    15825  run, but this will probably cause problems later if not rectified by
    15826  renumbering.
    15827 
    15828  Chain BJ, residue 60 specifies more than one residue! The simulation can
    15829  still
    15830  run, but this will probably cause problems later if not rectified by
    15831  renumbering.
    15832 
    15833  > select up
    15834 
    15835  140 atoms, 148 bonds, 1 residue, 1 model selected
    15836 
    15837  > isolde ignore sel
    15838 
    15839  ISOLDE: currently ignoring 1 residues in model 8.2
    15840 
    15841  Chain AH, residue 62 specifies more than one residue! The simulation can
    15842  still
    15843  run, but this will probably cause problems later if not rectified by
    15844  renumbering.
    15845 
    15846  Chain AK, residue 62 specifies more than one residue! The simulation can
    15847  still
    15848  run, but this will probably cause problems later if not rectified by
    15849  renumbering.
    15850 
    15851  Chain BJ, residue 60 specifies more than one residue! The simulation can
    15852  still
    15853  run, but this will probably cause problems later if not rectified by
    15854  renumbering.
    15855 
    15856  > isolde ~ignore
    15857 
    15858  Chain AH, residue 62 specifies more than one residue! The simulation can
    15859  still
    15860  run, but this will probably cause problems later if not rectified by
    15861  renumbering.
    15862 
    15863  Chain AK, residue 62 specifies more than one residue! The simulation can
    15864  still
    15865  run, but this will probably cause problems later if not rectified by
    15866  renumbering.
    15867 
    15868  > isolde add ligand LMT
    15869 
    15870  > ui mousemode right "translate selected atoms"
    15871 
    15872  > isolde ignore ~sel
    15873 
    15874  ISOLDE: currently ignoring 5388 residues in model 8.2
    15875  ISOLDE: currently ignoring 1 residues in model 2
    15876  ISOLDE: currently ignoring 1 residues in model 1.2
    15877 
    15878  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15879  bonded heavy atom.
    15880 
    15881  > isolde ~ignore
    15882 
    15883  > save working.cxs
    15884 
    15885  Taking snapshot of stepper: working_2.pdb
    15886 
    15887  > select ~protein
    15888 
    15889  33472 atoms, 34372 bonds, 14 pseudobonds, 313 residues, 39 models selected
    15890 
    15891  > select clear
    15892 
    15893  Chain AN, residue 62 specifies more than one residue! The simulation can
    15894  still
    15895  run, but this will probably cause problems later if not rectified by
    15896  renumbering.
    15897 
    15898  Chain AN, residue 62 specifies more than one residue! The simulation can
    15899  still
    15900  run, but this will probably cause problems later if not rectified by
    15901  renumbering.
    15902 
    15903  > select clear
    15904 
    15905  Chain AW, residue 62 specifies more than one residue! The simulation can
    15906  still
    15907  run, but this will probably cause problems later if not rectified by
    15908  renumbering.
    15909 
    15910  Chain BA, residue 60 specifies more than one residue! The simulation can
    15911  still
    15912  run, but this will probably cause problems later if not rectified by
    15913  renumbering.
    15914 
    15915  Chain BX, residue 60 specifies more than one residue! The simulation can
    15916  still
    15917  run, but this will probably cause problems later if not rectified by
    15918  renumbering.
    15919 
    15920  > select clear
    15921 
    15922  Chain AH, residue 62 specifies more than one residue! The simulation can
    15923  still
    15924  run, but this will probably cause problems later if not rectified by
    15925  renumbering.
    15926 
    15927  > save working.cxs
    15928 
    15929  Taking snapshot of stepper: working_2.pdb
    15930 
    15931  > save working.cif #8
    15932 
    15933  Not saving entity_poly_seq for non-authoritative sequences
    15934 
    15935  > select #1
    15936 
    15937  256 atoms, 255 bonds, 1 residue, 8 models selected
    15938 
    15939  > select #8
    15940 
    15941  113333 atoms, 115665 bonds, 14 pseudobonds, 5389 residues, 22 models
    15942  selected
    15943 
    15944  > select clear
    15945 
    15946  > view sel
    15947 
    15948  > select /ak:67&~protein
    15949 
    15950  140 atoms, 148 bonds, 1 residue, 1 model selected
    15951 
    15952  > view sel
    15953 
    15954  > select clear
    15955 
    15956  > view sel
    15957 
    15958  > select clear
    15959 
    15960  > view sel
    15961 
    15962  > select clear
    15963 
    15964  > view sel
    15965 
    15966  > select clear
    15967 
    15968  > view sel
    15969 
    15970  > select clear
    15971 
    15972  > view sel
    15973 
    15974  > select clear
    15975 
    15976  > view sel
    15977 
    15978  > select clear
    15979 
    15980  > view sel
    15981 
    15982  > select clear
    15983 
    15984  > view sel
    15985 
    15986  > select clear
    15987 
    15988  > view sel
    15989 
    15990  > select clear
    15991 
    15992  > view sel
    15993 
    15994  > view sel
    15995 
    15996  > select clear
    15997 
    15998  > select clear
    15999 
    16000  > select clear
    16001 
    16002  > select clear
    16003 
    16004  > select clear
    16005 
    16006  > select clear
    16007 
    16008  > select clear
    16009 
    16010  > select clear
    16011 
    16012  > select clear
    16013 
    16014  > select clear
    16015 
    16016  > select clear
    16017 
    16018  > select clear
    16019 
    16020  > select clear
    16021 
    16022  > select clear
    16023 
    16024  > select clear
    16025 
    16026  > select clear
    16027 
    16028  > select clear
    16029 
    16030  > select clear
    16031 
    16032  > select clear
    16033 
    16034  > select clear
    16035 
    16036  > select clear
    16037 
    16038  > select clear
    16039 
    16040  > select clear
    16041 
    16042  > save working.cif #8
    16043 
    16044  Not saving entity_poly_seq for non-authoritative sequences
    16045 
    16046  > select ~H
    16047 
    16048  55527 atoms, 116032 bonds, 14 pseudobonds, 5391 residues, 39 models
    16049  selected
    16050 
    16051  > save working_noh.cif #8 selectedOnly true
    16052 
    16053  Not saving entity_poly_seq for non-authoritative sequences
    16054 
    16055  > select clear
    16056 
    16057  > save working.pdb #8
    16058 
    16059  > view /CG:1
    16060 
    16061  > select /C
    16062 
    16063  4865 atoms, 4968 bonds, 4 pseudobonds, 303 residues, 2 models selected
    16064 
    16065  > select up
    16066 
    16067  78 atoms, 81 bonds, 4 residues, 1 model selected
    16068 
    16069  > view /MG:MAN
    16070 
    16071  > select up
    16072 
    16073  78 atoms, 81 bonds, 4 residues, 1 model selected
    16074 
    16075  > save working.cif #8
    16076 
    16077  Not saving entity_poly_seq for non-authoritative sequences
    16078 
    16079  > select clear
    16080 
    16081  > hide #!6 models
    16082 
    16083  > select up
    16084 
    16085  78 atoms, 81 bonds, 4 residues, 1 model selected
    16086 
    16087  > save working.cif #8
    16088 
    16089  Not saving entity_poly_seq for non-authoritative sequences
    16090 
    16091  > ui mousemode right "translate selected atoms"
    16092 
    16093  > select /C:1010-1020
    16094 
    16095  78 atoms, 81 bonds, 4 residues, 1 model selected
    16096 
    16097  > delete sel
    16098 
    16099  > select /C:1010-1020
    16100 
    16101  78 atoms, 81 bonds, 4 residues, 1 model selected
    16102 
    16103  > delete sel
    16104 
    16105  > select /M:20-50
    16106 
    16107  435 atoms, 440 bonds, 31 residues, 1 model selected
    16108 
    16109  > select /D:20-50
    16110 
    16111  Nothing selected
    16112 
    16113  > open
    16114  >
    16115  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16116 
    16117  Summary of feedback from opening
    16118  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16119  ---
    16120  warnings | Unknown polymer entity '1' near line 475
    16121  Unknown polymer entity '2' near line 2593
    16122  Unknown polymer entity '3' near line 5781
    16123  Unknown polymer entity '4' near line 26370
    16124  Unknown polymer entity '5' near line 27136
    16125  10 messages similar to the above omitted
    16126  Atom H is not in the residue template for MET /AA:1
    16127  Atom C1 is not in the residue template for GPC /AA:60
    16128  Atom H is not in the residue template for MET /AB:1
    16129  Atom C1 is not in the residue template for GPC /AB:60
    16130  Atom H is not in the residue template for MET /AC:1
    16131  Atom C1 is not in the residue template for GPC /AC:60
    16132  Atom H is not in the residue template for MET /AD:1
    16133  Atom C1 is not in the residue template for GPC /AD:60
    16134  Atom H is not in the residue template for MET /AE:1
    16135  Atom C1 is not in the residue template for GPC /AE:60
    16136  Atom H is not in the residue template for MET /AF:1
    16137  Atom C1 is not in the residue template for GPC /AF:60
    16138  Atom H is not in the residue template for MET /AG:1
    16139  Atom C1 is not in the residue template for GPC /AG:60
    16140  Atom H is not in the residue template for MET /AH:1
    16141  Atom C1 is not in the residue template for GPC /AH:60
    16142  Atom H is not in the residue template for MET /AI:1
    16143  Atom C1 is not in the residue template for GPC /AI:60
    16144  Atom H is not in the residue template for MET /AJ:1
    16145  Atom C1 is not in the residue template for GPC /AJ:60
    16146  Atom H is not in the residue template for MET /AK:1
    16147  Atom C1 is not in the residue template for GPC /AK:60
    16148  Atom C26 is not in the residue template for PEX /AK:62
    16149  Atom H is not in the residue template for MET /AL:1
    16150  Atom C1 is not in the residue template for GPC /AL:60
    16151  Atom H is not in the residue template for MET /AM:1
    16152  Atom C1 is not in the residue template for GPC /AM:60
    16153  Atom H is not in the residue template for MET /AN:1
    16154  Atom C1 is not in the residue template for GPC /AN:60
    16155  Atom H is not in the residue template for MET /AO:1
    16156  Atom C1 is not in the residue template for GPC /AO:60
    16157  Atom H is not in the residue template for MET /AP:1
    16158  Atom C1 is not in the residue template for GPC /AP:60
    16159  Atom H is not in the residue template for MET /AQ:1
    16160  Atom C1 is not in the residue template for GPC /AQ:60
    16161  Atom H is not in the residue template for MET /AR:1
    16162  Atom C1 is not in the residue template for GPC /AR:60
    16163  Atom H is not in the residue template for MET /AS:1
    16164  Atom C1 is not in the residue template for GPC /AS:60
    16165  Atom H is not in the residue template for MET /AT:1
    16166  Atom C1 is not in the residue template for GPC /AT:60
    16167  Atom H is not in the residue template for MET /AU:1
    16168  Atom C1 is not in the residue template for GPC /AU:60
    16169  Atom H is not in the residue template for MET /AV:1
    16170  Atom C1 is not in the residue template for GPC /AV:60
    16171  Atom H is not in the residue template for MET /AW:1
    16172  Atom C1 is not in the residue template for GPC /AW:60
    16173  Atom H is not in the residue template for MET /AX:1
    16174  Atom C1 is not in the residue template for GPC /AX:60
    16175  Atom H is not in the residue template for GLY /BQ:5
    16176  Atom H is not in the residue template for GLY /BR:5
    16177  Atom H is not in the residue template for GLY /BS:5
    16178  Atom H is not in the residue template for GLY /BT:5
    16179  Atom H11 is not in the residue template for BPH /L:606
    16180  Atom H11 is not in the residue template for BPH /M:605
    16181  Atom C1 is not in the residue template for RCC /M:701
    16182  Atom HN2 is not in the residue template for ARG /ak:71
    16183  Atom H is not in the residue template for GLY /C1:32
    16184  Atom C1 is not in the residue template for GPC /Ba:60
    16185  Atom C1 is not in the residue template for GPC /Bb:60
    16186  Atom C1 is not in the residue template for GPC /Bc:60
    16187  Atom C1 is not in the residue template for GPC /Bd:60
    16188  Atom C1 is not in the residue template for GPC /Be:60
    16189  11 messages similar to the above omitted
    16190  Missing or incomplete entity_poly_seq table. Inferred polymer
    16191  connectivity.
    16192 
    16193  Chain information for model1a.cif #5
    16194  ---
    16195  Chain | Description
    16196  AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?
    16197  AC AD | ?
    16198  BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk
    16199  bl
    16200  bm bo bp | ?
    16201  BB BD BE BI BQ BR BS BT BV BW bn | ?
    16202  C | ?
    16203  C1 | ?
    16204  H1 | ?
    16205  H2 | ?
    16206  L | ?
    16207  M | ?
    16208  aa | ?
    16209  ab ad ae af ag ah ai aj al am an ao ap | ?
    16210  ac | ?
    16211  ak | ?
    16212 
    16213 
    16214  > cartoon #5
    16215 
    16216  > hide #5
    16217 
    16218  > select /M:20-50
    16219 
    16220  736 atoms, 744 bonds, 2 pseudobonds, 52 residues, 3 models selected
    16221 
    16222  > view /C:1010
    16223 
    16224  No objects specified.
    16225 
    16226  > view /C:1001
    16227 
    16228  > dssp
    16229 
    16230  > select :BCL
    16231 
    16232  25620 atoms, 26748 bonds, 336 pseudobonds, 183 residues, 3 models selected
    16233 
    16234  > close #5
    16235 
    16236  > clipper spotlight radius 13.00
    16237 
    16238  > clipper spotlight radius 14.00
    16239 
    16240  > clipper spotlight radius 15.00
    16241 
    16242  > clipper spotlight radius 16.00
    16243 
    16244  > clipper spotlight radius 17.00
    16245 
    16246  > select /ak
    16247 
    16248  1347 atoms, 1369 bonds, 73 residues, 2 models selected
    16249 
    16250  > view /C:117
    16251 
    16252  > select #8&~protein
    16253 
    16254  33103 atoms, 34005 bonds, 14 pseudobonds, 311 residues, 22 models selected
    16255 
    16256  > select LMG
    16257 
    16258  Expected an objects specifier or a keyword
    16259 
    16260  > select :LMG
    16261 
    16262  141 atoms, 141 bonds, 1 residue, 1 model selected
    16263 
    16264  > view :LMG
    16265 
    16266  > select :LMX
    16267 
    16268  129 atoms, 129 bonds, 1 residue, 1 model selected
    16269 
    16270  > view sel
    16271 
    16272  > select clear
    16273 
    16274  > save working.cxs
    16275 
    16276  Taking snapshot of stepper: working_2.pdb
    16277  opened ChimeraX session
    16278 
    16279  > show #!6 models
    16280 
    16281  > volume #6 level 0.03545
    16282 
    16283  > ui tool show Shell
    16284 
    16285  /opt/UCSF/ChimeraX/lib/python3.7/site-
    16286  packages/IPython/core/history.py:226:
    16287  UserWarning: IPython History requires SQLite, your history will not be
    16288  saved
    16289  warn("IPython History requires SQLite, your history will not be saved")
    16290 
    16291  > isolde start
    16292 
    16293  > set selectionWidth 4
    16294 
    16295  Done loading forcefield
    16296 
    16297  > select #6
    16298 
    16299  4 models selected
    16300 
    16301  > select :HOH
    16302 
    16303  15 atoms, 10 bonds, 5 residues, 1 model selected
    16304 
    16305  > hide #!6 models
    16306 
    16307  > select :HOH
    16308 
    16309  3309 atoms, 2206 bonds, 1103 residues, 2 models selected
    16310 
    16311  > delete sel
    16312 
    16313  > select :HOH
    16314 
    16315  2505 atoms, 1670 bonds, 835 residues, 1 model selected
    16316 
    16317  > show #!6 models
    16318 
    16319  > hide #!6 models
    16320 
    16321  > delete :HOH
    16322 
    16323  > select :HOH
    16324 
    16325  498 atoms, 332 bonds, 166 residues, 1 model selected
    16326 
    16327  > show #!6 models
    16328 
    16329  > hide #!6 models
    16330 
    16331  > select :HOH
    16332 
    16333  498 atoms, 332 bonds, 166 residues, 1 model selected
    16334 
    16335  > show #!6 models
    16336 
    16337  > delete :HOH
    16338 
    16339  > select :HOH
    16340 
    16341  1497 atoms, 998 bonds, 499 residues, 1 model selected
    16342 
    16343  > hide #!6 models
    16344 
    16345  > show #!6 models
    16346 
    16347  > hide #!6 models
    16348 
    16349  > show #!6 models
    16350 
    16351  > select :HOH
    16352 
    16353  1926 atoms, 1284 bonds, 642 residues, 1 model selected
    16354 
    16355  > hide #!6 models
    16356 
    16357  Loading residue template for LMG from internal database
    16358  Loading residue template for PEE from internal database
    16359  Loading residue template for PEX from internal database
    16360  Loading residue template for PSF from internal database
    16361 
    16362  > select :HOH
    16363 
    16364  1926 atoms, 1284 bonds, 642 residues, 1 model selected
    16365  Map is too large for fast cubic interpolation on the GPU! Switching to
    16366  slower,
    16367  more memory-efficient implementation.
    16368  Map is too large for fast cubic interpolation on the GPU! Switching to
    16369  slower,
    16370  more memory-efficient implementation.
    16371 
    16372  > select clear
    16373 
    16374  > select clear
    16375 
    16376  > select clear
    16377 
    16378  > select :HOH
    16379 
    16380  1926 atoms, 1284 bonds, 642 residues, 1 model selected
    16381  Map is too large for fast cubic interpolation on the GPU! Switching to
    16382  slower,
    16383  more memory-efficient implementation.
    16384  Map is too large for fast cubic interpolation on the GPU! Switching to
    16385  slower,
    16386  more memory-efficient implementation.
    16387 
    16388  > select clear
    16389 
    16390  > select #8.1.1.1
    16391 
    16392  3 models selected
    16393 
    16394  > select clear
    16395 
    16396  > select :HOH
    16397 
    16398  2085 atoms, 1390 bonds, 695 residues, 1 model selected
    16399  Map is too large for fast cubic interpolation on the GPU! Switching to
    16400  slower,
    16401  more memory-efficient implementation.
    16402  Map is too large for fast cubic interpolation on the GPU! Switching to
    16403  slower,
    16404  more memory-efficient implementation.
    16405 
    16406  > select clear
    16407 
    16408  > close #6
    16409 
    16410  > select #1
    16411 
    16412  256 atoms, 255 bonds, 1 residue, 8 models selected
    16413  Traceback (most recent call last):
    16414  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16415  packages/chimerax/isolde/isolde.py", line 2580, in _xtal_mask_to_selection
    16416  self._xtal_mask_to_atoms(sel, focus)
    16417  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16418  packages/chimerax/isolde/isolde.py", line 2589, in _xtal_mask_to_atoms
    16419  atoms, 0, context, cutoff, focus=focus)
    16420  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16421  packages/chimerax/clipper/symmetry.py", line 982, in
    16422  isolate_and_cover_selection
    16423  extra_padding=extra_padding)
    16424  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16425  packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms
    16426  zm.set_symmetry_map(atoms, transforms, transform_indices)
    16427  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16428  packages/chimerax/clipper/maps/mask_handler.py", line 119, in
    16429  set_symmetry_map
    16430  self.structure = self._unique_structure(atoms)
    16431  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16432  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    16433  _unique_structure
    16434  raise TypeError('All atoms for zone mask must be from a single model!')
    16435  TypeError: All atoms for zone mask must be from a single model!
    16436 
    16437  TypeError: All atoms for zone mask must be from a single model!
    16438 
    16439  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    16440  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    16441  _unique_structure
    16442  raise TypeError('All atoms for zone mask must be from a single model!')
    16443 
    16444  See log for complete Python traceback.
    16445 
    16446 
    16447  > select #8
    16448 
    16449  115418 atoms, 117055 bonds, 14 pseudobonds, 6084 residues, 22 models
    16450  selected
    16451 
    16452  > select clear
    16453 
    16454  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    16455 
    16456  > volume subtract #8.1.1.1 #5
    16457 
    16458  > close #5
    16459 
    16460  > select clear
    16461 
    16462  > select clear
    16463 
    16464  > select :HOH
    16465 
    16466  2085 atoms, 1390 bonds, 695 residues, 1 model selected
    16467 
    16468  > select clear
    16469 
    16470  > hide #!6 models
    16471 
    16472  > show #!6 models
    16473 
    16474  > select clear
    16475 
    16476  > select #6
    16477 
    16478  4 models selected
    16479 
    16480  > select :HOH
    16481 
    16482  1494 atoms, 996 bonds, 498 residues, 1 model selected
    16483  Map is too large for fast cubic interpolation on the GPU! Switching to
    16484  slower,
    16485  more memory-efficient implementation.
    16486  Map is too large for fast cubic interpolation on the GPU! Switching to
    16487  slower,
    16488  more memory-efficient implementation.
    16489 
    16490  > hide #!6 models
    16491 
    16492  > select clear
    16493 
    16494  > select :HOH
    16495 
    16496  1494 atoms, 996 bonds, 498 residues, 1 model selected
    16497 
    16498  > isolde add water
    16499 
    16500  > isolde sim start sel
    16501 
    16502  > select :HOH
    16503 
    16504  1095 atoms, 730 bonds, 365 residues, 1 model selected
    16505 
    16506  > select clear
    16507 
    16508  > save working.cxs
    16509 
    16510  Taking snapshot of stepper: working_2.pdb
    16511 
    16512  > delete sel
    16513 
    16514  > delete sel
    16515 
    16516  > isolde add water
    16517 
    16518  > isolde sim start sel
    16519 
    16520  > isolde add water
    16521 
    16522  > isolde sim start sel
    16523 
    16524  > isolde add water
    16525 
    16526  > isolde sim start sel
    16527 
    16528  > isolde add water
    16529 
    16530  > isolde sim start sel
    16531 
    16532  > delete sel
    16533 
    16534  > setattr sel atoms name H
    16535 
    16536  Assigning name attribute to 1 item
    16537 
    16538  > isolde add water
    16539 
    16540  > isolde sim start sel
    16541 
    16542  > select up
    16543 
    16544  3 atoms, 2 bonds, 1 residue, 1 model selected
    16545 
    16546  > delete sel
    16547 
    16548  > isolde add water
    16549 
    16550  > isolde sim start sel
    16551 
    16552  > isolde add water
    16553 
    16554  > isolde sim start sel
    16555 
    16556  > isolde add water
    16557 
    16558  > isolde sim start sel
    16559 
    16560  > isolde add water simSettle false
    16561 
    16562  > isolde add water simSettle false
    16563 
    16564  > show #!6 models
    16565 
    16566  > hide #!6 models
    16567 
    16568  > show #!6 models
    16569 
    16570  > isolde add water
    16571 
    16572  > isolde sim start sel
    16573 
    16574  > hide #!6 models
    16575 
    16576  > isolde add water
    16577 
    16578  > isolde sim start sel
    16579 
    16580  > isolde add water simSettle false
    16581 
    16582  > isolde add water simSettle false
    16583 
    16584  > isolde add water simSettle false
    16585 
    16586  > isolde add water
    16587 
    16588  > isolde sim start sel
    16589 
    16590  > isolde add water
    16591 
    16592  > isolde sim start sel
    16593 
    16594  > isolde add water simSettle false
    16595 
    16596  > isolde add water simSettle false
    16597 
    16598  > isolde add water simSettle false
    16599 
    16600  > isolde add water
    16601 
    16602  > isolde sim start sel
    16603 
    16604  > isolde add water
    16605 
    16606  > isolde sim start sel
    16607 
    16608  > show #!6 models
    16609 
    16610  > hide #!6 models
    16611 
    16612  > show #!6 models
    16613 
    16614  > hide #!6 models
    16615 
    16616  > isolde add water simSettle false
    16617 
    16618  > isolde add water simSettle false
    16619 
    16620  > isolde add water
    16621 
    16622  > isolde sim start sel
    16623 
    16624  > show #!6 models
    16625 
    16626  > volume #6 level 0.02957
    16627 
    16628  > volume #6 level 0.02196
    16629 
    16630  > volume #6 level 0.02872
    16631 
    16632  > hide #!6 models
    16633 
    16634  > isolde add water
    16635 
    16636  > isolde sim start sel
    16637 
    16638  > isolde add water
    16639 
    16640  > isolde sim start sel
    16641 
    16642  > isolde add water simSettle false
    16643 
    16644  > isolde add water simSettle false
    16645 
    16646  > select /ak
    16647 
    16648  1380 atoms, 1391 bonds, 84 residues, 2 models selected
    16649 
    16650  > isolde add water simSettle false
    16651 
    16652  > select /ak
    16653 
    16654  1380 atoms, 1391 bonds, 84 residues, 2 models selected
    16655 
    16656  > select up
    16657 
    16658  114625 atoms, 116562 bonds, 5784 residues, 2 models selected
    16659 
    16660  > select clear
    16661 
    16662  > isolde add water simSettle false
    16663 
    16664  > select /ak
    16665 
    16666  1383 atoms, 1393 bonds, 85 residues, 2 models selected
    16667 
    16668  > select /ak
    16669 
    16670  1383 atoms, 1393 bonds, 85 residues, 2 models selected
    16671 
    16672  > isolde add water simSettle false
    16673 
    16674  > isolde add water simSettle false
    16675 
    16676  > isolde add water simSettle false
    16677 
    16678  > isolde add water simSettle false
    16679 
    16680  > select clear
    16681 
    16682  > isolde add water simSettle false
    16683 
    16684  > select clear
    16685 
    16686  > view /aa:45
    16687 
    16688  > view /ab:45
    16689 
    16690  > isolde add water simSettle false
    16691 
    16692  > isolde add water simSettle false
    16693 
    16694  > view /ac:45
    16695 
    16696  > select clear
    16697 
    16698  > view /ad:45
    16699 
    16700  > view /ae:45
    16701 
    16702  > view /af:45
    16703 
    16704  > view /ag:45
    16705 
    16706  > view /ah:45
    16707 
    16708  > isolde add water simSettle false
    16709 
    16710  > select clear
    16711 
    16712  > view /ai:45
    16713 
    16714  > view /aj:45
    16715 
    16716  > view /ak:45
    16717 
    16718  > view /al:45
    16719 
    16720  > isolde add water simSettle false
    16721 
    16722  > isolde add water simSettle false
    16723 
    16724  > select clear
    16725 
    16726  > view /am:45
    16727 
    16728  > isolde add water simSettle false
    16729 
    16730  > select clear
    16731 
    16732  > view /an:45
    16733 
    16734  > isolde add water simSettle false
    16735 
    16736  > select clear
    16737 
    16738  > view /ao:45
    16739 
    16740  > view /ap:45
    16741 
    16742  > isolde add water simSettle false
    16743 
    16744  > select clear
    16745 
    16746  > view /aa:5
    16747 
    16748  > view /AA:45
    16749 
    16750  > view /AB:4
    16751 
    16752  > view /AB:43
    16753 
    16754  > view /AC:43
    16755 
    16756  > view /AD:43
    16757 
    16758  > view /AE:43
    16759 
    16760  > select clear
    16761 
    16762  > view /AF:43
    16763 
    16764  > view /AG:43
    16765 
    16766  > view /AH:43
    16767 
    16768  > view /AI:43
    16769 
    16770  > save working.cxs
    16771 
    16772  Taking snapshot of stepper: working_2.pdb
    16773 
    16774  > close #8.1
    16775 
    16776  > clipper associate #3 toModel #8
    16777 
    16778  > volume gaussian #8 bfactor 50
    16779 
    16780  > clipper associate #3 toModel #1
    16781 
    16782  > close #1.1
    16783 
    16784  > volume gaussian #8 bfactor 50
    16785 
    16786  > clipper associate #3 toModel #8
    16787 
    16788  > clipper set contourSensitivity 0.25
    16789 
    16790  > select /D1
    16791 
    16792  Nothing selected
    16793 
    16794  > delete /C2
    16795 
    16796  > select /H1
    16797 
    16798  1580 atoms, 1586 bonds, 75 residues, 1 model selected
    16799 
    16800  > select /M
    16801 
    16802  6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected
    16803 
    16804  > select clear
    16805 
    16806  > isolde restrain distances #8
    16807 
    16808  > select :HOH
    16809 
    16810  1218 atoms, 812 bonds, 406 residues, 1 model selected
    16811 
    16812  > select /M
    16813 
    16814  6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected
    16815 
    16816  > select clear
    16817 
    16818  > select /M:20-50
    16819 
    16820  435 atoms, 440 bonds, 31 residues, 1 model selected
    16821 
    16822  > isolde release distances sel
    16823 
    16824  > select clear
    16825 
    16826  > select #8
    16827 
    16828  112951 atoms, 114855 bonds, 14 pseudobonds, 5695 residues, 22 models
    16829  selected
    16830  Map is too large for fast cubic interpolation on the GPU! Switching to
    16831  slower,
    16832  more memory-efficient implementation.
    16833  Map is too large for fast cubic interpolation on the GPU! Switching to
    16834  slower,
    16835  more memory-efficient implementation.
    16836 
    16837  > select clear
    16838 
    16839  > close #8.2.10
    16840 
    16841  > select clear
    16842 
    16843  > select /M:20-50
    16844 
    16845  435 atoms, 440 bonds, 31 residues, 1 model selected
    16846 
    16847  > open
    16848  >
    16849  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16850 
    16851  Summary of feedback from opening
    16852  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16853  ---
    16854  warnings | Unknown polymer entity '1' near line 475
    16855  Unknown polymer entity '2' near line 2593
    16856  Unknown polymer entity '3' near line 5781
    16857  Unknown polymer entity '4' near line 26370
    16858  Unknown polymer entity '5' near line 27136
    16859  10 messages similar to the above omitted
    16860  Atom H is not in the residue template for MET /AA:1
    16861  Atom C1 is not in the residue template for GPC /AA:60
    16862  Atom H is not in the residue template for MET /AB:1
    16863  Atom C1 is not in the residue template for GPC /AB:60
    16864  Atom H is not in the residue template for MET /AC:1
    16865  Atom C1 is not in the residue template for GPC /AC:60
    16866  Atom H is not in the residue template for MET /AD:1
    16867  Atom C1 is not in the residue template for GPC /AD:60
    16868  Atom H is not in the residue template for MET /AE:1
    16869  Atom C1 is not in the residue template for GPC /AE:60
    16870  Atom H is not in the residue template for MET /AF:1
    16871  Atom C1 is not in the residue template for GPC /AF:60
    16872  Atom H is not in the residue template for MET /AG:1
    16873  Atom C1 is not in the residue template for GPC /AG:60
    16874  Atom H is not in the residue template for MET /AH:1
    16875  Atom C1 is not in the residue template for GPC /AH:60
    16876  Atom H is not in the residue template for MET /AI:1
    16877  Atom C1 is not in the residue template for GPC /AI:60
    16878  Atom H is not in the residue template for MET /AJ:1
    16879  Atom C1 is not in the residue template for GPC /AJ:60
    16880  Atom H is not in the residue template for MET /AK:1
    16881  Atom C1 is not in the residue template for GPC /AK:60
    16882  Atom C26 is not in the residue template for PEX /AK:62
    16883  Atom H is not in the residue template for MET /AL:1
    16884  Atom C1 is not in the residue template for GPC /AL:60
    16885  Atom H is not in the residue template for MET /AM:1
    16886  Atom C1 is not in the residue template for GPC /AM:60
    16887  Atom H is not in the residue template for MET /AN:1
    16888  Atom C1 is not in the residue template for GPC /AN:60
    16889  Atom H is not in the residue template for MET /AO:1
    16890  Atom C1 is not in the residue template for GPC /AO:60
    16891  Atom H is not in the residue template for MET /AP:1
    16892  Atom C1 is not in the residue template for GPC /AP:60
    16893  Atom H is not in the residue template for MET /AQ:1
    16894  Atom C1 is not in the residue template for GPC /AQ:60
    16895  Atom H is not in the residue template for MET /AR:1
    16896  Atom C1 is not in the residue template for GPC /AR:60
    16897  Atom H is not in the residue template for MET /AS:1
    16898  Atom C1 is not in the residue template for GPC /AS:60
    16899  Atom H is not in the residue template for MET /AT:1
    16900  Atom C1 is not in the residue template for GPC /AT:60
    16901  Atom H is not in the residue template for MET /AU:1
    16902  Atom C1 is not in the residue template for GPC /AU:60
    16903  Atom H is not in the residue template for MET /AV:1
    16904  Atom C1 is not in the residue template for GPC /AV:60
    16905  Atom H is not in the residue template for MET /AW:1
    16906  Atom C1 is not in the residue template for GPC /AW:60
    16907  Atom H is not in the residue template for MET /AX:1
    16908  Atom C1 is not in the residue template for GPC /AX:60
    16909  Atom H is not in the residue template for GLY /BQ:5
    16910  Atom H is not in the residue template for GLY /BR:5
    16911  Atom H is not in the residue template for GLY /BS:5
    16912  Atom H is not in the residue template for GLY /BT:5
    16913  Atom H11 is not in the residue template for BPH /L:606
    16914  Atom H11 is not in the residue template for BPH /M:605
    16915  Atom C1 is not in the residue template for RCC /M:701
    16916  Atom HN2 is not in the residue template for ARG /ak:71
    16917  Atom H is not in the residue template for GLY /C1:32
    16918  Atom C1 is not in the residue template for GPC /Ba:60
    16919  Atom C1 is not in the residue template for GPC /Bb:60
    16920  Atom C1 is not in the residue template for GPC /Bc:60
    16921  Atom C1 is not in the residue template for GPC /Bd:60
    16922  Atom C1 is not in the residue template for GPC /Be:60
    16923  11 messages similar to the above omitted
    16924  Missing or incomplete entity_poly_seq table. Inferred polymer
    16925  connectivity.
    16926 
    16927  Chain information for model1a.cif #3
    16928  ---
    16929  Chain | Description
    16930  AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?
    16931  AC AD | ?
    16932  BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk
    16933  bl
    16934  bm bo bp | ?
    16935  BB BD BE BI BQ BR BS BT BV BW bn | ?
    16936  C | ?
    16937  C1 | ?
    16938  H1 | ?
    16939  H2 | ?
    16940  L | ?
    16941  M | ?
    16942  aa | ?
    16943  ab ad ae af ag ah ai aj al am an ao ap | ?
    16944  ac | ?
    16945  ak | ?
    16946 
    16947 
    16948  > delete #3&~/M
    16949 
    16950  > select #3/M
    16951 
    16952  5881 atoms, 5992 bonds, 16 pseudobonds, 333 residues, 3 models selected
    16953 
    16954  > style sel stick
    16955 
    16956  Changed 5881 atom styles
    16957 
    16958  > hide HC
    16959 
    16960  > color sel green
    16961 
    16962  > color sel byhetero
    16963 
    16964  > select clear
    16965 
    16966  > select #8/M:20-50
    16967 
    16968  435 atoms, 440 bonds, 31 residues, 1 model selected
    16969 
    16970  > select clear
    16971 
    16972  > hide #!3 models
    16973 
    16974  > select #8/M:20-50
    16975 
    16976  435 atoms, 440 bonds, 31 residues, 1 model selected
    16977 
    16978  > delete #8/M:22-35
    16979 
    16980  > select #8/M:20-50
    16981 
    16982  242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected
    16983 
    16984  > select #8/M:20-50
    16985 
    16986  242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected
    16987 
    16988  > isolde add water simSettle false
    16989 
    16990  > select clear
    16991 
    16992  > save working.cxs
    16993 
    16994  Taking snapshot of stepper: working_2.pdb
    16995 
    16996  > close #6
    16997 
    16998  > close #4
    16999 
    17000  > close #3
    17001 
    17002  > close #2
    17003 
    17004  > close #1
    17005 
    17006  > save working.cxs
    17007 
    17008  Taking snapshot of stepper: working_2.pdb
    17009 
    17010  > select #8
    17011 
    17012  112761 atoms, 114661 bonds, 15 pseudobonds, 5682 residues, 23 models
    17013  selected
    17014 
    17015  > select clear
    17016 
    17017  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    17018 
    17019  > volume subtract #8.1.1.1 #1
    17020 
    17021  > close #1
    17022 
    17023  > select /M:4-12
    17024 
    17025  162 atoms, 163 bonds, 9 residues, 1 model selected
    17026 
    17027  > select clear
    17028 
    17029  > select up
    17030 
    17031  14 atoms, 13 bonds, 1 residue, 1 model selected
    17032 
    17033  > select up
    17034 
    17035  215 atoms, 216 bonds, 12 residues, 1 model selected
    17036 
    17037  > select clear
    17038 
    17039  > select clear
    17040 
    17041  > select /AA/AX:BCL
    17042 
    17043  1311 atoms, 1345 bonds, 57 residues, 1 model selected
    17044 
    17045  > select /AA-AX:BCL
    17046 
    17047  5460 atoms, 5772 bonds, 39 residues, 1 model selected
    17048 
    17049  > select /AA-AX:BCL
    17050 
    17051  5460 atoms, 5772 bonds, 39 residues, 1 model selected
    17052 
    17053  > isolde add water sel f
    17054 
    17055  Expected a keyword
    17056 
    17057  > isolde add water simSettle false
    17058 
    17059  > select /AA-AX:BCL
    17060 
    17061  5460 atoms, 5772 bonds, 39 residues, 1 model selected
    17062 
    17063  > select /AA-AX:BCL
    17064 
    17065  5460 atoms, 5772 bonds, 39 residues, 1 model selected
    17066 
    17067  > select /AA-AX:BCL
    17068 
    17069  5460 atoms, 5772 bonds, 39 residues, 1 model selected
    17070 
    17071  > select up
    17072 
    17073  140 atoms, 148 bonds, 1 residue, 1 model selected
    17074 
    17075  > select /AD:10-40@CA
    17076 
    17077  31 atoms, 31 residues, 1 model selected
    17078 
    17079  > select /AB:10-40@CA
    17080 
    17081  31 atoms, 31 residues, 1 model selected
    17082 
    17083  > select /AB
    17084 
    17085  1212 atoms, 1234 bonds, 53 residues, 1 model selected
    17086 
    17087  > select /AA-AX:BCL
    17088 
    17089  5600 atoms, 5920 bonds, 40 residues, 1 model selected
    17090 
    17091  > select clear
    17092 
    17093  > select /AB
    17094 
    17095  1352 atoms, 1382 bonds, 54 residues, 1 model selected
    17096 
    17097  > select /AA-AX:BCL
    17098 
    17099  5600 atoms, 5920 bonds, 40 residues, 1 model selected
    17100 
    17101  > select /AX:10-40@CA
    17102 
    17103  31 atoms, 31 residues, 1 model selected
    17104 
    17105  > select /AX
    17106 
    17107  1302 atoms, 1322 bonds, 57 residues, 1 model selected
    17108 
    17109  > delete /AX:73
    17110 
    17111  > select /AX:10-40@CA
    17112 
    17113  31 atoms, 31 residues, 1 model selected
    17114 
    17115  > select /AA-AX:BCL
    17116 
    17117  5740 atoms, 6068 bonds, 41 residues, 1 model selected
    17118 
    17119  > select up
    17120 
    17121  3 atoms, 2 bonds, 1 residue, 1 model selected
    17122 
    17123  > delete sel
    17124 
    17125  > select /AA-AX:BCL
    17126 
    17127  5740 atoms, 6068 bonds, 41 residues, 1 model selected
    17128 
    17129  > select /AU:10-40@CA
    17130 
    17131  31 atoms, 31 residues, 1 model selected
    17132 
    17133  > select /AU
    17134 
    17135  1218 atoms, 1238 bonds, 55 residues, 1 model selected
    17136 
    17137  > select /AA-AX:BCL
    17138 
    17139  5880 atoms, 6216 bonds, 42 residues, 1 model selected
    17140 
    17141  > select /AA-AX:BCL
    17142 
    17143  5880 atoms, 6216 bonds, 42 residues, 1 model selected
    17144 
    17145  > select up
    17146 
    17147  3 atoms, 2 bonds, 1 residue, 1 model selected
    17148 
    17149  > delete sel
    17150 
    17151  > select /AA-AX:BCL
    17152 
    17153  5880 atoms, 6216 bonds, 42 residues, 1 model selected
    17154 
    17155  > select /AR:10-40@CA
    17156 
    17157  31 atoms, 31 residues, 1 model selected
    17158 
    17159  > select /AR
    17160 
    17161  1215 atoms, 1236 bonds, 54 residues, 1 model selected
    17162 
    17163  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17164  bonded heavy atom.
    17165 
    17166  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17167  bonded heavy atom.
    17168 
    17169  > select /AA-AX:BCL
    17170 
    17171  6020 atoms, 6364 bonds, 43 residues, 1 model selected
    17172 
    17173  > select /AA-AX:BCL
    17174 
    17175  6020 atoms, 6364 bonds, 43 residues, 1 model selected
    17176 
    17177  > select /AA-AX:BCL
    17178 
    17179  6020 atoms, 6364 bonds, 43 residues, 1 model selected
    17180 
    17181  > select /Ao:10-40@CA
    17182 
    17183  Nothing selected
    17184 
    17185  > select /AO:10-40@CA
    17186 
    17187  31 atoms, 31 residues, 1 model selected
    17188 
    17189  > select /AO
    17190 
    17191  1134 atoms, 1154 bonds, 53 residues, 1 model selected
    17192 
    17193  > select up
    17194 
    17195  3 atoms, 2 bonds, 1 residue, 1 model selected
    17196 
    17197  > delete sel
    17198 
    17199  > select /AO
    17200 
    17201  1274 atoms, 1302 bonds, 54 residues, 1 model selected
    17202 
    17203  > select /AA-AX:BCL
    17204 
    17205  6160 atoms, 6512 bonds, 44 residues, 1 model selected
    17206 
    17207  > select /AL:10-40@CA
    17208 
    17209  31 atoms, 31 residues, 1 model selected
    17210 
    17211  > select /AL
    17212 
    17213  1305 atoms, 1324 bonds, 58 residues, 1 model selected
    17214 
    17215  > select /AL:10-40@CA
    17216 
    17217  31 atoms, 31 residues, 1 model selected
    17218 
    17219  > select /AA-AX:BCL
    17220 
    17221  6300 atoms, 6660 bonds, 45 residues, 1 model selected
    17222 
    17223  > select clear
    17224 
    17225  > select up
    17226 
    17227  3 atoms, 2 bonds, 1 residue, 1 model selected
    17228 
    17229  > delete sel
    17230 
    17231  > select /AA-AX:BCL
    17232 
    17233  6300 atoms, 6660 bonds, 45 residues, 1 model selected
    17234 
    17235  > select /AA-AX:BCL
    17236 
    17237  6300 atoms, 6660 bonds, 45 residues, 1 model selected
    17238 
    17239  > select clear
    17240 
    17241  > select up
    17242 
    17243  81 atoms, 82 bonds, 1 residue, 1 model selected
    17244 
    17245  > delete sel
    17246 
    17247  > select /AF:10-40@CA
    17248 
    17249  31 atoms, 31 residues, 1 model selected
    17250 
    17251  > select /AF
    17252 
    17253  1389 atoms, 1408 bonds, 60 residues, 1 model selected
    17254 
    17255  > select clear
    17256 
    17257  > select /AA-AX:BCL
    17258 
    17259  6440 atoms, 6808 bonds, 46 residues, 1 model selected
    17260 
    17261  > select /AA-AX:BCL
    17262 
    17263  6440 atoms, 6808 bonds, 46 residues, 1 model selected
    17264 
    17265  > select /AI:10-40@CA
    17266 
    17267  31 atoms, 31 residues, 1 model selected
    17268 
    17269  > select /AI
    17270 
    17271  1464 atoms, 1486 bonds, 59 residues, 1 model selected
    17272 
    17273  > select up
    17274 
    17275  81 atoms, 82 bonds, 1 residue, 1 model selected
    17276 
    17277  > delete sel
    17278 
    17279  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17280  bonded heavy atom.
    17281 
    17282  > select /AA-AX:BCL
    17283 
    17284  6580 atoms, 6956 bonds, 47 residues, 1 model selected
    17285 
    17286  > select /AC:10-40@CA
    17287 
    17288  31 atoms, 31 residues, 1 model selected
    17289 
    17290  > select /AC
    17291 
    17292  1207 atoms, 1225 bonds, 55 residues, 1 model selected
    17293 
    17294  > select up
    17295 
    17296  140 atoms, 148 bonds, 1 residue, 1 model selected
    17297 
    17298  > isolde ignore sel
    17299 
    17300  ISOLDE: currently ignoring 1 residues in model 8.2
    17301 
    17302  > isolde ~ignore
    17303 
    17304  > select /AA-AX:BCL
    17305 
    17306  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    17307 
    17308  > select /AA-AX:BCL
    17309 
    17310  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    17311 
    17312  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17313  bonded heavy atom.
    17314 
    17315  > select /AA-AX:BCL
    17316 
    17317  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    17318 
    17319  > select clear
    17320 
    17321  > save working.cxs
    17322 
    17323  Taking snapshot of stepper: working_2.pdb
    17324 
    17325  > select /ba-bp:BCL
    17326 
    17327  2240 atoms, 2368 bonds, 16 residues, 1 model selected
    17328 
    17329  > select /ba-bp,aa-ap:BCL
    17330 
    17331  4480 atoms, 4736 bonds, 32 residues, 1 model selected
    17332 
    17333  > select clear
    17334 
    17335  > select clear
    17336 
    17337  > isolde add water simSettle false
    17338 
    17339  > view /aa:26
    17340 
    17341  > view /ab:26
    17342 
    17343  > select clear
    17344 
    17345  > view /ac:26
    17346 
    17347  > view /ad:26
    17348 
    17349  > view /ae:26
    17350 
    17351  > view /af:26
    17352 
    17353  > view /ag:26
    17354 
    17355  > view /ah:26
    17356 
    17357  > view /ai:26
    17358 
    17359  > view /ap:26
    17360 
    17361  > view /aj:26
    17362 
    17363  > select clear
    17364 
    17365  > select clear
    17366 
    17367  > save working.cxs
    17368 
    17369  Taking snapshot of stepper: working_2.pdb
    17370 
    17371  > isolde add water simSettle false
    17372 
    17373  > select :HOH
    17374 
    17375  1218 atoms, 812 bonds, 406 residues, 1 model selected
    17376 
    17377  > select #8.1.1.1
    17378 
    17379  3 models selected
    17380 
    17381  > select clear
    17382 
    17383  > close #2
    17384 
    17385  > select #8
    17386 
    17387  113595 atoms, 115653 bonds, 15 pseudobonds, 5601 residues, 23 models
    17388  selected
    17389 
    17390  > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    17391 
    17392  > volume subtract #8.1.1.1 #1
    17393 
    17394  > close #1
    17395 
    17396  > select clear
    17397 
    17398  > select #2
    17399 
    17400  4 models selected
    17401 
    17402  > select clear
    17403 
    17404  > select :HOH
    17405 
    17406  2655 atoms, 1770 bonds, 885 residues, 1 model selected
    17407  Map is too large for fast cubic interpolation on the GPU! Switching to
    17408  slower,
    17409  more memory-efficient implementation.
    17410  Map is too large for fast cubic interpolation on the GPU! Switching to
    17411  slower,
    17412  more memory-efficient implementation.
    17413 
    17414  > select clear
    17415 
    17416  > select clear
    17417 
    17418  > select :HOH
    17419 
    17420  2655 atoms, 1770 bonds, 885 residues, 1 model selected
    17421 
    17422  > select clear
    17423 
    17424  > select :HOH
    17425 
    17426  2799 atoms, 1866 bonds, 933 residues, 1 model selected
    17427 
    17428  > select clear
    17429 
    17430  > style sel sphere
    17431 
    17432  Changed 672 atom styles
    17433 
    17434  > select :HOH
    17435 
    17436  2799 atoms, 1866 bonds, 933 residues, 1 model selected
    17437  Map is too large for fast cubic interpolation on the GPU! Switching to
    17438  slower,
    17439  more memory-efficient implementation.
    17440  Map is too large for fast cubic interpolation on the GPU! Switching to
    17441  slower,
    17442  more memory-efficient implementation.
    17443 
    17444  > select clear
    17445 
    17446  > select :HOH
    17447 
    17448  2799 atoms, 1866 bonds, 933 residues, 1 model selected
    17449 
    17450  > style sel stick
    17451 
    17452  Changed 2799 atom styles
    17453 
    17454  > select :HOH
    17455 
    17456  2334 atoms, 1556 bonds, 778 residues, 1 model selected
    17457 
    17458  > select clear
    17459 
    17460  > hide #!2 models
    17461 
    17462  > select ~:HOH&~H
    17463 
    17464  55004 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 27 models
    17465  selected
    17466 
    17467  > select up
    17468 
    17469  3 atoms, 2 bonds, 1 residue, 1 model selected
    17470 
    17471  > delete sel
    17472 
    17473  > select up
    17474 
    17475  9 atoms, 6 bonds, 3 residues, 1 model selected
    17476 
    17477  > delete sel
    17478 
    17479  > delete sel
    17480 
    17481  > select up
    17482 
    17483  9 atoms, 6 bonds, 3 residues, 1 model selected
    17484 
    17485  > delete sel
    17486 
    17487  > select #8
    17488 
    17489  114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models
    17490  selected
    17491 
    17492  > select clear
    17493 
    17494  > select #8
    17495 
    17496  114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models
    17497  selected
    17498 
    17499  > select clear
    17500 
    17501  > select #8
    17502 
    17503  114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models
    17504  selected
    17505 
    17506  > select clear
    17507 
    17508  > select clear
    17509 
    17510  > select #8
    17511 
    17512  114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models
    17513  selected
    17514 
    17515  > select clear
    17516 
    17517  > select up
    17518 
    17519  405 atoms, 410 bonds, 5 residues, 1 model selected
    17520 
    17521  > style sel sphere
    17522 
    17523  Changed 405 atom styles
    17524 
    17525  > style sel ball
    17526 
    17527  Changed 405 atom styles
    17528 
    17529  > style sel stick
    17530 
    17531  Changed 405 atom styles
    17532 
    17533  > color sel lightgreen
    17534 
    17535  > color sel byhetero
    17536 
    17537  > color ~sel lightgrey
    17538 
    17539  > color ~sel byhetero
    17540 
    17541  > color sel green
    17542 
    17543  > color sel byhetero
    17544 
    17545  > select clear
    17546 
    17547  > hide :HOH
    17548 
    17549  > select clear
    17550 
    17551  > save sideways_detergents.jpg
    17552 
    17553  > save sideways_detergents.jpg
    17554 
    17555  > color bychain
    17556 
    17557  > color byhetero
    17558 
    17559  > save working.cxs
    17560 
    17561  Taking snapshot of stepper: working_2.pdb
    17562  opened ChimeraX session
    17563 
    17564  > select /aa-ap,ba-bp&~protein
    17565 
    17566  6585 atoms, 6636 bonds, 253 residues, 1 model selected
    17567 
    17568  > isolde start
    17569 
    17570  > set selectionWidth 4
    17571 
    17572  Done loading forcefield
    17573 
    17574  > ui tool show Shell
    17575 
    17576  /opt/UCSF/ChimeraX/lib/python3.7/site-
    17577  packages/IPython/core/history.py:226:
    17578  UserWarning: IPython History requires SQLite, your history will not be
    17579  saved
    17580  warn("IPython History requires SQLite, your history will not be saved")
    17581 
    17582  > select /aa-ap,ba-bp&~protein
    17583 
    17584  6585 atoms, 6636 bonds, 253 residues, 1 model selected
    17585 
    17586  > select up
    17587 
    17588  81 atoms, 82 bonds, 1 residue, 1 model selected
    17589 
    17590  > select /aa-ap,ba-bp,AA-AX,BA-BX
    17591 
    17592  89079 atoms, 90638 bonds, 4388 residues, 1 model selected
    17593 
    17594  > select clear
    17595 
    17596  > select up
    17597 
    17598  81 atoms, 82 bonds, 1 residue, 1 model selected
    17599 
    17600  > select /AH
    17601 
    17602  1463 atoms, 1484 bonds, 65 residues, 1 model selected
    17603 
    17604  > select up
    17605 
    17606  81 atoms, 82 bonds, 1 residue, 1 model selected
    17607 
    17608  > select up
    17609 
    17610  3 atoms, 2 bonds, 1 residue, 1 model selected
    17611 
    17612  > delete sel
    17613 
    17614  Loading residue template for PEE from internal database
    17615  Loading residue template for PEX from internal database
    17616  Loading residue template for LMG from internal database
    17617  Loading residue template for PSF from internal database
    17618 
    17619  > select /aa-ap,ba-bp,AA-AX,BA-BX
    17620 
    17621  89076 atoms, 90636 bonds, 4387 residues, 1 model selected
    17622 
    17623  > select /aa-ap,ba-bp,AA-AX,BA-BX&~protein
    17624 
    17625  30204 atoms, 30692 bonds, 676 residues, 1 model selected
    17626 
    17627  > hide protein
    17628 
    17629  > select /aa-ap,ba-bp&~protein
    17630 
    17631  6501 atoms, 6552 bonds, 251 residues, 1 model selected
    17632 
    17633  > select clear
    17634 
    17635  > select up
    17636 
    17637  81 atoms, 82 bonds, 1 residue, 1 model selected
    17638 
    17639  > select /NA
    17640 
    17641  Nothing selected
    17642 
    17643  > select /AN
    17644 
    17645  1364 atoms, 1390 bonds, 58 residues, 1 model selected
    17646 
    17647  > select up
    17648 
    17649  81 atoms, 82 bonds, 1 residue, 1 model selected
    17650 
    17651  > select /AT
    17652 
    17653  1367 atoms, 1392 bonds, 59 residues, 1 model selected
    17654 
    17655  > select up
    17656 
    17657  81 atoms, 82 bonds, 1 residue, 1 model selected
    17658 
    17659  > select up
    17660 
    17661  81 atoms, 82 bonds, 1 residue, 1 model selected
    17662 
    17663  > select /AE
    17664 
    17665  1370 atoms, 1394 bonds, 60 residues, 1 model selected
    17666 
    17667  > select up
    17668 
    17669  81 atoms, 82 bonds, 1 residue, 1 model selected
    17670 
    17671  > select /aa-ap,ba-bp&~protein
    17672 
    17673  6258 atoms, 6306 bonds, 248 residues, 1 model selected
    17674 
    17675  > select clear
    17676 
    17677  > select /AK
    17678 
    17679  1361 atoms, 1388 bonds, 57 residues, 1 model selected
    17680 
    17681  > select up
    17682 
    17683  81 atoms, 82 bonds, 1 residue, 1 model selected
    17684 
    17685  > select up
    17686 
    17687  419 atoms, 426 bonds, 27 residues, 1 model selected
    17688 
    17689  > select /AS
    17690 
    17691  1251 atoms, 1278 bonds, 57 residues, 1 model selected
    17692 
    17693  > select up
    17694 
    17695  81 atoms, 82 bonds, 1 residue, 1 model selected
    17696 
    17697  > select /AT
    17698 
    17699  1448 atoms, 1474 bonds, 60 residues, 1 model selected
    17700 
    17701  > select up
    17702 
    17703  81 atoms, 82 bonds, 1 residue, 1 model selected
    17704 
    17705  > select /aa-ap,ba-bp&~protein&~:HOH
    17706 
    17707  5391 atoms, 5644 bonds, 37 residues, 1 model selected
    17708 
    17709  > select clear
    17710 
    17711  > select /AA-AX,BA-BX&~protein&~:HOH
    17712 
    17713  23574 atoms, 24222 bonds, 226 residues, 1 model selected
    17714 
    17715  > select clear
    17716 
    17717  > select /aa-ap,ba-bp
    17718 
    17719  31156 atoms, 31603 bonds, 1836 residues, 1 model selected
    17720 
    17721  > select /aa-ap,ba-bp&protein
    17722 
    17723  25141 atoms, 25543 bonds, 1591 residues, 1 model selected
    17724 
    17725  > select clear
    17726 
    17727  > select /AA-AX,BA-BX&~protein&~:HOH
    17728 
    17729  23574 atoms, 24222 bonds, 226 residues, 1 model selected
    17730 
    17731  > select zone /aa-ap,ba-bp range 4 & sel
    17732 
    17733  Missing or invalid "range" argument: Expected a number
    17734 
    17735  > select zone /aa-ap,ba-bp range 4
    17736 
    17737  Missing or invalid "range" argument: Expected a number
    17738 
    17739  > select zone /aa-ap,ba-bp 4
    17740 
    17741  Selected 10127 atoms, 2 surfaces
    17742 
    17743  > select sel&/AA-AX,BA-BX&~protein&~:HOH
    17744 
    17745  4211 atoms, 3646 bonds, 114 residues, 1 model selected
    17746 
    17747  > select zone /aa-ap,ba-bp&protein 4
    17748 
    17749  Selected 13233 atoms, 2 surfaces
    17750 
    17751  > select sel&/AA-AX,BA-BX&~protein&~:HOH
    17752 
    17753  3584 atoms, 2961 bonds, 107 residues, 1 model selected
    17754 
    17755  > select sel&:PEX,LMT
    17756 
    17757  2797 atoms, 2354 bonds, 57 residues, 1 model selected
    17758 
    17759  > select up
    17760 
    17761  2638 atoms, 2181 bonds, 57 residues, 1 model selected
    17762 
    17763  > select up
    17764 
    17765  2634 atoms, 2173 bonds, 57 residues, 1 model selected
    17766 
    17767  > select down
    17768 
    17769  2218 atoms, 1914 bonds, 57 residues, 1 model selected
    17770 
    17771  > select up
    17772 
    17773  2560 atoms, 2075 bonds, 57 residues, 1 model selected
    17774 
    17775  > select down
    17776 
    17777  1819 atoms, 1586 bonds, 57 residues, 1 model selected
    17778 
    17779  > show sel
    17780 
    17781  > select up
    17782 
    17783  849 atoms, 659 bonds, 44 residues, 1 model selected
    17784 
    17785  > select up
    17786 
    17787  4076 atoms, 4088 bonds, 44 residues, 1 model selected
    17788 
    17789  > save reassigning_ligands.cxs
    17790 
    17791  Taking snapshot of stepper: working_2.pdb
    17792 
    17793  > select /AA-AX,BA-BX&~protein&~:HOH
    17794 
    17795  19498 atoms, 20134 bonds, 182 residues, 1 model selected
    17796 
    17797  > save reassigning_ligands.cxs
    17798 
    17799  Taking snapshot of stepper: working_2.pdb
    17800  Restoring stepper: working_2.pdb
    17801  opened ChimeraX session
    17802 
    17803  > select :GPC
    17804 
    17805  4000 atoms, 3960 bonds, 40 residues, 1 model selected
    17806 
    17807  > select /Ba-Bp
    17808 
    17809  1603 atoms, 1586 bonds, 17 residues, 1 model selected
    17810 
    17811  > select /Ba-Bp
    17812 
    17813  Nothing selected
    17814 
    17815  > select /Aa-Ap
    17816 
    17817  Nothing selected
    17818 
    17819  > save reassigning_ligands.cxs
    17820 
    17821  Taking snapshot of stepper: working_2.pdb
    17822  Restoring stepper: working_2.pdb
    17823  opened ChimeraX session
    17824  Traceback (most recent call last):
    17825  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17826  packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>
    17827  QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
    17828  RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
    17829 
    17830  RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
    17831 
    17832  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17833  packages/chimerax/map/volume_viewer.py", line 1530, in
    17834  QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
    17835 
    17836  See log for complete Python traceback.
    17837 
    17838 
    17839  > select ~:HOH
    17840 
    17841  112638 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 24 models
    17842  selected
    17843 
    17844  > select zone sel 3
    17845 
    17846  Selected 1994 atoms
    17847 
    17848  > select up
    17849 
    17850  2145 atoms, 1430 bonds, 715 residues, 1 model selected
    17851 
    17852  > select :HOH&~sel
    17853 
    17854  120 atoms, 80 bonds, 40 residues, 1 model selected
    17855 
    17856  > delete sel
    17857 
    17858  > view /L:40
    17859 
    17860  > select up
    17861 
    17862  6 atoms, 4 bonds, 2 residues, 1 model selected
    17863 
    17864  > delete sel
    17865 
    17866  > isolde add ligand MQ9
    17867 
    17868  > delete sel
    17869 
    17870  > isolde add ligand MQ8
    17871 
    17872  > ui mousemode right "translate selected atoms"
    17873 
    17874  > isolde ignore ~sel
    17875 
    17876  ISOLDE: currently ignoring 5995 residues in model 8.2
    17877 
    17878  > isolde ~ignore
    17879 
    17880  > save working.cxs
    17881 
    17882  Taking snapshot of stepper: working_2.pdb
    17883 
    17884  > select #8
    17885 
    17886  114902 atoms, 116567 bonds, 15 pseudobonds, 5996 residues, 23 models
    17887  selected
    17888 
    17889  > show #!2 models
    17890 
    17891  > select /aa-ap
    17892 
    17893  18677 atoms, 18860 bonds, 1123 residues, 1 model selected
    17894 
    17895  > select clear
    17896 
    17897  > select /aa-ap
    17898 
    17899  18677 atoms, 18860 bonds, 1123 residues, 1 model selected
    17900 
    17901  > select clear
    17902 
    17903  > select #8
    17904 
    17905  114902 atoms, 116567 bonds, 15 pseudobonds, 5996 residues, 23 models
    17906  selected
    17907 
    17908  > select /aa-ap
    17909 
    17910  18677 atoms, 18860 bonds, 1123 residues, 1 model selected
    17911 
    17912  > select clear
    17913 
    17914  > select clear
    17915 
    17916  > select /aa-ap
    17917 
    17918  18677 atoms, 18860 bonds, 1123 residues, 1 model selected
    17919 
    17920  > swapaa mousemode sel MET
    17921 
    17922  > swapaa mousemode sel SER
    17923 
    17924  > swapaa mousemode sel PRO
    17925 
    17926  > swapaa mousemode sel LEU
    17927 
    17928  > swapaa mousemode sel GLY
    17929 
    17930  > delete sel
    17931 
    17932  > hide #!2 models
    17933 
    17934  > select up
    17935 
    17936  14 atoms, 14 bonds, 1 residue, 1 model selected
    17937 
    17938  > select up
    17939 
    17940  159 atoms, 161 bonds, 12 residues, 1 model selected
    17941 
    17942  > swapaa mousemode sel ARG
    17943 
    17944  > swapaa mousemode sel ARG
    17945 
    17946  Traceback (most recent call last):
    17947  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17948  packages/chimerax/atomic/molarray.py", line 112, in __init__
    17949  pointers = numpy.array([i._c_pointer.value for i in items], cptr)
    17950  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17951  packages/chimerax/atomic/molarray.py", line 112, in <listcomp>
    17952  pointers = numpy.array([i._c_pointer.value for i in items], cptr)
    17953  AttributeError: 'Rotamer' object has no attribute '_c_pointer'
    17954 
    17955  During handling of the above exception, another exception occurred:
    17956 
    17957  Traceback (most recent call last):
    17958  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17959  packages/chimerax/isolde/isolde.py", line 2089, in _commit_rotamer
    17960  rrm.commit_preview(rot)
    17961  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17962  packages/chimerax/isolde/molobject.py", line 4169, in commit_preview
    17963  rr = self.add_restraint(rotamer)
    17964  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17965  packages/chimerax/isolde/molobject.py", line 4077, in add_restraint
    17966  rr = self._get_restraints(_rotamers([r]), True)
    17967  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17968  packages/chimerax/isolde/molobject.py", line 78, in _rotamers
    17969  return Rotamers(p)
    17970  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17971  packages/chimerax/isolde/molarray.py", line 269, in __init__
    17972  super().__init__(c_pointers, Rotamer, Rotamers)
    17973  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17974  packages/chimerax/atomic/molarray.py", line 117, in __init__
    17975  raise ValueError('Collection items of unrecognized type "%s"' % t)
    17976  ValueError: Collection items of unrecognized type "<class 'list'>"
    17977 
    17978  ValueError: Collection items of unrecognized type ""
    17979 
    17980  File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17981  packages/chimerax/atomic/molarray.py", line 117, in __init__
    17982  raise ValueError('Collection items of unrecognized type "%s"' % t)
    17983 
    17984  See log for complete Python traceback.
    17985 
    17986 
    17987  No rotamer preview selected! Ignoring command.
    17988 
    17989  > isolde ignore ~sel
    17990 
    17991  ISOLDE: currently ignoring 5994 residues in model 8.2
    17992  Traceback (most recent call last):
    17993  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17994  packages/chimerax/isolde/isolde.py", line 2707, in
    17995  _start_sim_or_toggle_pause
    17996  self.start_sim()
    17997  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17998  packages/chimerax/isolde/isolde.py", line 2727, in start_sim
    17999  self.params, self.sim_params, excluded_residues = self.ignored_residues)
    18000  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18001  packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in
    18002  __init__
    18003  self._prepare_mdff_managers()
    18004  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18005  packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    18006  _prepare_mdff_managers
    18007  focus = False)
    18008  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18009  packages/chimerax/clipper/symmetry.py", line 982, in
    18010  isolate_and_cover_selection
    18011  extra_padding=extra_padding)
    18012  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18013  packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms
    18014  zm.set_symmetry_map(atoms, transforms, transform_indices)
    18015  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18016  packages/chimerax/clipper/maps/mask_handler.py", line 119, in
    18017  set_symmetry_map
    18018  self.structure = self._unique_structure(atoms)
    18019  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18020  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    18021  _unique_structure
    18022  raise TypeError('All atoms for zone mask must be from a single model!')
    18023  TypeError: All atoms for zone mask must be from a single model!
    18024 
    18025  TypeError: All atoms for zone mask must be from a single model!
    18026 
    18027  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    18028  packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    18029  _unique_structure
    18030  raise TypeError('All atoms for zone mask must be from a single model!')
    18031 
    18032  See log for complete Python traceback.
    18033 
    18034 
    18035  > isolde ~ignore
    18036 
    18037  > color bychain
    18038 
    18039  > color byhetero
    18040 
    18041  > cartoon
    18042 
    18043  > select up
    18044 
    18045  24 atoms, 23 bonds, 1 residue, 1 model selected
    18046 
    18047  > isolde ignore ~sel
    18048 
    18049  ISOLDE: currently ignoring 5993 residues in model 8.2
    18050 
    18051  > isolde ~ignore
    18052 
    18053  Added a C-terminal OXT to chain C1
    18054 
    18055  > select up
    18056 
    18057  24 atoms, 23 bonds, 1 residue, 1 model selected
    18058 
    18059  > show sel
    18060 
    18061  > swapaa sel mousem GLU
    18062 
    18063  Expected a keyword
    18064 
    18065  > swapaa mousemode sel GLU
    18066 
    18067  > swapaa mousemode sel ALA
    18068 
    18069  > swapaa mousemode sel ALA
    18070 
    18071  > select up
    18072 
    18073  3 atoms, 2 bonds, 1 residue, 1 model selected
    18074 
    18075  > delete sel
    18076 
    18077  > select up
    18078 
    18079  10 atoms, 9 bonds, 1 residue, 1 model selected
    18080 
    18081  > select up
    18082 
    18083  162 atoms, 164 bonds, 12 residues, 1 model selected
    18084 
    18085  > select /ap:50-100
    18086 
    18087  291 atoms, 295 bonds, 23 residues, 1 model selected
    18088 
    18089  Chain ap, residue 60 specifies more than one residue! The simulation can
    18090  still
    18091  run, but this will probably cause problems later if not rectified by
    18092  renumbering.
    18093 
    18094  > select clear
    18095 
    18096  > swapaa mousemode sel ALA
    18097 
    18098  > select up
    18099 
    18100  10 atoms, 9 bonds, 1 residue, 1 model selected
    18101 
    18102  > delete sel
    18103 
    18104  > select /ap:50-100
    18105 
    18106  294 atoms, 298 bonds, 23 residues, 1 model selected
    18107 
    18108  > select clear
    18109 
    18110  Residue ALA ap61 is not a C-terminal residue!
    18111  Residue ALA ap61 is not a C-terminal residue!
    18112 
    18113  > isolde add ligand TRP
    18114 
    18115  place_ligand() was called with use_md_template=True, but no suitable
    18116  template
    18117  was found. This command has been ignored.
    18118 
    18119  > select up
    18120 
    18121  27 atoms, 28 bonds, 1 residue, 1 model selected
    18122 
    18123  > delete sel
    18124 
    18125  > select :MQ8
    18126 
    18127  125 atoms, 126 bonds, 1 residue, 1 model selected
    18128 
    18129  > select clear
    18130 
    18131  > select /ap
    18132 
    18133  1268 atoms, 1283 bonds, 81 residues, 1 model selected
    18134  Added a C-terminal OXT to chain ap
    18135 
    18136  > isolde add water
    18137 
    18138  > isolde sim start sel
    18139 
    18140  > select up
    18141 
    18142  3 atoms, 2 bonds, 1 residue, 1 model selected
    18143 
    18144  > style sel stick
    18145 
    18146  Changed 3 atom styles
    18147 
    18148  > color sel byhetero
    18149 
    18150  > select clear
    18151 
    18152  > isolde add water simSettle false
    18153 
    18154  > isolde add water simSettle false
    18155 
    18156  > isolde add water simSettle false
    18157 
    18158  > select clear
    18159 
    18160  > clipper spotlight radius 19.00
    18161 
    18162  > clipper spotlight radius 20.00
    18163 
    18164  > select up
    18165 
    18166  17 atoms, 16 bonds, 1 residue, 1 model selected
    18167 
    18168  > select up
    18169 
    18170  159 atoms, 161 bonds, 11 residues, 1 model selected
    18171 
    18172  Chain bk, residue 100 specifies more than one residue! The simulation can
    18173  still run, but this will probably cause problems later if not rectified by
    18174  renumbering.
    18175 
    18176  Deleted the following atoms from residue GLU an63: HN2
    18177  Deleted the following atoms from residue SER an65: HN2
    18178  Deleted the following atoms from residue LEU an67: HN2
    18179  Deleted the following atoms from residue ARG an71: HN2
    18180 
    18181  Chain bk, residue 100 specifies more than one residue! The simulation can
    18182  still run, but this will probably cause problems later if not rectified by
    18183  renumbering.
    18184 
    18185  > select up
    18186 
    18187  11 atoms, 10 bonds, 1 residue, 1 model selected
    18188 
    18189  > select up
    18190 
    18191  155 atoms, 157 bonds, 11 residues, 1 model selected
    18192 
    18193  > select clear
    18194 
    18195  > show #!2 models
    18196 
    18197  > hide #!2 models
    18198 
    18199  > isolde add ligand LMT chain ba
    18200 
    18201  > ui mousemode right "translate selected atoms"
    18202 
    18203  > select clear
    18204 
    18205  > select up
    18206 
    18207  3 atoms, 2 bonds, 1 residue, 1 model selected
    18208 
    18209  > delete sel
    18210 
    18211  > select up
    18212 
    18213  9 atoms, 6 bonds, 3 residues, 1 model selected
    18214 
    18215  > select up
    18216 
    18217  12 atoms, 8 bonds, 4 residues, 1 model selected
    18218 
    18219  > delete sel
    18220 
    18221  > select up
    18222 
    18223  3 atoms, 2 bonds, 1 residue, 1 model selected
    18224 
    18225  > select up
    18226 
    18227  6 atoms, 4 bonds, 2 residues, 1 model selected
    18228 
    18229  > select up
    18230 
    18231  9 atoms, 6 bonds, 3 residues, 1 model selected
    18232 
    18233  > select up
    18234 
    18235  15 atoms, 10 bonds, 5 residues, 1 model selected
    18236 
    18237  > select up
    18238 
    18239  18 atoms, 12 bonds, 6 residues, 1 model selected
    18240 
    18241  > select up
    18242 
    18243  27 atoms, 18 bonds, 9 residues, 1 model selected
    18244 
    18245  > delete sel
    18246 
    18247  > select clear
    18248 
    18249  > select ~:HOH
    18250 
    18251  112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 27 models
    18252  selected
    18253 
    18254  > usage sel
    18255 
    18256  select [objects] [residues true or false] [polymer an atoms specifier]
    18257  [minimumLength a number] [maximumLength a number] [sequence a text string]
    18258  — select specified objects
    18259  Subcommands are:
    18260 
    18261    * select add
    18262    * select clear
    18263    * select down
    18264    * select intersect
    18265    * select subtract
    18266    * select up
    18267    * select zone
    18268 
    18269 
    18270 
    18271  > select #8.2&~:HOH
    18272 
    18273  112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models
    18274  selected
    18275 
    18276  > select zone sel 3
    18277 
    18278  Selected 1954 atoms, 5 surfaces
    18279 
    18280  > select up
    18281 
    18282  2103 atoms, 1402 bonds, 701 residues, 6 models selected
    18283 
    18284  > select :HOH&~sel
    18285 
    18286  3 atoms, 2 bonds, 1 residue, 1 model selected
    18287 
    18288  > select clear
    18289 
    18290  > select #8.2&~:HOH
    18291 
    18292  112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models
    18293  selected
    18294 
    18295  > select zone sel 3
    18296 
    18297  Selected 1954 atoms, 5 surfaces
    18298 
    18299  > select up
    18300 
    18301  2103 atoms, 1402 bonds, 701 residues, 6 models selected
    18302 
    18303  > select down
    18304 
    18305  1954 atoms, 701 residues, 6 models selected
    18306 
    18307  > select clear
    18308 
    18309  > select #8.2&~:HOH&~H
    18310 
    18311  55156 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models
    18312  selected
    18313 
    18314  > select zone sel 3
    18315 
    18316  Selected 59310 atoms, 5 surfaces
    18317 
    18318  > select up
    18319 
    18320  114877 atoms, 116626 bonds, 5926 residues, 6 models selected
    18321 
    18322  > select :HOH&~sel
    18323 
    18324  204 atoms, 136 bonds, 68 residues, 1 model selected
    18325 
    18326  > delete sel
    18327 
    18328  > isolde add ligand MQ8
    18329 
    18330  > ui mousemode right "translate selected atoms"
    18331 
    18332  > isolde ignore ~sel
    18333 
    18334  ISOLDE: currently ignoring 5927 residues in model 8.2
    18335 
    18336  > isolde ~ignore
    18337 
    18338  Chain bk, residue 100 specifies more than one residue! The simulation can
    18339  still run, but this will probably cause problems later if not rectified by
    18340  renumbering.
    18341 
    18342  > select clear
    18343 
    18344  > select up
    18345 
    18346  125 atoms, 126 bonds, 1 residue, 1 model selected
    18347 
    18348  > show sel
    18349 
    18350  > select clear
    18351 
    18352  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    18353  bonded heavy atom.
    18354 
    18355  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    18356  bonded heavy atom.
    18357 
    18358  Chain bk, residue 100 specifies more than one residue! The simulation can
    18359  still run, but this will probably cause problems later if not rectified by
    18360  renumbering.
    18361 
    18362  > select :MQ9
    18363 
    18364  138 atoms, 139 bonds, 1 residue, 1 model selected
    18365 
    18366  > select :MQ8,MQ9
    18367 
    18368  388 atoms, 391 bonds, 3 residues, 1 model selected
    18369 
    18370  > select up
    18371 
    18372  3 atoms, 2 bonds, 1 residue, 1 model selected
    18373 
    18374  > delete sel
    18375 
    18376  > select up
    18377 
    18378  3 atoms, 2 bonds, 1 residue, 1 model selected
    18379 
    18380  > delete sel
    18381 
    18382  > select up
    18383 
    18384  3 atoms, 2 bonds, 1 residue, 1 model selected
    18385 
    18386  > delete sel
    18387 
    18388  > select clear
    18389 
    18390  > select clear
    18391 
    18392  > select up
    18393 
    18394  15 atoms, 10 bonds, 5 residues, 1 model selected
    18395 
    18396  > delete sel
    18397 
    18398  > select clear
    18399 
    18400  > select up
    18401 
    18402  256 atoms, 255 bonds, 1 residue, 1 model selected
    18403 
    18404  > select clear
    18405 
    18406  > isolde add water simSettle false
    18407 
    18408  > select up
    18409 
    18410  6 atoms, 4 bonds, 2 residues, 1 model selected
    18411 
    18412  > delete sel
    18413 
    18414  > isolde add water simSettle false
    18415 
    18416  > isolde add water simSettle false
    18417 
    18418  > isolde add water simSettle false
    18419 
    18420  > isolde add water simSettle false
    18421 
    18422  > isolde add water simSettle false
    18423 
    18424  > isolde add water simSettle false
    18425 
    18426  > isolde add water simSettle false
    18427 
    18428  > isolde add water simSettle false
    18429 
    18430  No existing atoms found within the given distance cutoff of the target
    18431  position. You may repeat with a larger cutoff or explicitly specify the
    18432  B-factor and chain ID, but keep in mind that placing waters outside of
    18433  H-bonding distance to the model is generally inadvisable.
    18434 
    18435  > isolde add water simSettle false
    18436 
    18437  > isolde add water simSettle false
    18438 
    18439  > isolde add water simSettle false
    18440 
    18441  > select clear
    18442 
    18443  > save working.cxs
    18444 
    18445  Taking snapshot of stepper: working_2.pdb
    18446  opened ChimeraX session
    18447 
    18448  > view /M:GCU
    18449 
    18450  > open
    18451  >
    18452  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/GUX.xml
    18453 
    18454  Opened GUX.xml
    18455 
    18456  > open
    18457  >
    18458  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    18459 
    18460  > select #1
    18461 
    18462  29 atoms, 29 bonds, 1 residue, 1 model selected
    18463 
    18464  > ui mousemode right "translate selected atoms"
    18465 
    18466  > select up
    18467 
    18468  2 atoms, 1 bond, 1 residue, 1 model selected
    18469 
    18470  > select up
    18471 
    18472  29 atoms, 29 bonds, 1 residue, 1 model selected
    18473 
    18474  > delete sel
    18475 
    18476  > isolde start
    18477 
    18478  > set selectionWidth 4
    18479 
    18480  Done loading forcefield
    18481 
    18482  > pwd
    18483 
    18484  Current working directory is:
    18485  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a
    18486 
    18487  > open
    18488  >
    18489  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    18490 
    18491  > select #1
    18492 
    18493  29 atoms, 29 bonds, 1 residue, 1 model selected
    18494 
    18495  > delete #1/M:GCU
    18496 
    18497  > open
    18498  >
    18499  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    18500 
    18501  > select #1
    18502 
    18503  29 atoms, 29 bonds, 1 residue, 1 model selected
    18504 
    18505  > delete #8/M:GCU
    18506 
    18507  > ui tool show Shell
    18508 
    18509  /opt/UCSF/ChimeraX/lib/python3.7/site-
    18510  packages/IPython/core/history.py:226:
    18511  UserWarning: IPython History requires SQLite, your history will not be
    18512  saved
    18513  warn("IPython History requires SQLite, your history will not be saved")
    18514 
    18515  > hide #1 models
    18516 
    18517  > select up
    18518 
    18519  67 atoms, 69 bonds, 3 residues, 1 model selected
    18520 
    18521  Chain bk, residue 100 specifies more than one residue! The simulation can
    18522  still run, but this will probably cause problems later if not rectified by
    18523  renumbering.
    18524 
    18525  > select up
    18526 
    18527  29 atoms, 29 bonds, 1 residue, 1 model selected
    18528 
    18529  > select clear
    18530 
    18531  > select /C
    18532 
    18533  5190 atoms, 5214 bonds, 4 pseudobonds, 390 residues, 2 models selected
    18534 
    18535  > select clear
    18536 
    18537  > view :GUX
    18538 
    18539  > select up
    18540 
    18541  29 atoms, 29 bonds, 1 residue, 1 model selected
    18542 
    18543  > save acetylated_gcu.jpg
    18544 
    18545  > select clear
    18546 
    18547  > view /M:GCU
    18548 
    18549  > view #8:GCU
    18550 
    18551  > view #8:GUX
    18552 
    18553  > close #1#2
    18554 
    18555  > view :GCU
    18556 
    18557  > open
    18558  >
    18559  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    18560 
    18561  > select #1
    18562 
    18563  29 atoms, 29 bonds, 1 residue, 1 model selected
    18564 
    18565  > ui mousemode right "translate selected atoms"
    18566 
    18567  > select up
    18568 
    18569  19 atoms, 19 bonds, 1 residue, 1 model selected
    18570 
    18571  > delete sel
    18572 
    18573  > hide #1 models
    18574 
    18575  > select up
    18576 
    18577  67 atoms, 69 bonds, 3 residues, 1 model selected
    18578 
    18579  Chain bk, residue 100 specifies more than one residue! The simulation can
    18580  still run, but this will probably cause problems later if not rectified by
    18581  renumbering.
    18582 
    18583  > select up
    18584 
    18585  29 atoms, 29 bonds, 1 residue, 1 model selected
    18586 
    18587  > select clear
    18588 
    18589  > save model1a_2020_11_02.pdb #1
    18590 
    18591  > save model1a_2020_11_02.pdb #8
    18592 
    18593  > view /M:GUX
    18594 
    18595  > select clear
    18596 
    18597  > isolde add water simSettle false
    18598 
    18599  > save model1a_2020_11_02.pdb #8
    18600 
    18601  > isolde add water simSettle false
    18602 
    18603  > isolde add water simSettle false
    18604 
    18605  > select up
    18606 
    18607  3 atoms, 2 bonds, 1 residue, 1 model selected
    18608 
    18609  > delete sel
    18610 
    18611  > isolde add water simSettle false
    18612 
    18613  > isolde add water simSettle false
    18614 
    18615  > select up
    18616 
    18617  3 atoms, 2 bonds, 1 residue, 1 model selected
    18618 
    18619  > delete sel
    18620 
    18621  > isolde add water simSettle false
    18622 
    18623  > isolde add water simSettle false
    18624 
    18625  > isolde add water simSettle false
    18626 
    18627  > isolde add water simSettle false
    18628 
    18629  > isolde add water simSettle false
    18630 
    18631  > isolde add water simSettle false
    18632 
    18633  > isolde add water simSettle false
    18634 
    18635  > isolde add water simSettle false
    18636 
    18637  > isolde add water simSettle false
    18638 
    18639  > isolde add water simSettle false
    18640 
    18641  > select clear
    18642 
    18643  > isolde add water simSettle false
    18644 
    18645  > isolde add water simSettle false
    18646 
    18647  > isolde add water simSettle false
    18648 
    18649  > isolde add water simSettle false
    18650 
    18651  > isolde add water simSettle false
    18652 
    18653  > isolde add water simSettle false
    18654 
    18655  > isolde add water simSettle false
    18656 
    18657  > isolde add water simSettle false
    18658 
    18659  > isolde add water simSettle false
    18660 
    18661  > isolde add water simSettle false
    18662 
    18663  > select clear
    18664 
    18665  > isolde add water simSettle false
    18666 
    18667  > isolde add water simSettle false
    18668 
    18669  > select clear
    18670 
    18671  > isolde add water simSettle false
    18672 
    18673  > select clear
    18674 
    18675  > isolde add water simSettle false
    18676 
    18677  > select clear
    18678 
    18679  > isolde add water simSettle false
    18680 
    18681  > isolde add water simSettle false
    18682 
    18683  > isolde add water simSettle false
    18684 
    18685  > isolde add water simSettle false
    18686 
    18687  > isolde add water simSettle false
    18688 
    18689  > select up
    18690 
    18691  3 atoms, 2 bonds, 1 residue, 1 model selected
    18692 
    18693  > delete sel
    18694 
    18695  > select /a*:50-60
    18696 
    18697  2020 atoms, 2035 bonds, 172 residues, 1 model selected
    18698 
    18699  > select clear
    18700 
    18701  > isolde add water simSettle false
    18702 
    18703  > select clear
    18704 
    18705  > select clear
    18706 
    18707  > select clear
    18708 
    18709  > isolde add water simSettle false
    18710 
    18711  > select clear
    18712 
    18713  > isolde add water simSettle false
    18714 
    18715  > isolde add water simSettle false
    18716 
    18717  > select clear
    18718 
    18719  > isolde add water simSettle false
    18720 
    18721  > select clear
    18722 
    18723  > isolde add water simSettle false
    18724 
    18725  > isolde add water simSettle false
    18726 
    18727  > isolde add water simSettle false
    18728 
    18729  > select up
    18730 
    18731  6 atoms, 4 bonds, 2 residues, 1 model selected
    18732 
    18733  > delete sel
    18734 
    18735  > select up
    18736 
    18737  3 atoms, 2 bonds, 1 residue, 1 model selected
    18738 
    18739  > delete sel
    18740 
    18741  > select up
    18742 
    18743  3 atoms, 2 bonds, 1 residue, 1 model selected
    18744 
    18745  > delete sel
    18746 
    18747  > select clear
    18748 
    18749  > save model1a_2020_11_02.cxs
    18750 
    18751  Taking snapshot of stepper: Model 1a
    18752 
    18753  > save model1a_2020_11_02.pdb #8
    18754 
    18755  > select clear
    18756 
    18757  > delete sel
    18758 
    18759  > dssp
    18760 
    18761  > save model1a_2020_11_02.cxs
    18762 
    18763  Taking snapshot of stepper: Model 1a
    18764  opened ChimeraX session
    18765 
    18766  > close #8.1.1.2
    18767 
    18768  > open
    18769  >
    18770  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/class1a_r_2.35A.mrc
    18771 
    18772  Opened class1a_r_2.35A.mrc, grid size 400,400,400, pixel 0.999, shown at
    18773  level
    18774  0.0164, step 2, values float32
    18775 
    18776  > clipper associate #2 toModel #8
    18777 
    18778  > close #1
    18779 
    18780  > isolde start
    18781 
    18782  > set selectionWidth 4
    18783 
    18784  Done loading forcefield
    18785 
    18786  > view /M:MAN
    18787 
    18788  > select clear
    18789 
    18790  > clipper spotlight radius 11.00
    18791 
    18792  > clipper spotlight radius 10.00
    18793 
    18794  > clipper spotlight radius 9.00
    18795 
    18796  > clipper spotlight radius 8.00
    18797 
    18798  > clipper spotlight radius 7.00
    18799 
    18800  > clipper spotlight radius 6.00
    18801 
    18802  > clipper spotlight radius 5.00
    18803 
    18804  > clipper spotlight radius 6.00
    18805 
    18806  > clipper spotlight radius 7.00
    18807 
    18808  > clipper spotlight radius 8.00
    18809 
    18810  > clipper spotlight radius 9.00
    18811 
    18812  > clipper spotlight radius 10.00
    18813 
    18814  > clipper spotlight radius 11.00
    18815 
    18816  > clipper spotlight radius 12.00
    18817 
    18818  > clipper spotlight radius 13.00
    18819 
    18820  > clipper spotlight radius 14.00
    18821 
    18822  > clipper spotlight radius 15.00
    18823 
    18824  > clipper spotlight radius 16.00
    18825 
    18826  > select clear
    18827 
    18828  > select clear
    18829 
    18830  > save man.jpg
    18831 
    18832  > select clear
    18833 
    18834  > save model1a_2020_11_04.cxs
    18835 
    18836  Taking snapshot of stepper: Model 1a
    18837  opened ChimeraX session
    18838 
    18839  > ui tool show Shell
    18840 
    18841  /opt/UCSF/ChimeraX/lib/python3.7/site-
    18842  packages/IPython/core/history.py:226:
    18843  UserWarning: IPython History requires SQLite, your history will not be
    18844  saved
    18845  warn("IPython History requires SQLite, your history will not be saved")
    18846 
    18847  > open class4b_r_2.35A_postprocess_masked.mrc
    18848 
    18849  Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400,
    18850  pixel
    18851  0.999, shown at level 0.0164, step 2, values float32
    18852 
    18853  > volume gaussian #1 bfactor 50
    18854 
    18855  > close #8.1
    18856 
    18857  > clipper associate #1,2 toModel #8
    18858 
    18859  > isolde start
    18860 
    18861  > set selectionWidth 4
    18862 
    18863  Done loading forcefield
    18864 
    18865  > clipper set contourSensitivity 0.25
    18866 
    18867  > select clear
    18868 
    18869  > ui tool show Shell
    18870 
    18871  > alias keep setattr sel residues isolde_keep true
    18872 
    18873  > alias st isolde step $*
    18874 
    18875  > alias aw isolde add water $*
    18876 
    18877  > keep
    18878 
    18879  Assigning isolde_keep attribute to 1 item
    18880 
    18881  > keep
    18882 
    18883  Assigning isolde_keep attribute to 1 item
    18884 
    18885  > keep
    18886 
    18887  Assigning isolde_keep attribute to 1 item
    18888 
    18889  > keep
    18890 
    18891  Assigning isolde_keep attribute to 1 item
    18892 
    18893  > keep
    18894 
    18895  Assigning isolde_keep attribute to 1 item
    18896 
    18897  > keep
    18898 
    18899  Assigning isolde_keep attribute to 1 item
    18900 
    18901  > keep
    18902 
    18903  Assigning isolde_keep attribute to 1 item
    18904 
    18905  > select clear
    18906 
    18907  > keep
    18908 
    18909  Assigning isolde_keep attribute to 1 item
    18910 
    18911  > keep
    18912 
    18913  Assigning isolde_keep attribute to 1 item
    18914 
    18915  > keep
    18916 
    18917  Assigning isolde_keep attribute to 1 item
    18918 
    18919  > keep
    18920 
    18921  Assigning isolde_keep attribute to 1 item
    18922 
    18923  > keep
    18924 
    18925  Assigning isolde_keep attribute to 1 item
    18926 
    18927  > keep
    18928 
    18929  Assigning isolde_keep attribute to 1 item
    18930 
    18931  > keep
    18932 
    18933  Assigning isolde_keep attribute to 1 item
    18934 
    18935  > keep
    18936 
    18937  Assigning isolde_keep attribute to 1 item
    18938 
    18939  > keep
    18940 
    18941  Assigning isolde_keep attribute to 1 item
    18942 
    18943  > keep
    18944 
    18945  Assigning isolde_keep attribute to 1 item
    18946 
    18947  > keep
    18948 
    18949  Assigning isolde_keep attribute to 1 item
    18950 
    18951  > keep
    18952 
    18953  Assigning isolde_keep attribute to 1 item
    18954 
    18955  > keep
    18956 
    18957  Assigning isolde_keep attribute to 1 item
    18958 
    18959  > keep
    18960 
    18961  Assigning isolde_keep attribute to 1 item
    18962 
    18963  > keep
    18964 
    18965  Assigning isolde_keep attribute to 1 item
    18966 
    18967  > keep
    18968 
    18969  Assigning isolde_keep attribute to 1 item
    18970 
    18971  > select clear
    18972 
    18973  > select clear
    18974 
    18975  > select clear
    18976 
    18977  > select up
    18978 
    18979  3 atoms, 2 bonds, 1 residue, 1 model selected
    18980 
    18981  > keep
    18982 
    18983  Assigning isolde_keep attribute to 1 item
    18984 
    18985  > keep
    18986 
    18987  Assigning isolde_keep attribute to 1 item
    18988 
    18989  > keep
    18990 
    18991  Assigning isolde_keep attribute to 1 item
    18992 
    18993  > keep
    18994 
    18995  Assigning isolde_keep attribute to 1 item
    18996 
    18997  > keep
    18998 
    18999  Assigning isolde_keep attribute to 1 item
    19000 
    19001  > keep
    19002 
    19003  Assigning isolde_keep attribute to 1 item
    19004 
    19005  > keep
    19006 
    19007  Assigning isolde_keep attribute to 1 item
    19008 
    19009  > keep
    19010 
    19011  Assigning isolde_keep attribute to 1 item
    19012 
    19013  > keep
    19014 
    19015  Assigning isolde_keep attribute to 1 item
    19016 
    19017  > keep
    19018 
    19019  Assigning isolde_keep attribute to 1 item
    19020 
    19021  > keep
    19022 
    19023  Assigning isolde_keep attribute to 1 item
    19024 
    19025  > keep
    19026 
    19027  Assigning isolde_keep attribute to 1 item
    19028 
    19029  > keep
    19030 
    19031  Assigning isolde_keep attribute to 1 item
    19032 
    19033  > keep
    19034 
    19035  Assigning isolde_keep attribute to 1 item
    19036 
    19037  > aw
    19038 
    19039  > isolde sim start sel
    19040 
    19041  > keep
    19042 
    19043  Assigning isolde_keep attribute to 1 item
    19044 
    19045  > keep
    19046 
    19047  Assigning isolde_keep attribute to 1 item
    19048 
    19049  > select clear
    19050 
    19051  > keep
    19052 
    19053  Assigning isolde_keep attribute to 1 item
    19054 
    19055  > keep
    19056 
    19057  Assigning isolde_keep attribute to 1 item
    19058 
    19059  > keep
    19060 
    19061  Assigning isolde_keep attribute to 1 item
    19062 
    19063  > keep
    19064 
    19065  Assigning isolde_keep attribute to 1 item
    19066 
    19067  > keep
    19068 
    19069  Assigning isolde_keep attribute to 1 item
    19070 
    19071  > keep
    19072 
    19073  Assigning isolde_keep attribute to 1 item
    19074 
    19075  > keep
    19076 
    19077  Assigning isolde_keep attribute to 1 item
    19078 
    19079  > keep
    19080 
    19081  Assigning isolde_keep attribute to 1 item
    19082 
    19083  > keep
    19084 
    19085  Assigning isolde_keep attribute to 1 item
    19086 
    19087  > keep
    19088 
    19089  Assigning isolde_keep attribute to 1 item
    19090 
    19091  > keep
    19092 
    19093  Assigning isolde_keep attribute to 1 item
    19094 
    19095  > keep
    19096 
    19097  Assigning isolde_keep attribute to 1 item
    19098 
    19099  > keep
    19100 
    19101  Assigning isolde_keep attribute to 1 item
    19102 
    19103  > save working.cxs
    19104 
    19105  Taking snapshot of stepper: Model 1a
    19106 
    19107  > keep
    19108 
    19109  Assigning isolde_keep attribute to 1 item
    19110 
    19111  > keep
    19112 
    19113  Assigning isolde_keep attribute to 1 item
    19114 
    19115  > keep
    19116 
    19117  Assigning isolde_keep attribute to 1 item
    19118 
    19119  > keep
    19120 
    19121  Assigning isolde_keep attribute to 1 item
    19122 
    19123  > keep
    19124 
    19125  Assigning isolde_keep attribute to 1 item
    19126 
    19127  > keep
    19128 
    19129  Assigning isolde_keep attribute to 1 item
    19130 
    19131  > keep
    19132 
    19133  Assigning isolde_keep attribute to 1 item
    19134 
    19135  > keep
    19136 
    19137  Assigning isolde_keep attribute to 1 item
    19138 
    19139  > keep
    19140 
    19141  Assigning isolde_keep attribute to 1 item
    19142 
    19143  > keep
    19144 
    19145  Assigning isolde_keep attribute to 1 item
    19146 
    19147  > keep
    19148 
    19149  Assigning isolde_keep attribute to 1 item
    19150 
    19151  > keep
    19152 
    19153  Assigning isolde_keep attribute to 1 item
    19154 
    19155  > keep
    19156 
    19157  Assigning isolde_keep attribute to 1 item
    19158 
    19159  > keep
    19160 
    19161  Assigning isolde_keep attribute to 1 item
    19162 
    19163  > keep
    19164 
    19165  Assigning isolde_keep attribute to 1 item
    19166 
    19167  > keep
    19168 
    19169  Assigning isolde_keep attribute to 1 item
    19170 
    19171  > select clear
    19172 
    19173  > keep
    19174 
    19175  Assigning isolde_keep attribute to 1 item
    19176 
    19177  > keep
    19178 
    19179  Assigning isolde_keep attribute to 1 item
    19180 
    19181  > keep
    19182 
    19183  Assigning isolde_keep attribute to 1 item
    19184 
    19185  > keep
    19186 
    19187  Assigning isolde_keep attribute to 1 item
    19188 
    19189  > select clear
    19190 
    19191  > keep
    19192 
    19193  Assigning isolde_keep attribute to 1 item
    19194 
    19195  > keep
    19196 
    19197  Assigning isolde_keep attribute to 1 item
    19198 
    19199  > keep
    19200 
    19201  Assigning isolde_keep attribute to 1 item
    19202 
    19203  > keep
    19204 
    19205  Assigning isolde_keep attribute to 1 item
    19206 
    19207  > keep
    19208 
    19209  Assigning isolde_keep attribute to 1 item
    19210 
    19211  > keep
    19212 
    19213  Assigning isolde_keep attribute to 1 item
    19214 
    19215  > keep
    19216 
    19217  Assigning isolde_keep attribute to 1 item
    19218 
    19219  > keep
    19220 
    19221  Assigning isolde_keep attribute to 1 item
    19222 
    19223  > keep
    19224 
    19225  Assigning isolde_keep attribute to 1 item
    19226 
    19227  > keep
    19228 
    19229  Assigning isolde_keep attribute to 1 item
    19230 
    19231  > keep
    19232 
    19233  Assigning isolde_keep attribute to 1 item
    19234 
    19235  > keep
    19236 
    19237  Assigning isolde_keep attribute to 1 item
    19238 
    19239  > keep
    19240 
    19241  Assigning isolde_keep attribute to 1 item
    19242 
    19243  > keep
    19244 
    19245  Assigning isolde_keep attribute to 1 item
    19246 
    19247  > select clear
    19248 
    19249  > keep
    19250 
    19251  Assigning isolde_keep attribute to 1 item
    19252 
    19253  > keep
    19254 
    19255  Assigning isolde_keep attribute to 1 item
    19256 
    19257  > keep
    19258 
    19259  Assigning isolde_keep attribute to 1 item
    19260 
    19261  > keep
    19262 
    19263  Assigning isolde_keep attribute to 1 item
    19264 
    19265  > select clear
    19266 
    19267  > keep
    19268 
    19269  Assigning isolde_keep attribute to 1 item
    19270 
    19271  > keep
    19272 
    19273  Assigning isolde_keep attribute to 1 item
    19274 
    19275  > keep
    19276 
    19277  Assigning isolde_keep attribute to 1 item
    19278 
    19279  > keep
    19280 
    19281  Assigning isolde_keep attribute to 1 item
    19282 
    19283  > keep
    19284 
    19285  Assigning isolde_keep attribute to 1 item
    19286 
    19287  > keep
    19288 
    19289  Assigning isolde_keep attribute to 1 item
    19290 
    19291  > keep
    19292 
    19293  Assigning isolde_keep attribute to 1 item
    19294 
    19295  > keep
    19296 
    19297  Assigning isolde_keep attribute to 1 item
    19298 
    19299  > keep
    19300 
    19301  Assigning isolde_keep attribute to 1 item
    19302 
    19303  > keep
    19304 
    19305  Assigning isolde_keep attribute to 1 item
    19306 
    19307  > keep
    19308 
    19309  Assigning isolde_keep attribute to 1 item
    19310 
    19311  > keep
    19312 
    19313  Assigning isolde_keep attribute to 1 item
    19314 
    19315  > keep
    19316 
    19317  Assigning isolde_keep attribute to 1 item
    19318 
    19319  > select clear
    19320 
    19321  > keep
    19322 
    19323  Assigning isolde_keep attribute to 1 item
    19324 
    19325  > keep
    19326 
    19327  Assigning isolde_keep attribute to 1 item
    19328 
    19329  > keep
    19330 
    19331  Assigning isolde_keep attribute to 1 item
    19332 
    19333  > keep
    19334 
    19335  Assigning isolde_keep attribute to 1 item
    19336 
    19337  > keep
    19338 
    19339  Assigning isolde_keep attribute to 1 item
    19340 
    19341  > keep
    19342 
    19343  Assigning isolde_keep attribute to 1 item
    19344 
    19345  > keep
    19346 
    19347  Assigning isolde_keep attribute to 1 item
    19348 
    19349  > keep
    19350 
    19351  Assigning isolde_keep attribute to 1 item
    19352 
    19353  > keep
    19354 
    19355  Assigning isolde_keep attribute to 1 item
    19356 
    19357  > keep
    19358 
    19359  Assigning isolde_keep attribute to 1 item
    19360 
    19361  > keep
    19362 
    19363  Assigning isolde_keep attribute to 1 item
    19364 
    19365  > keep
    19366 
    19367  Assigning isolde_keep attribute to 1 item
    19368 
    19369  > keep
    19370 
    19371  Assigning isolde_keep attribute to 1 item
    19372 
    19373  > keep
    19374 
    19375  Assigning isolde_keep attribute to 1 item
    19376 
    19377  > keep
    19378 
    19379  Assigning isolde_keep attribute to 1 item
    19380 
    19381  > keep
    19382 
    19383  Assigning isolde_keep attribute to 1 item
    19384 
    19385  > keep
    19386 
    19387  Assigning isolde_keep attribute to 1 item
    19388 
    19389  > select clear
    19390 
    19391  > keep
    19392 
    19393  Assigning isolde_keep attribute to 1 item
    19394 
    19395  > select clear
    19396 
    19397  > keep
    19398 
    19399  Assigning isolde_keep attribute to 1 item
    19400 
    19401  > keep
    19402 
    19403  Assigning isolde_keep attribute to 1 item
    19404 
    19405  > keep
    19406 
    19407  Assigning isolde_keep attribute to 1 item
    19408 
    19409  > keep
    19410 
    19411  Assigning isolde_keep attribute to 1 item
    19412 
    19413  > view /aa:4
    19414 
    19415  > view /aa:47
    19416 
    19417  > view /ab:47
    19418 
    19419  > view /ac:47
    19420 
    19421  > view /ad:47
    19422 
    19423  > view /ae:47
    19424 
    19425  > view /af:47
    19426 
    19427  > view /ag:47
    19428 
    19429  > view /ah:47
    19430 
    19431  > view /ai:47
    19432 
    19433  > view /aj:47
    19434 
    19435  > view /ak:47
    19436 
    19437  > view /al:47
    19438 
    19439  > view /am:47
    19440 
    19441  > view /an:47
    19442 
    19443  > view /ao:47
    19444 
    19445  > view /ap:47
    19446 
    19447  > view /aq:47
    19448 
    19449  No objects specified.
    19450 
    19451  > keep
    19452 
    19453  Assigning isolde_keep attribute to 1 item
    19454 
    19455  > keep
    19456 
    19457  Assigning isolde_keep attribute to 1 item
    19458 
    19459  > select clear
    19460 
    19461  > keep
    19462 
    19463  Assigning isolde_keep attribute to 1 item
    19464 
    19465  > keep
    19466 
    19467  Assigning isolde_keep attribute to 1 item
    19468 
    19469  > keep
    19470 
    19471  Assigning isolde_keep attribute to 1 item
    19472 
    19473  > setattr sel residues isolde_keep false
    19474 
    19475  Assigning isolde_keep attribute to 1 item
    19476 
    19477  > keep
    19478 
    19479  Assigning isolde_keep attribute to 1 item
    19480 
    19481  > keep
    19482 
    19483  Assigning isolde_keep attribute to 1 item
    19484 
    19485  > keep
    19486 
    19487  Assigning isolde_keep attribute to 1 item
    19488 
    19489  > keep
    19490 
    19491  Assigning isolde_keep attribute to 1 item
    19492 
    19493  > keep
    19494 
    19495  Assigning isolde_keep attribute to 1 item
    19496 
    19497  > keep
    19498 
    19499  Assigning isolde_keep attribute to 1 item
    19500 
    19501  > keep
    19502 
    19503  Assigning isolde_keep attribute to 1 item
    19504 
    19505  > keep
    19506 
    19507  Assigning isolde_keep attribute to 1 item
    19508 
    19509  > keep
    19510 
    19511  Assigning isolde_keep attribute to 1 item
    19512 
    19513  > keep
    19514 
    19515  Assigning isolde_keep attribute to 1 item
    19516 
    19517  > select clear
    19518 
    19519  > keep
    19520 
    19521  Assigning isolde_keep attribute to 1 item
    19522 
    19523  > select up
    19524 
    19525  3 atoms, 2 bonds, 1 residue, 1 model selected
    19526 
    19527  > keep
    19528 
    19529  Assigning isolde_keep attribute to 1 item
    19530 
    19531  > keep
    19532 
    19533  Assigning isolde_keep attribute to 1 item
    19534 
    19535  > keep
    19536 
    19537  Assigning isolde_keep attribute to 1 item
    19538 
    19539  > keep
    19540 
    19541  Assigning isolde_keep attribute to 1 item
    19542 
    19543  > keep
    19544 
    19545  Assigning isolde_keep attribute to 1 item
    19546 
    19547  > keep
    19548 
    19549  Assigning isolde_keep attribute to 1 item
    19550 
    19551  > setattr sel residues isolde_keep false
    19552 
    19553  Assigning isolde_keep attribute to 1 item
    19554 
    19555  > keep
    19556 
    19557  Assigning isolde_keep attribute to 1 item
    19558 
    19559  > keep
    19560 
    19561  Assigning isolde_keep attribute to 1 item
    19562 
    19563  > keep
    19564 
    19565  Assigning isolde_keep attribute to 1 item
    19566 
    19567  > keep
    19568 
    19569  Assigning isolde_keep attribute to 1 item
    19570 
    19571  > keep
    19572 
    19573  Assigning isolde_keep attribute to 1 item
    19574 
    19575  > keep
    19576 
    19577  Assigning isolde_keep attribute to 1 item
    19578 
    19579  > select clear
    19580 
    19581  > keep
    19582 
    19583  Assigning isolde_keep attribute to 1 item
    19584 
    19585  > keep
    19586 
    19587  Assigning isolde_keep attribute to 1 item
    19588 
    19589  > keep
    19590 
    19591  Assigning isolde_keep attribute to 1 item
    19592 
    19593  > keep
    19594 
    19595  Assigning isolde_keep attribute to 1 item
    19596 
    19597  > keep
    19598 
    19599  Assigning isolde_keep attribute to 1 item
    19600 
    19601  > keep
    19602 
    19603  Assigning isolde_keep attribute to 1 item
    19604 
    19605  > setattr sel residues isolde_keep false
    19606 
    19607  Assigning isolde_keep attribute to 1 item
    19608 
    19609  > keep
    19610 
    19611  Assigning isolde_keep attribute to 1 item
    19612 
    19613  > keep
    19614 
    19615  Assigning isolde_keep attribute to 1 item
    19616 
    19617  > keep
    19618 
    19619  Assigning isolde_keep attribute to 1 item
    19620 
    19621  > keep
    19622 
    19623  Assigning isolde_keep attribute to 1 item
    19624 
    19625  > select clear
    19626 
    19627  > keep
    19628 
    19629  Assigning isolde_keep attribute to 1 item
    19630 
    19631  > keep
    19632 
    19633  Assigning isolde_keep attribute to 1 item
    19634 
    19635  > keep
    19636 
    19637  Assigning isolde_keep attribute to 1 item
    19638 
    19639  > keep
    19640 
    19641  Assigning isolde_keep attribute to 1 item
    19642 
    19643  > keep
    19644 
    19645  Assigning isolde_keep attribute to 1 item
    19646 
    19647  > keep
    19648 
    19649  Assigning isolde_keep attribute to 1 item
    19650 
    19651  > keep
    19652 
    19653  Assigning isolde_keep attribute to 1 item
    19654 
    19655  > keep
    19656 
    19657  Assigning isolde_keep attribute to 1 item
    19658 
    19659  > keep
    19660 
    19661  Assigning isolde_keep attribute to 1 item
    19662 
    19663  > keep
    19664 
    19665  Assigning isolde_keep attribute to 1 item
    19666 
    19667  > keep
    19668 
    19669  Assigning isolde_keep attribute to 1 item
    19670 
    19671  > keep
    19672 
    19673  Assigning isolde_keep attribute to 1 item
    19674 
    19675  > keep
    19676 
    19677  Assigning isolde_keep attribute to 1 item
    19678 
    19679  > keep
    19680 
    19681  Assigning isolde_keep attribute to 1 item
    19682 
    19683  > keep
    19684 
    19685  Assigning isolde_keep attribute to 1 item
    19686 
    19687  > keep
    19688 
    19689  Assigning isolde_keep attribute to 1 item
    19690 
    19691  > select up
    19692 
    19693  5218 atoms, 5236 bonds, 396 residues, 1 model selected
    19694 
    19695  > keep
    19696 
    19697  Assigning isolde_keep attribute to 1 item
    19698 
    19699  > keep
    19700 
    19701  Assigning isolde_keep attribute to 1 item
    19702 
    19703  > keep
    19704 
    19705  Assigning isolde_keep attribute to 1 item
    19706 
    19707  > keep
    19708 
    19709  Assigning isolde_keep attribute to 1 item
    19710 
    19711  > keep
    19712 
    19713  Assigning isolde_keep attribute to 1 item
    19714 
    19715  > keep
    19716 
    19717  Assigning isolde_keep attribute to 1 item
    19718 
    19719  > keep
    19720 
    19721  Assigning isolde_keep attribute to 1 item
    19722 
    19723  > keep
    19724 
    19725  Assigning isolde_keep attribute to 1 item
    19726 
    19727  > keep
    19728 
    19729  Assigning isolde_keep attribute to 1 item
    19730 
    19731  > keep
    19732 
    19733  Assigning isolde_keep attribute to 1 item
    19734 
    19735  > keep
    19736 
    19737  Assigning isolde_keep attribute to 1 item
    19738 
    19739  > keep
    19740 
    19741  Assigning isolde_keep attribute to 1 item
    19742 
    19743  > keep
    19744 
    19745  Assigning isolde_keep attribute to 1 item
    19746 
    19747  > keep
    19748 
    19749  Assigning isolde_keep attribute to 1 item
    19750 
    19751  > keep
    19752 
    19753  Assigning isolde_keep attribute to 1 item
    19754 
    19755  > keep
    19756 
    19757  Assigning isolde_keep attribute to 1 item
    19758 
    19759  > keep
    19760 
    19761  Assigning isolde_keep attribute to 1 item
    19762 
    19763  > keep
    19764 
    19765  Assigning isolde_keep attribute to 1 item
    19766 
    19767  > keep
    19768 
    19769  Assigning isolde_keep attribute to 1 item
    19770 
    19771  > keep
    19772 
    19773  Assigning isolde_keep attribute to 1 item
    19774 
    19775  > select up
    19776 
    19777  3 atoms, 2 bonds, 1 residue, 1 model selected
    19778 
    19779  > keep
    19780 
    19781  Assigning isolde_keep attribute to 1 item
    19782 
    19783  > keep
    19784 
    19785  Assigning isolde_keep attribute to 1 item
    19786 
    19787  > keep
    19788 
    19789  Assigning isolde_keep attribute to 1 item
    19790 
    19791  > keep
    19792 
    19793  Assigning isolde_keep attribute to 1 item
    19794 
    19795  > select clear
    19796 
    19797  > keep
    19798 
    19799  Assigning isolde_keep attribute to 1 item
    19800 
    19801  > keep
    19802 
    19803  Assigning isolde_keep attribute to 1 item
    19804 
    19805  > keep
    19806 
    19807  Assigning isolde_keep attribute to 1 item
    19808 
    19809  > keep
    19810 
    19811  Assigning isolde_keep attribute to 1 item
    19812 
    19813  > keep
    19814 
    19815  Assigning isolde_keep attribute to 1 item
    19816 
    19817  > aw sim f
    19818 
    19819  > aw sim f
    19820 
    19821  > keep
    19822 
    19823  Assigning isolde_keep attribute to 2 items
    19824 
    19825  > keep
    19826 
    19827  Assigning isolde_keep attribute to 1 item
    19828 
    19829  > keep
    19830 
    19831  Assigning isolde_keep attribute to 1 item
    19832 
    19833  > keep
    19834 
    19835  Assigning isolde_keep attribute to 1 item
    19836 
    19837  > keep
    19838 
    19839  Assigning isolde_keep attribute to 1 item
    19840 
    19841  > keep
    19842 
    19843  Assigning isolde_keep attribute to 1 item
    19844 
    19845  > keep
    19846 
    19847  Assigning isolde_keep attribute to 1 item
    19848 
    19849  > keep
    19850 
    19851  Assigning isolde_keep attribute to 1 item
    19852 
    19853  > keep
    19854 
    19855  Assigning isolde_keep attribute to 1 item
    19856 
    19857  > keep
    19858 
    19859  Assigning isolde_keep attribute to 1 item
    19860 
    19861  > keep
    19862 
    19863  Assigning isolde_keep attribute to 1 item
    19864 
    19865  > keep
    19866 
    19867  Assigning isolde_keep attribute to 1 item
    19868 
    19869  > keep
    19870 
    19871  Assigning isolde_keep attribute to 1 item
    19872 
    19873  > keep
    19874 
    19875  Assigning isolde_keep attribute to 1 item
    19876 
    19877  > select up
    19878 
    19879  3 atoms, 2 bonds, 1 residue, 1 model selected
    19880 
    19881  > keep
    19882 
    19883  Assigning isolde_keep attribute to 1 item
    19884 
    19885  > keep
    19886 
    19887  Assigning isolde_keep attribute to 1 item
    19888 
    19889  > keep
    19890 
    19891  Assigning isolde_keep attribute to 1 item
    19892 
    19893  > keep
    19894 
    19895  Assigning isolde_keep attribute to 1 item
    19896 
    19897  > keep
    19898 
    19899  Assigning isolde_keep attribute to 1 item
    19900 
    19901  > setattr sel residues isolde_keep false
    19902 
    19903  Assigning isolde_keep attribute to 1 item
    19904 
    19905  > keep
    19906 
    19907  Assigning isolde_keep attribute to 1 item
    19908 
    19909  > keep
    19910 
    19911  Assigning isolde_keep attribute to 1 item
    19912 
    19913  > keep
    19914 
    19915  Assigning isolde_keep attribute to 1 item
    19916 
    19917  > keep
    19918 
    19919  Assigning isolde_keep attribute to 1 item
    19920 
    19921  > keep
    19922 
    19923  Assigning isolde_keep attribute to 1 item
    19924 
    19925  > keep
    19926 
    19927  Assigning isolde_keep attribute to 1 item
    19928 
    19929  > keep
    19930 
    19931  Assigning isolde_keep attribute to 1 item
    19932 
    19933  > setattr sel residues isolde_keep false
    19934 
    19935  Assigning isolde_keep attribute to 1 item
    19936 
    19937  > keep
    19938 
    19939  Assigning isolde_keep attribute to 1 item
    19940 
    19941  > keep
    19942 
    19943  Assigning isolde_keep attribute to 1 item
    19944 
    19945  > keep
    19946 
    19947  Assigning isolde_keep attribute to 1 item
    19948 
    19949  > keep
    19950 
    19951  Assigning isolde_keep attribute to 1 item
    19952 
    19953  > keep
    19954 
    19955  Assigning isolde_keep attribute to 1 item
    19956 
    19957  > keep
    19958 
    19959  Assigning isolde_keep attribute to 1 item
    19960 
    19961  > keep
    19962 
    19963  Assigning isolde_keep attribute to 1 item
    19964 
    19965  > keep
    19966 
    19967  Assigning isolde_keep attribute to 1 item
    19968 
    19969  > keep
    19970 
    19971  Assigning isolde_keep attribute to 1 item
    19972 
    19973  > keep
    19974 
    19975  Assigning isolde_keep attribute to 1 item
    19976 
    19977  > keep
    19978 
    19979  Assigning isolde_keep attribute to 1 item
    19980 
    19981  > keep
    19982 
    19983  Assigning isolde_keep attribute to 1 item
    19984 
    19985  > keep
    19986 
    19987  Assigning isolde_keep attribute to 1 item
    19988 
    19989  > keep
    19990 
    19991  Assigning isolde_keep attribute to 1 item
    19992 
    19993  > keep
    19994 
    19995  Assigning isolde_keep attribute to 1 item
    19996 
    19997  > keep
    19998 
    19999  Assigning isolde_keep attribute to 1 item
    20000 
    20001  > keep
    20002 
    20003  Assigning isolde_keep attribute to 1 item
    20004 
    20005  > keep
    20006 
    20007  Assigning isolde_keep attribute to 1 item
    20008 
    20009  > keep
    20010 
    20011  Assigning isolde_keep attribute to 1 item
    20012 
    20013  > keep
    20014 
    20015  Assigning isolde_keep attribute to 1 item
    20016 
    20017  > keep
    20018 
    20019  Assigning isolde_keep attribute to 1 item
    20020 
    20021  > keep
    20022 
    20023  Assigning isolde_keep attribute to 1 item
    20024 
    20025  > keep
    20026 
    20027  Assigning isolde_keep attribute to 1 item
    20028 
    20029  > keep
    20030 
    20031  Assigning isolde_keep attribute to 1 item
    20032 
    20033  > aw
    20034 
    20035  > isolde sim start sel
    20036 
    20037  > select up
    20038 
    20039  6 atoms, 4 bonds, 2 residues, 1 model selected
    20040 
    20041  > aw
    20042 
    20043  > isolde sim start sel
    20044 
    20045  > select up
    20046 
    20047  3 atoms, 2 bonds, 1 residue, 1 model selected
    20048 
    20049  > delete sel
    20050 
    20051  > select up
    20052 
    20053  6 atoms, 4 bonds, 2 residues, 1 model selected
    20054 
    20055  > keep
    20056 
    20057  Assigning isolde_keep attribute to 2 items
    20058 
    20059  > keep
    20060 
    20061  Assigning isolde_keep attribute to 1 item
    20062 
    20063  > keep
    20064 
    20065  Assigning isolde_keep attribute to 1 item
    20066 
    20067  > keep
    20068 
    20069  Assigning isolde_keep attribute to 1 item
    20070 
    20071  > keep
    20072 
    20073  Assigning isolde_keep attribute to 1 item
    20074 
    20075  > keep
    20076 
    20077  Assigning isolde_keep attribute to 1 item
    20078 
    20079  > keep
    20080 
    20081  Assigning isolde_keep attribute to 1 item
    20082 
    20083  > keep
    20084 
    20085  Assigning isolde_keep attribute to 1 item
    20086 
    20087  > keep
    20088 
    20089  Assigning isolde_keep attribute to 1 item
    20090 
    20091  > keep
    20092 
    20093  Assigning isolde_keep attribute to 1 item
    20094 
    20095  > keep
    20096 
    20097  Assigning isolde_keep attribute to 1 item
    20098 
    20099  > keep
    20100 
    20101  Assigning isolde_keep attribute to 1 item
    20102 
    20103  > keep
    20104 
    20105  Assigning isolde_keep attribute to 1 item
    20106 
    20107  > keep
    20108 
    20109  Assigning isolde_keep attribute to 1 item
    20110 
    20111  > select clear
    20112 
    20113  > select up
    20114 
    20115  1257 atoms, 1282 bonds, 59 residues, 1 model selected
    20116 
    20117  > keep
    20118 
    20119  Assigning isolde_keep attribute to 1 item
    20120 
    20121  > select clear
    20122 
    20123  > keep
    20124 
    20125  Assigning isolde_keep attribute to 1 item
    20126 
    20127  > select clear
    20128 
    20129  > keep
    20130 
    20131  Assigning isolde_keep attribute to 1 item
    20132 
    20133  > keep
    20134 
    20135  Assigning isolde_keep attribute to 1 item
    20136 
    20137  > keep
    20138 
    20139  Assigning isolde_keep attribute to 1 item
    20140 
    20141  > keep
    20142 
    20143  Assigning isolde_keep attribute to 1 item
    20144 
    20145  > select clear
    20146 
    20147  > keep
    20148 
    20149  Assigning isolde_keep attribute to 1 item
    20150 
    20151  > keep
    20152 
    20153  Assigning isolde_keep attribute to 1 item
    20154 
    20155  > keep
    20156 
    20157  Assigning isolde_keep attribute to 1 item
    20158 
    20159  > keep
    20160 
    20161  Assigning isolde_keep attribute to 1 item
    20162 
    20163  > select clear
    20164 
    20165  > select clear
    20166 
    20167  > save working.cxs
    20168 
    20169  Taking snapshot of stepper: Model 1a
    20170 
    20171  > select :HOH
    20172 
    20173  828 atoms, 552 bonds, 276 residues, 1 model selected
    20174 
    20175  > select #1
    20176 
    20177  Nothing selected
    20178 
    20179  > select #8
    20180 
    20181  113879 atoms, 115985 bonds, 15 pseudobonds, 5566 residues, 23 models
    20182  selected
    20183  Map is too large for fast cubic interpolation on the GPU! Switching to
    20184  slower,
    20185  more memory-efficient implementation.
    20186  Map is too large for fast cubic interpolation on the GPU! Switching to
    20187  slower,
    20188  more memory-efficient implementation.
    20189 
    20190  > select clear
    20191 
    20192  > select up
    20193 
    20194  215 atoms, 216 bonds, 12 residues, 1 model selected
    20195 
    20196  > select clear
    20197 
    20198  > select clear
    20199 
    20200  > select clear
    20201 
    20202  > select clear
    20203 
    20204  > select clear
    20205 
    20206  > select clear
    20207 
    20208  > select clear
    20209 
    20210  > select clear
    20211 
    20212  > select clear
    20213 
    20214  > select clear
    20215 
    20216  > select clear
    20217 
    20218  > select clear
    20219 
    20220  > select clear
    20221 
    20222  > select clear
    20223 
    20224  > select clear
    20225 
    20226  > select clear
    20227 
    20228  > select clear
    20229 
    20230  > select clear
    20231 
    20232  > select clear
    20233 
    20234  > select clear
    20235 
    20236  > select clear
    20237 
    20238  > select clear
    20239 
    20240  > select clear
    20241 
    20242  > select clear
    20243 
    20244  > select clear
    20245 
    20246  > select clear
    20247 
    20248  > select clear
    20249 
    20250  > select clear
    20251 
    20252  > select clear
    20253 
    20254  > select clear
    20255 
    20256  > select clear
    20257 
    20258  > select clear
    20259 
    20260  > select clear
    20261 
    20262  > select clear
    20263 
    20264  > select clear
    20265 
    20266  > select clear
    20267 
    20268  > select clear
    20269 
    20270  > select clear
    20271 
    20272  > select clear
    20273 
    20274  > select clear
    20275 
    20276  > select clear
    20277 
    20278  > select clear
    20279 
    20280  > select clear
    20281 
    20282  > view /ba:32
    20283 
    20284  > view /bb:32
    20285 
    20286  > view /bc:32
    20287 
    20288  > view /bd:32
    20289 
    20290  > view /ba:32
    20291 
    20292  > view /bb:32
    20293 
    20294  > view /bc:32
    20295 
    20296  > view /bd:32
    20297 
    20298  > view /ba:27-32
    20299 
    20300  > view /bb:27-32
    20301 
    20302  > view /bc:27-32
    20303 
    20304  > view /be:27-32
    20305 
    20306  > select clear
    20307 
    20308  > view /bf:27-32
    20309 
    20310  > view /bg:27-32
    20311 
    20312  > view /bh:27-32
    20313 
    20314  > view /bi:27-32
    20315 
    20316  > select clear
    20317 
    20318  > view /bj:27-32
    20319 
    20320  > select clear
    20321 
    20322  > view /bk:27-32
    20323 
    20324  > select clear
    20325 
    20326  > view /bl:27-32
    20327 
    20328  > view /bl:27-32
    20329 
    20330  > view /bm:27-32
    20331 
    20332  > select clear
    20333 
    20334  > select clear
    20335 
    20336  > select clear
    20337 
    20338  > select clear
    20339 
    20340  > view /bn:27-32
    20341 
    20342  > select up
    20343 
    20344  16 atoms, 15 bonds, 1 residue, 1 model selected
    20345 
    20346  > select up
    20347 
    20348  503 atoms, 512 bonds, 32 residues, 1 model selected
    20349 
    20350  > select clear
    20351 
    20352  > select clear
    20353 
    20354  > view /bo:27-32
    20355 
    20356  > select up
    20357 
    20358  16 atoms, 15 bonds, 1 residue, 1 model selected
    20359 
    20360  > select up
    20361 
    20362  503 atoms, 512 bonds, 32 residues, 1 model selected
    20363 
    20364  > select clear
    20365 
    20366  > view /bp:27-32
    20367 
    20368  > select up
    20369 
    20370  16 atoms, 15 bonds, 1 residue, 1 model selected
    20371 
    20372  > select up
    20373 
    20374  503 atoms, 512 bonds, 32 residues, 1 model selected
    20375 
    20376  > select clear
    20377 
    20378  > select clear
    20379 
    20380  > view /bq:27-32
    20381 
    20382  No objects specified.
    20383 
    20384  > save working.cxs
    20385 
    20386  Taking snapshot of stepper: Model 1a
    20387  Restoring stepper: Model 1a
    20388  opened ChimeraX session
    20389 
    20390  > select :MAN
    20391 
    20392  40 atoms, 40 bonds, 2 residues, 1 model selected
    20393 
    20394  > select clear
    20395 
    20396  > select :XYS
    20397 
    20398  36 atoms, 36 bonds, 2 residues, 1 model selected
    20399 
    20400  > select :XYS
    20401 
    20402  36 atoms, 36 bonds, 2 residues, 1 model selected
    20403 
    20404  > select clear
    20405 
    20406  > movie record
    20407 
    20408  > movie stop
    20409 
    20410  > movie reset
    20411 
    20412  > movie record
    20413 
    20414  > movie stop
    20415 
    20416  > movie encode glycan.mp4
    20417 
    20418  Movie saved to glycan.mp4
    20419 
    20420 
    20421  > ui tool show "Change Substituents"
    20422 
    20423  > substitute sel substituents COCH3 guessAttachment true modify true
    20424  minimize
    20425  > false
    20426 
    20427  > substitute sel substituents OH guessAttachment true modify true minimize
    20428  > false
    20429 
    20430  > substitute sel substituents COCH3 guessAttachment true modify true
    20431  minimize
    20432  > false
    20433 
    20434  > select up
    20435 
    20436  23 atoms, 23 bonds, 1 residue, 1 model selected
    20437 
    20438  > setattr sel residues name XYX
    20439 
    20440  Assigning name attribute to 1 item
    20441 
    20442  > show sel
    20443 
    20444  > setattr sel atoms name O2
    20445 
    20446  Assigning name attribute to 1 item
    20447 
    20448  > select up
    20449 
    20450  23 atoms, 23 bonds, 1 residue, 1 model selected
    20451 
    20452  > show sel
    20453 
    20454  > select up
    20455 
    20456  23 atoms, 23 bonds, 1 residue, 1 model selected
    20457 
    20458  > show sel
    20459 
    20460  > open 3e80
    20461 
    20462  3e80 title:
    20463  Structure of Heparinase II complexed with heparan sulfate degradation
    20464  disaccharide product [more info...]
    20465 
    20466  Chain information for 3e80 #1
    20467  ---
    20468  Chain | Description
    20469  A B C | Heparinase II protein
    20470 
    20471  Non-standard residues in 3e80 #1
    20472  ---
    20473  GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid
    20474  GCU — alpha-D-glucopyranuronic acid
    20475  MAN — alpha-D-mannopyranose
    20476  NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose
    20477  PO4 — phosphate ion
    20478  RAM — alpha-L-rhamnopyranose
    20479  XYS — alpha-D-xylopyranose
    20480  ZN — zinc ion
    20481 
    20482  3e80 mmCIF Assemblies
    20483  ---
    20484  1| author_and_software_defined_assembly
    20485  2| author_and_software_defined_assembly
    20486  3| author_and_software_defined_assembly
    20487 
    20488 
    20489  > select #1/A:RAM
    20490 
    20491  Nothing selected
    20492 
    20493  > select #1/B:RAM
    20494 
    20495  Nothing selected
    20496 
    20497  > select #1/C:RAM
    20498 
    20499  Nothing selected
    20500 
    20501  > select #1/C:MAN
    20502 
    20503  Nothing selected
    20504 
    20505  > select #1:MAN
    20506 
    20507  33 atoms, 33 bonds, 3 residues, 1 model selected
    20508 
    20509  > select #1/F:MAN
    20510 
    20511  11 atoms, 11 bonds, 1 residue, 1 model selected
    20512 
    20513  > align sel #8/M:MAN&~H
    20514 
    20515  Expected a keyword
    20516 
    20517  > align sel toAtoms #8/M:MAN&~H
    20518 
    20519  RMSD between 11 atom pairs is 0.195 angstroms
    20520 
    20521  > close #1
    20522 
    20523  > open 2fuq
    20524 
    20525  2fuq title:
    20526  Crystal Structure of Heparinase II [more info...]
    20527 
    20528  Chain information for 2fuq #1
    20529  ---
    20530  Chain | Description
    20531  A B | heparinase II protein
    20532 
    20533  Non-standard residues in 2fuq #1
    20534  ---
    20535  FMT — formic acid
    20536  GCU — alpha-D-glucopyranuronic acid
    20537  MAN — alpha-D-mannopyranose
    20538  PO4 — phosphate ion
    20539  RAM — alpha-L-rhamnopyranose
    20540  XYS — alpha-D-xylopyranose
    20541  ZN — zinc ion
    20542 
    20543 
    20544  > select #1/C:MAN
    20545 
    20546  11 atoms, 11 bonds, 1 residue, 1 model selected
    20547 
    20548  > align sel toAtoms #8/M:MAN&~H
    20549 
    20550  RMSD between 11 atom pairs is 0.151 angstroms
    20551 
    20552  > hide #!8 models
    20553 
    20554  > show #1
    20555 
    20556  > hide #1&protein
    20557 
    20558  > delete #1&:HOH
    20559 
    20560  > show #!8 models
    20561 
    20562  > hide #!1 models
    20563 
    20564  > select up
    20565 
    20566  23 atoms, 23 bonds, 1 residue, 1 model selected
    20567 
    20568  > select clear
    20569 
    20570  > ui mousemode right "translate selected atoms"
    20571 
    20572  > setattr sel atoms name C2A
    20573 
    20574  Assigning name attribute to 1 item
    20575 
    20576  > select clear
    20577 
    20578  > setattr sel atoms name O2A
    20579 
    20580  Assigning name attribute to 1 item
    20581 
    20582  > setattr sel atoms name C2B
    20583 
    20584  Assigning name attribute to 1 item
    20585 
    20586  > setattr sel atoms name H2B1
    20587 
    20588  Assigning name attribute to 1 item
    20589 
    20590  > setattr sel atoms name H2B2
    20591 
    20592  Assigning name attribute to 1 item
    20593 
    20594  > setattr sel atoms name H2B3
    20595 
    20596  Assigning name attribute to 1 item
    20597 
    20598  > select :XYS
    20599 
    20600  34 atoms, 34 bonds, 3 residues, 2 models selected
    20601 
    20602  > select #8:XYS
    20603 
    20604  18 atoms, 18 bonds, 1 residue, 1 model selected
    20605 
    20606  > view sel
    20607 
    20608  > ui tool show "Change Substituents"
    20609 
    20610  > substitute sel substituents COCH3 newName XYX guessAttachment true
    20611  modify
    20612  > true minimize false
    20613 
    20614  > select clear
    20615 
    20616  > setattr sel atoms name C2A
    20617 
    20618  Assigning name attribute to 1 item
    20619 
    20620  > select up
    20621 
    20622  23 atoms, 23 bonds, 1 residue, 1 model selected
    20623 
    20624  > show sel
    20625 
    20626  > setattr sel atoms name O2A
    20627 
    20628  Assigning name attribute to 1 item
    20629 
    20630  > setattr sel atoms name C2B
    20631 
    20632  Assigning name attribute to 1 item
    20633 
    20634  > setattr sel atoms name H2B1
    20635 
    20636  Assigning name attribute to 1 item
    20637 
    20638  > setattr sel atoms name H2B2
    20639 
    20640  Assigning name attribute to 1 item
    20641 
    20642  > setattr sel atoms name H2B3
    20643 
    20644  Assigning name attribute to 1 item
    20645 
    20646  > select clear
    20647 
    20648  > save working.cxs
    20649 
    20650  Taking snapshot of stepper: Model 1a
    20651 
    20652  > select clear
    20653 
    20654  > select ~H
    20655 
    20656  67529 atoms, 128381 bonds, 21 pseudobonds, 7075 residues, 25 models
    20657  selected
    20658 
    20659  > save model1a_working_noh.cif #8 selectedOnly true
    20660 
    20661  Not saving entity_poly_seq for non-authoritative sequences
    20662 
    20663  > select clear
    20664 
    20665  > isolde add ligand NDG
    20666 
    20667  Deleted the following atoms from residue NDG M1175: HO1, O1
    20668 
    20669  > ui mousemode right "translate selected atoms"
    20670 
    20671  > show sel
    20672 
    20673  > isolde add ligand A2G
    20674 
    20675  Deleted the following atoms from residue A2G M1176: HO1, O1
    20676 
    20677  > ui mousemode right "translate selected atoms"
    20678 
    20679  > show sel
    20680 
    20681  > delete sel
    20682 
    20683  > select up
    20684 
    20685  23 atoms, 23 bonds, 1 residue, 1 model selected
    20686 
    20687  > delete sel
    20688 
    20689  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    20690  bonded heavy atom.
    20691 
    20692  > select clear
    20693 
    20694  > view :XYX
    20695 
    20696  > select up
    20697 
    20698  23 atoms, 23 bonds, 1 residue, 1 model selected
    20699 
    20700  > delete sel
    20701 
    20702  > isolde add ligand NDG
    20703 
    20704  Deleted the following atoms from residue NDG C1155: HO1, O1
    20705 
    20706  > show sel
    20707 
    20708  > ui mousemode right "translate selected atoms"
    20709 
    20710  > view /M:NDG
    20711 
    20712  > select ~H
    20713 
    20714  67533 atoms, 128391 bonds, 21 pseudobonds, 7075 residues, 25 models
    20715  selected
    20716 
    20717  > save model1a_working_noh.cif #8 selectedOnly true
    20718 
    20719  Not saving entity_poly_seq for non-authoritative sequences
    20720 
    20721  > select clear
    20722 
    20723  > save working.cxs
    20724 
    20725  Taking snapshot of stepper: Model 1a
    20726  opened ChimeraX session
    20727 
    20728  > close #1
    20729 
    20730  > isolde start
    20731 
    20732  > set selectionWidth 4
    20733 
    20734  Done loading forcefield
    20735 
    20736  > select ~protein&~:HOH
    20737 
    20738  34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected
    20739 
    20740  > select clear
    20741 
    20742  > st first
    20743 
    20744  > st
    20745 
    20746  > select clear
    20747 
    20748  > st
    20749 
    20750  > st interp 5
    20751 
    20752  > st interp 5
    20753 
    20754  > st
    20755 
    20756  > st
    20757 
    20758  > st
    20759 
    20760  > st
    20761 
    20762  > delete sel
    20763 
    20764  > aw
    20765 
    20766  > isolde sim start sel
    20767 
    20768  > st
    20769 
    20770  > st
    20771 
    20772  > st
    20773 
    20774  > st
    20775 
    20776  > st
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    20778  > st
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    20780  > st
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    20800  > st
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    20871 
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    20874  > st
    20875 
    20876  > st
    20877 
    20878  > st
    20879 
    20880  > st
    20881 
    20882  > isolde jumpto
    20883 
    20884  > isolde jumpto
    20885 
    20886  > isolde jumpto
    20887 
    20888  > isolde jumpto
    20889 
    20890  > isolde jumpto
    20891 
    20892  > isolde jumpto
    20893 
    20894  > isolde jumpto
    20895 
    20896  > isolde jumpto
    20897 
    20898  > isolde jumpto
    20899 
    20900  > isolde jumpto
    20901 
    20902  > isolde jumpto
    20903 
    20904  > isolde jumpto
    20905 
    20906  > isolde jumpto
    20907 
    20908  > isolde jumpto
    20909 
    20910  > isolde jumpto
    20911 
    20912  > isolde jumpto
    20913 
    20914  > isolde jumpto
    20915 
    20916  > isolde jumpto
    20917 
    20918  > isolde jumpto
    20919 
    20920  > isolde jumpto
    20921 
    20922  > isolde jumpto
    20923 
    20924  > isolde jumpto
    20925 
    20926  > isolde jumpto
    20927 
    20928  > isolde jumpto
    20929 
    20930  > isolde jumpto
    20931 
    20932  > isolde jumpto
    20933 
    20934  > isolde jumpto
    20935 
    20936  > isolde jumpto
    20937 
    20938  > isolde jumpto
    20939 
    20940  > isolde jumpto
    20941 
    20942  > isolde jumpto
    20943 
    20944  > isolde jumpto
    20945 
    20946  > isolde jumpto
    20947 
    20948  > isolde jumpto
    20949 
    20950  > isolde jumpto
    20951 
    20952  > isolde jumpto
    20953 
    20954  > isolde jumpto
    20955 
    20956  > isolde jumpto
    20957 
    20958  > isolde jumpto
    20959 
    20960  > isolde jumpto
    20961 
    20962  > isolde jumpto
    20963 
    20964  > isolde jumpto
    20965 
    20966  > isolde jumpto
    20967 
    20968  > isolde jumpto
    20969 
    20970  > isolde jumpto
    20971 
    20972  > isolde jumpto
    20973 
    20974  > isolde jumpto
    20975 
    20976  > st
    20977 
    20978  > st
    20979 
    20980  > st
    20981 
    20982  > st
    20983 
    20984  > st
    20985 
    20986  > awsf
    20987 
    20988  > awsf
    20989 
    20990  > awsf
    20991 
    20992  > awsf
    20993 
    20994  > aw
    20995 
    20996  > isolde sim start sel
    20997 
    20998  > aw
    20999 
    21000  > isolde sim start sel
    21001 
    21002  > st
    21003 
    21004  > st
    21005 
    21006  > st
    21007 
    21008  > st
    21009 
    21010  > aw
    21011 
    21012  > isolde sim start sel
    21013 
    21014  > aw
    21015 
    21016  > isolde sim start sel
    21017 
    21018  > aw
    21019 
    21020  > isolde sim start sel
    21021 
    21022  > st
    21023 
    21024  > st
    21025 
    21026  > st
    21027 
    21028  > st
    21029 
    21030  > st
    21031 
    21032  > st
    21033 
    21034  > st
    21035 
    21036  > st
    21037 
    21038  > aw
    21039 
    21040  > isolde sim start sel
    21041 
    21042  > st
    21043 
    21044  > awsf
    21045 
    21046  > awsf
    21047 
    21048  > awsf
    21049 
    21050  > awsf
    21051 
    21052  > awsf
    21053 
    21054  > awsf
    21055 
    21056  > awsf
    21057 
    21058  > awsf
    21059 
    21060  > st
    21061 
    21062  > aw
    21063 
    21064  > isolde sim start sel
    21065 
    21066  > st
    21067 
    21068  > st
    21069 
    21070  > st
    21071 
    21072  > st
    21073 
    21074  > st
    21075 
    21076  > st
    21077 
    21078  > st
    21079 
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    21081 
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    21087 
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    21091 
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    21095 
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    21097 
    21098  > st
    21099 
    21100  > st
    21101 
    21102  > st
    21103 
    21104  > st
    21105 
    21106  > st
    21107 
    21108  > st
    21109 
    21110  > st
    21111 
    21112  > st
    21113 
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    21115 
    21116  > st
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    21118  > st
    21119 
    21120  > st
    21121 
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    21123 
    21124  > st
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    21126  > st
    21127 
    21128  > st
    21129 
    21130  > st
    21131 
    21132  > st
    21133 
    21134  > st
    21135 
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    21137 
    21138  > st
    21139 
    21140  > st
    21141 
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    21143 
    21144  > st
    21145 
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    21147 
    21148  > st
    21149 
    21150  > st
    21151 
    21152  > st
    21153 
    21154  > st
    21155 
    21156  > st
    21157 
    21158  > select clear
    21159 
    21160  > st
    21161 
    21162  > st
    21163 
    21164  > st
    21165 
    21166  > st
    21167 
    21168  > st
    21169 
    21170  > st
    21171 
    21172  > st
    21173 
    21174  > select clear
    21175 
    21176  > st
    21177 
    21178  > st
    21179 
    21180  > st
    21181 
    21182  > st
    21183 
    21184  > st
    21185 
    21186  > st
    21187 
    21188  > st
    21189 
    21190  > st
    21191 
    21192  > select clear
    21193 
    21194  > st
    21195 
    21196  > st
    21197 
    21198  > st
    21199 
    21200  > st
    21201 
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    21203 
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    21205 
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    21207 
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    21211 
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    21213 
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    21215 
    21216  > st
    21217 
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    21219 
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    21221 
    21222  > st
    21223 
    21224  > st
    21225 
    21226  > st
    21227 
    21228  > st
    21229 
    21230  > select clear
    21231 
    21232  > st
    21233 
    21234  > st
    21235 
    21236  > st
    21237 
    21238  > st
    21239 
    21240  > st
    21241 
    21242  > st
    21243 
    21244  > select clear
    21245 
    21246  > st
    21247 
    21248  > st
    21249 
    21250  > st
    21251 
    21252  > st
    21253 
    21254  > st
    21255 
    21256  > st
    21257 
    21258  > st
    21259 
    21260  > st
    21261 
    21262  > st
    21263 
    21264  > st
    21265 
    21266  > st
    21267 
    21268  > st
    21269 
    21270  > st
    21271 
    21272  > st
    21273 
    21274  > st
    21275 
    21276  > st
    21277 
    21278  > aw
    21279 
    21280  > isolde sim start sel
    21281 
    21282  > st
    21283 
    21284  > st
    21285 
    21286  > st
    21287 
    21288  > st
    21289 
    21290  > st
    21291 
    21292  > st
    21293 
    21294  > st
    21295 
    21296  > st
    21297 
    21298  > st
    21299 
    21300  > st
    21301 
    21302  > awsf
    21303 
    21304  > select clear
    21305 
    21306  > select clear
    21307 
    21308  > st
    21309 
    21310  > st
    21311 
    21312  > st
    21313 
    21314  > st
    21315 
    21316  > st
    21317 
    21318  > st
    21319 
    21320  > st
    21321 
    21322  > st
    21323 
    21324  > aw
    21325 
    21326  > isolde sim start sel
    21327 
    21328  > aw
    21329 
    21330  > isolde sim start sel
    21331 
    21332  > st
    21333 
    21334  > st
    21335 
    21336  > st
    21337 
    21338  > st
    21339 
    21340  > st
    21341 
    21342  > st
    21343 
    21344  > st
    21345 
    21346  > awsf
    21347 
    21348  > awsf
    21349 
    21350  > st
    21351 
    21352  > st
    21353 
    21354  > st
    21355 
    21356  > aw
    21357 
    21358  > isolde sim start sel
    21359 
    21360  > select up
    21361 
    21362  3 atoms, 2 bonds, 1 residue, 1 model selected
    21363 
    21364  > delete sel
    21365 
    21366  > st
    21367 
    21368  > awsf
    21369 
    21370  > awsf
    21371 
    21372  > awsf
    21373 
    21374  > select up
    21375 
    21376  6 atoms, 4 bonds, 2 residues, 1 model selected
    21377 
    21378  > delete sel
    21379 
    21380  > st
    21381 
    21382  > awsf
    21383 
    21384  > awsf
    21385 
    21386  > st
    21387 
    21388  > st
    21389 
    21390  > st
    21391 
    21392  > st
    21393 
    21394  > st
    21395 
    21396  > st
    21397 
    21398  > st
    21399 
    21400  > st
    21401 
    21402  > st
    21403 
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    21405 
    21406  > st
    21407 
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    21409 
    21410  > st
    21411 
    21412  > st
    21413 
    21414  > st
    21415 
    21416  > st
    21417 
    21418  > st
    21419 
    21420  > st
    21421 
    21422  > awsf
    21423 
    21424  > awsf
    21425 
    21426  > select up
    21427 
    21428  3 atoms, 2 bonds, 1 residue, 1 model selected
    21429 
    21430  > delete sel
    21431 
    21432  > st
    21433 
    21434  > st
    21435 
    21436  > st
    21437 
    21438  > st
    21439 
    21440  > st
    21441 
    21442  > st
    21443 
    21444  > st
    21445 
    21446  > st
    21447 
    21448  > st
    21449 
    21450  > aw
    21451 
    21452  > isolde sim start sel
    21453 
    21454  > st
    21455 
    21456  > st
    21457 
    21458  > st
    21459 
    21460  > aw
    21461 
    21462  > isolde sim start sel
    21463 
    21464  > st
    21465 
    21466  > st
    21467 
    21468  > st
    21469 
    21470  > st
    21471 
    21472  > aw
    21473 
    21474  > isolde sim start sel
    21475 
    21476  > select up
    21477 
    21478  3 atoms, 2 bonds, 1 residue, 1 model selected
    21479 
    21480  > delete sel
    21481 
    21482  > st
    21483 
    21484  > aw
    21485 
    21486  > isolde sim start sel
    21487 
    21488  > st
    21489 
    21490  > st
    21491 
    21492  > st
    21493 
    21494  > st
    21495 
    21496  > st
    21497 
    21498  > st
    21499 
    21500  > aw
    21501 
    21502  > isolde sim start sel
    21503 
    21504  > st
    21505 
    21506  > aw
    21507 
    21508  > isolde sim start sel
    21509 
    21510  > select up
    21511 
    21512  3 atoms, 2 bonds, 1 residue, 1 model selected
    21513 
    21514  > delete sel
    21515 
    21516  > st
    21517 
    21518  > st
    21519 
    21520  > st
    21521 
    21522  > st
    21523 
    21524  > st
    21525 
    21526  > st
    21527 
    21528  > st
    21529 
    21530  > st
    21531 
    21532  > st
    21533 
    21534  > st
    21535 
    21536  > st
    21537 
    21538  > st
    21539 
    21540  > st
    21541 
    21542  > st
    21543 
    21544  > st
    21545 
    21546  > st
    21547 
    21548  > st
    21549 
    21550  > aw
    21551 
    21552  > isolde sim start sel
    21553 
    21554  > aw
    21555 
    21556  > isolde sim start sel
    21557 
    21558  > st
    21559 
    21560  > st
    21561 
    21562  > st
    21563 
    21564  > st
    21565 
    21566  > st
    21567 
    21568  > st
    21569 
    21570  > st
    21571 
    21572  > st
    21573 
    21574  > st
    21575 
    21576  > st
    21577 
    21578  > st
    21579 
    21580  > st
    21581 
    21582  > st
    21583 
    21584  > st
    21585 
    21586  > st
    21587 
    21588  > st
    21589 
    21590  > select clear
    21591 
    21592  > st
    21593 
    21594  > st
    21595 
    21596  > st
    21597 
    21598  > st
    21599 
    21600  > st
    21601 
    21602  > st
    21603 
    21604  > st
    21605 
    21606  > st
    21607 
    21608  > st
    21609 
    21610  > st
    21611 
    21612  > st
    21613 
    21614  > st
    21615 
    21616  > st
    21617 
    21618  > st
    21619 
    21620  > st
    21621 
    21622  > st
    21623 
    21624  > st
    21625 
    21626  > st
    21627 
    21628  > st
    21629 
    21630  > st
    21631 
    21632  > st
    21633 
    21634  > st
    21635 
    21636  > st
    21637 
    21638  > st
    21639 
    21640  > st
    21641 
    21642  > st
    21643 
    21644  > st
    21645 
    21646  > st
    21647 
    21648  > st
    21649 
    21650  > st
    21651 
    21652  > st
    21653 
    21654  > st
    21655 
    21656  > st
    21657 
    21658  > st
    21659 
    21660  > st
    21661 
    21662  > st
    21663 
    21664  > st
    21665 
    21666  > st
    21667 
    21668  > st
    21669 
    21670  > st
    21671 
    21672  > st
    21673 
    21674  > st
    21675 
    21676  > st
    21677 
    21678  > st
    21679 
    21680  > st
    21681 
    21682  > st
    21683 
    21684  > st
    21685 
    21686  > st
    21687 
    21688  > st
    21689 
    21690  > st
    21691 
    21692  > st
    21693 
    21694  > st
    21695 
    21696  > st
    21697 
    21698  > st
    21699 
    21700  > st
    21701 
    21702  > st
    21703 
    21704  > st
    21705 
    21706  > st
    21707 
    21708  > st
    21709 
    21710  > st
    21711 
    21712  > st
    21713 
    21714  > st
    21715 
    21716  > st
    21717 
    21718  > st
    21719 
    21720  > st
    21721 
    21722  > st
    21723 
    21724  > st
    21725 
    21726  > st
    21727 
    21728  > st
    21729 
    21730  > st
    21731 
    21732  > st
    21733 
    21734  > st
    21735 
    21736  > st
    21737 
    21738  > st
    21739 
    21740  > st
    21741 
    21742  > st
    21743 
    21744  > st
    21745 
    21746  > st
    21747 
    21748  > st
    21749 
    21750  > st
    21751 
    21752  > st
    21753 
    21754  > st
    21755 
    21756  > st
    21757 
    21758  > st
    21759 
    21760  > st
    21761 
    21762  > aw
    21763 
    21764  > isolde sim start sel
    21765 
    21766  > st
    21767 
    21768  > st
    21769 
    21770  > st
    21771 
    21772  > st
    21773 
    21774  > st
    21775 
    21776  > st
    21777 
    21778  > st
    21779 
    21780  > st
    21781 
    21782  > st
    21783 
    21784  > st
    21785 
    21786  > st
    21787 
    21788  > st
    21789 
    21790  > st
    21791 
    21792  > st
    21793 
    21794  > st
    21795 
    21796  > st
    21797 
    21798  > aw
    21799 
    21800  > isolde sim start sel
    21801 
    21802  > st
    21803 
    21804  > aw
    21805 
    21806  > isolde sim start sel
    21807 
    21808  > aw
    21809 
    21810  > isolde sim start sel
    21811 
    21812  > st
    21813 
    21814  > st
    21815 
    21816  > st
    21817 
    21818  > st
    21819 
    21820  > st
    21821 
    21822  > st
    21823 
    21824  > select clear
    21825 
    21826  > st
    21827 
    21828  > st
    21829 
    21830  > st
    21831 
    21832  > select clear
    21833 
    21834  > aw
    21835 
    21836  > isolde sim start sel
    21837 
    21838  > st
    21839 
    21840  > st
    21841 
    21842  > st
    21843 
    21844  > st
    21845 
    21846  > st
    21847 
    21848  > st
    21849 
    21850  > st
    21851 
    21852  > st
    21853 
    21854  > st
    21855 
    21856  > st
    21857 
    21858  > st
    21859 
    21860  > st
    21861 
    21862  > st
    21863 
    21864  > st
    21865 
    21866  > st
    21867 
    21868  > st
    21869 
    21870  > st
    21871 
    21872  > st
    21873 
    21874  > st
    21875 
    21876  > st
    21877 
    21878  > st
    21879 
    21880  > st
    21881 
    21882  > st
    21883 
    21884  > st
    21885 
    21886  > st
    21887 
    21888  > st
    21889 
    21890  > st
    21891 
    21892  > st
    21893 
    21894  > st
    21895 
    21896  > st
    21897 
    21898  > aw
    21899 
    21900  > isolde sim start sel
    21901 
    21902  > st
    21903 
    21904  > aw
    21905 
    21906  > isolde sim start sel
    21907 
    21908  > st
    21909 
    21910  > st
    21911 
    21912  > st
    21913 
    21914  > st
    21915 
    21916  > st
    21917 
    21918  > st
    21919 
    21920  > st
    21921 
    21922  > st
    21923 
    21924  > st
    21925 
    21926  > st
    21927 
    21928  > st
    21929 
    21930  > st
    21931 
    21932  > st
    21933 
    21934  > st
    21935 
    21936  > st
    21937 
    21938  > aw
    21939 
    21940  > isolde sim start sel
    21941 
    21942  > st
    21943 
    21944  > awsf
    21945 
    21946  > st
    21947 
    21948  > st
    21949 
    21950  > aw
    21951 
    21952  > isolde sim start sel
    21953 
    21954  > awsf
    21955 
    21956  > awsf
    21957 
    21958  > select clear
    21959 
    21960  > st
    21961 
    21962  > st
    21963 
    21964  > st
    21965 
    21966  > st
    21967 
    21968  > st
    21969 
    21970  > aw
    21971 
    21972  > isolde sim start sel
    21973 
    21974  > st
    21975 
    21976  > st
    21977 
    21978  > st
    21979 
    21980  > st
    21981 
    21982  > st
    21983 
    21984  > st
    21985 
    21986  > select clear
    21987 
    21988  > st
    21989 
    21990  > st
    21991 
    21992  > st
    21993 
    21994  > st
    21995 
    21996  > st
    21997 
    21998  > st
    21999 
    22000  > st
    22001 
    22002  > st
    22003 
    22004  > st
    22005 
    22006  > st
    22007 
    22008  > st
    22009 
    22010  > st
    22011 
    22012  > st
    22013 
    22014  > st
    22015 
    22016  > st
    22017 
    22018  > st
    22019 
    22020  > st
    22021 
    22022  > st
    22023 
    22024  > st
    22025 
    22026  > st
    22027 
    22028  > st
    22029 
    22030  > st
    22031 
    22032  > st
    22033 
    22034  > st
    22035 
    22036  > st
    22037 
    22038  > st
    22039 
    22040  > st
    22041 
    22042  > st
    22043 
    22044  > st
    22045 
    22046  > select clear
    22047 
    22048  > st
    22049 
    22050  > st
    22051 
    22052  > aw
    22053 
    22054  > isolde sim start sel
    22055 
    22056  > st
    22057 
    22058  > st
    22059 
    22060  > st
    22061 
    22062  > st
    22063 
    22064  > st
    22065 
    22066  > st
    22067 
    22068  > st
    22069 
    22070  > st
    22071 
    22072  > st
    22073 
    22074  > st
    22075 
    22076  > st
    22077 
    22078  > st
    22079 
    22080  > st
    22081 
    22082  > st
    22083 
    22084  > st
    22085 
    22086  > st
    22087 
    22088  > st
    22089 
    22090  > st
    22091 
    22092  > st
    22093 
    22094  > st
    22095 
    22096  > st
    22097 
    22098  > st
    22099 
    22100  > st
    22101 
    22102  > aw
    22103 
    22104  > isolde sim start sel
    22105 
    22106  > st
    22107 
    22108  > st
    22109 
    22110  > st
    22111 
    22112  > st
    22113 
    22114  > st
    22115 
    22116  > aw
    22117 
    22118  > isolde sim start sel
    22119 
    22120  > st
    22121 
    22122  > st
    22123 
    22124  > st
    22125 
    22126  > st
    22127 
    22128  > st
    22129 
    22130  > st
    22131 
    22132  > st
    22133 
    22134  > st
    22135 
    22136  > st
    22137 
    22138  > st
    22139 
    22140  > st
    22141 
    22142  > st
    22143 
    22144  > st
    22145 
    22146  > st
    22147 
    22148  > st
    22149 
    22150  > st
    22151 
    22152  > st
    22153 
    22154  > st
    22155 
    22156  > st
    22157 
    22158  > st
    22159 
    22160  > st
    22161 
    22162  > aw
    22163 
    22164  > isolde sim start sel
    22165 
    22166  > st
    22167 
    22168  > st
    22169 
    22170  > st
    22171 
    22172  > st
    22173 
    22174  > st
    22175 
    22176  > st
    22177 
    22178  > st
    22179 
    22180  > st
    22181 
    22182  > st
    22183 
    22184  > st
    22185 
    22186  > st
    22187 
    22188  > st
    22189 
    22190  > st
    22191 
    22192  > awsf
    22193 
    22194  > awsf
    22195 
    22196  > st
    22197 
    22198  > st
    22199 
    22200  > st
    22201 
    22202  > st
    22203 
    22204  > st
    22205 
    22206  > aw
    22207 
    22208  > isolde sim start sel
    22209 
    22210  > st
    22211 
    22212  > st
    22213 
    22214  > st
    22215 
    22216  > st
    22217 
    22218  > st
    22219 
    22220  > st
    22221 
    22222  > st
    22223 
    22224  > st
    22225 
    22226  > st
    22227 
    22228  > st
    22229 
    22230  > st
    22231 
    22232  > st
    22233 
    22234  > st
    22235 
    22236  > st
    22237 
    22238  > st
    22239 
    22240  > st
    22241 
    22242  > st
    22243 
    22244  > st
    22245 
    22246  > st
    22247 
    22248  > st
    22249 
    22250  > st
    22251 
    22252  > aw
    22253 
    22254  > isolde sim start sel
    22255 
    22256  > st
    22257 
    22258  > st
    22259 
    22260  > st
    22261 
    22262  > st
    22263 
    22264  > st
    22265 
    22266  > st
    22267 
    22268  > select clear
    22269 
    22270  > st
    22271 
    22272  > st
    22273 
    22274  > st
    22275 
    22276  > st
    22277 
    22278  > st
    22279 
    22280  > st
    22281 
    22282  > st
    22283 
    22284  > st
    22285 
    22286  > st
    22287 
    22288  > st
    22289 
    22290  > st
    22291 
    22292  > st
    22293 
    22294  > st
    22295 
    22296  > st
    22297 
    22298  > st
    22299 
    22300  > st
    22301 
    22302  > st
    22303 
    22304  > st
    22305 
    22306  > st
    22307 
    22308  > st
    22309 
    22310  > st
    22311 
    22312  > st
    22313 
    22314  > st
    22315 
    22316  > st
    22317 
    22318  > st
    22319 
    22320  > st
    22321 
    22322  > st
    22323 
    22324  > select clear
    22325 
    22326  > st
    22327 
    22328  > st
    22329 
    22330  > st
    22331 
    22332  > st
    22333 
    22334  > st
    22335 
    22336  > st
    22337 
    22338  > st
    22339 
    22340  > st
    22341 
    22342  > st
    22343 
    22344  > st
    22345 
    22346  > aw
    22347 
    22348  > isolde sim start sel
    22349 
    22350  > st
    22351 
    22352  > st
    22353 
    22354  > st
    22355 
    22356  > st
    22357 
    22358  > st
    22359 
    22360  > st
    22361 
    22362  > st
    22363 
    22364  > st
    22365 
    22366  > st
    22367 
    22368  > st
    22369 
    22370  > st
    22371 
    22372  > st
    22373 
    22374  > st
    22375 
    22376  > st
    22377 
    22378  > st
    22379 
    22380  > st
    22381 
    22382  > st
    22383 
    22384  > st
    22385 
    22386  > st
    22387 
    22388  > st
    22389 
    22390  > st
    22391 
    22392  > st
    22393 
    22394  > st
    22395 
    22396  > st
    22397 
    22398  > st
    22399 
    22400  > st
    22401 
    22402  > st
    22403 
    22404  > st
    22405 
    22406  > st
    22407 
    22408  > st
    22409 
    22410  > select clear
    22411 
    22412  > st
    22413 
    22414  > st
    22415 
    22416  > st
    22417 
    22418  > st
    22419 
    22420  > st
    22421 
    22422  > st
    22423 
    22424  > st
    22425 
    22426  > st
    22427 
    22428  > st
    22429 
    22430  > st
    22431 
    22432  > st
    22433 
    22434  > st
    22435 
    22436  > st
    22437 
    22438  > st
    22439 
    22440  > st
    22441 
    22442  > st
    22443 
    22444  > st
    22445 
    22446  > st
    22447 
    22448  > st
    22449 
    22450  > st
    22451 
    22452  > st
    22453 
    22454  > st
    22455 
    22456  > st
    22457 
    22458  > st
    22459 
    22460  > st
    22461 
    22462  > st
    22463 
    22464  > st
    22465 
    22466  > st
    22467 
    22468  > st
    22469 
    22470  > st
    22471 
    22472  > st
    22473 
    22474  > st
    22475 
    22476  > st
    22477 
    22478  > st
    22479 
    22480  > st
    22481 
    22482  > st
    22483 
    22484  > st
    22485 
    22486  > st
    22487 
    22488  > st
    22489 
    22490  > st
    22491 
    22492  > st
    22493 
    22494  > st
    22495 
    22496  > st
    22497 
    22498  > st
    22499 
    22500  > st
    22501 
    22502  > st
    22503 
    22504  > st
    22505 
    22506  > st
    22507 
    22508  > st
    22509 
    22510  > st
    22511 
    22512  > st
    22513 
    22514  > st
    22515 
    22516  > st
    22517 
    22518  > st
    22519 
    22520  > st
    22521 
    22522  > st
    22523 
    22524  > st
    22525 
    22526  > st
    22527 
    22528  > aw
    22529 
    22530  > isolde sim start sel
    22531 
    22532  > aw
    22533 
    22534  > isolde sim start sel
    22535 
    22536  > st
    22537 
    22538  > st
    22539 
    22540  > st
    22541 
    22542  > st
    22543 
    22544  > st
    22545 
    22546  > awsf
    22547 
    22548  > awsf
    22549 
    22550  > st
    22551 
    22552  > st
    22553 
    22554  > st
    22555 
    22556  > aw
    22557 
    22558  > isolde sim start sel
    22559 
    22560  > st
    22561 
    22562  > st
    22563 
    22564  > st
    22565 
    22566  > st
    22567 
    22568  > st
    22569 
    22570  > st
    22571 
    22572  > st
    22573 
    22574  > st
    22575 
    22576  > st
    22577 
    22578  > aw
    22579 
    22580  > isolde sim start sel
    22581 
    22582  > st
    22583 
    22584  > st
    22585 
    22586  > st
    22587 
    22588  > st
    22589 
    22590  > aw
    22591 
    22592  > isolde sim start sel
    22593 
    22594  > st
    22595 
    22596  > st
    22597 
    22598  > st
    22599 
    22600  > st
    22601 
    22602  > st
    22603 
    22604  > st
    22605 
    22606  > st
    22607 
    22608  > st
    22609 
    22610  > st
    22611 
    22612  > st
    22613 
    22614  > st
    22615 
    22616  > st
    22617 
    22618  > st
    22619 
    22620  > st
    22621 
    22622  > st
    22623 
    22624  > st
    22625 
    22626  > st
    22627 
    22628  > st
    22629 
    22630  > st
    22631 
    22632  > st
    22633 
    22634  > st
    22635 
    22636  > st
    22637 
    22638  > st
    22639 
    22640  > st
    22641 
    22642  > st
    22643 
    22644  > st
    22645 
    22646  > st
    22647 
    22648  > st
    22649 
    22650  > st
    22651 
    22652  > st
    22653 
    22654  > st
    22655 
    22656  > st
    22657 
    22658  > st
    22659 
    22660  > st
    22661 
    22662  > st
    22663 
    22664  > awsf
    22665 
    22666  > select clear
    22667 
    22668  > st
    22669 
    22670  > st
    22671 
    22672  > st
    22673 
    22674  > st
    22675 
    22676  > st
    22677 
    22678  > st
    22679 
    22680  > aw
    22681 
    22682  > isolde sim start sel
    22683 
    22684  > st
    22685 
    22686  > st
    22687 
    22688  > st
    22689 
    22690  > st
    22691 
    22692  > st
    22693 
    22694  > st
    22695 
    22696  > st
    22697 
    22698  > st
    22699 
    22700  > st
    22701 
    22702  > st
    22703 
    22704  > aw
    22705 
    22706  > isolde sim start sel
    22707 
    22708  > aw
    22709 
    22710  > isolde sim start sel
    22711 
    22712  > st
    22713 
    22714  > select clear
    22715 
    22716  > st
    22717 
    22718  > st
    22719 
    22720  > st
    22721 
    22722  > st
    22723 
    22724  > st
    22725 
    22726  > st
    22727 
    22728  > st
    22729 
    22730  > st
    22731 
    22732  > st
    22733 
    22734  > st
    22735 
    22736  > st
    22737 
    22738  > st
    22739 
    22740  > st
    22741 
    22742  > st
    22743 
    22744  > st
    22745 
    22746  > st
    22747 
    22748  > st
    22749 
    22750  > st
    22751 
    22752  > st
    22753 
    22754  > st
    22755 
    22756  > st
    22757 
    22758  > st
    22759 
    22760  > st
    22761 
    22762  > st
    22763 
    22764  > st
    22765 
    22766  > st
    22767 
    22768  > st
    22769 
    22770  > st
    22771 
    22772  > st
    22773 
    22774  > st
    22775 
    22776  > st
    22777 
    22778  > st
    22779 
    22780  > st
    22781 
    22782  > st
    22783 
    22784  > st
    22785 
    22786  > st
    22787 
    22788  > st
    22789 
    22790  > st
    22791 
    22792  > st
    22793 
    22794  > st
    22795 
    22796  > st
    22797 
    22798  > st
    22799 
    22800  > st
    22801 
    22802  > st
    22803 
    22804  > st
    22805 
    22806  > st
    22807 
    22808  > st
    22809 
    22810  > st
    22811 
    22812  > st
    22813 
    22814  > st
    22815 
    22816  > st
    22817 
    22818  > st
    22819 
    22820  > st
    22821 
    22822  > st
    22823 
    22824  > st
    22825 
    22826  > st
    22827 
    22828  > st
    22829 
    22830  > st
    22831 
    22832  > st
    22833 
    22834  > st
    22835 
    22836  > st
    22837 
    22838  > st
    22839 
    22840  > st
    22841 
    22842  > st
    22843 
    22844  > st
    22845 
    22846  > st
    22847 
    22848  > st
    22849 
    22850  > st
    22851 
    22852  > st
    22853 
    22854  > st
    22855 
    22856  > st
    22857 
    22858  > st
    22859 
    22860  > st
    22861 
    22862  > st
    22863 
    22864  > st
    22865 
    22866  > st
    22867 
    22868  > st
    22869 
    22870  > st
    22871 
    22872  > st
    22873 
    22874  > st
    22875 
    22876  > st
    22877 
    22878  > st
    22879 
    22880  > st
    22881 
    22882  > st
    22883 
    22884  > st
    22885 
    22886  > st
    22887 
    22888  > st
    22889 
    22890  > st
    22891 
    22892  > st
    22893 
    22894  > st
    22895 
    22896  > st
    22897 
    22898  > st
    22899 
    22900  > st
    22901 
    22902  > st
    22903 
    22904  > st
    22905 
    22906  > st
    22907 
    22908  > st
    22909 
    22910  > st
    22911 
    22912  > st
    22913 
    22914  > st
    22915 
    22916  > st
    22917 
    22918  > st
    22919 
    22920  > st
    22921 
    22922  > st
    22923 
    22924  > st
    22925 
    22926  > st
    22927 
    22928  > st
    22929 
    22930  > st
    22931 
    22932  > st
    22933 
    22934  > st
    22935 
    22936  > st
    22937 
    22938  > st
    22939 
    22940  > st
    22941 
    22942  > st
    22943 
    22944  > st
    22945 
    22946  > st
    22947 
    22948  > st
    22949 
    22950  > select clear
    22951 
    22952  > st
    22953 
    22954  > st
    22955 
    22956  > st
    22957 
    22958  > st
    22959 
    22960  > st
    22961 
    22962  > st
    22963 
    22964  > st
    22965 
    22966  > st
    22967 
    22968  > st
    22969 
    22970  > st
    22971 
    22972  > st
    22973 
    22974  > st
    22975 
    22976  > st
    22977 
    22978  > st
    22979 
    22980  > st
    22981 
    22982  > st
    22983 
    22984  > st
    22985 
    22986  > st
    22987 
    22988  > st
    22989 
    22990  > st
    22991 
    22992  > st
    22993 
    22994  > st
    22995 
    22996  > st
    22997 
    22998  > st
    22999 
    23000  > st
    23001 
    23002  > st
    23003 
    23004  > st
    23005 
    23006  > st
    23007 
    23008  > st
    23009 
    23010  > st
    23011 
    23012  > st
    23013 
    23014  > st
    23015 
    23016  > st
    23017 
    23018  > st
    23019 
    23020  > st
    23021 
    23022  > st
    23023 
    23024  > st
    23025 
    23026  > st
    23027 
    23028  > st
    23029 
    23030  > st
    23031 
    23032  > st
    23033 
    23034  > st
    23035 
    23036  > st
    23037 
    23038  > st
    23039 
    23040  > st
    23041 
    23042  > st
    23043 
    23044  > st
    23045 
    23046  > st
    23047 
    23048  > st
    23049 
    23050  > st
    23051 
    23052  > st
    23053 
    23054  > st
    23055 
    23056  > st
    23057 
    23058  > st
    23059 
    23060  > st
    23061 
    23062  > st
    23063 
    23064  > st
    23065 
    23066  > st
    23067 
    23068  > st
    23069 
    23070  > aw
    23071 
    23072  > isolde sim start sel
    23073 
    23074  > select up
    23075 
    23076  3 atoms, 2 bonds, 1 residue, 1 model selected
    23077 
    23078  > delete sel
    23079 
    23080  > st
    23081 
    23082  > st
    23083 
    23084  > st
    23085 
    23086  > st
    23087 
    23088  > st
    23089 
    23090  > st
    23091 
    23092  > st
    23093 
    23094  > st
    23095 
    23096  > st
    23097 
    23098  > st
    23099 
    23100  > st
    23101 
    23102  > st
    23103 
    23104  > st
    23105 
    23106  > st
    23107 
    23108  > st
    23109 
    23110  > st
    23111 
    23112  > st
    23113 
    23114  > st
    23115 
    23116  > st
    23117 
    23118  > select up
    23119 
    23120  215 atoms, 216 bonds, 12 residues, 1 model selected
    23121 
    23122  > select clear
    23123 
    23124  > st
    23125 
    23126  > st
    23127 
    23128  > st
    23129 
    23130  > st
    23131 
    23132  > st
    23133 
    23134  > st
    23135 
    23136  > st
    23137 
    23138  > select clear
    23139 
    23140  > st
    23141 
    23142  > st
    23143 
    23144  > st
    23145 
    23146  > st
    23147 
    23148  > st
    23149 
    23150  > st
    23151 
    23152  > st
    23153 
    23154  > st
    23155 
    23156  > st
    23157 
    23158  > st
    23159 
    23160  > st
    23161 
    23162  > st
    23163 
    23164  > st
    23165 
    23166  > st
    23167 
    23168  > st
    23169 
    23170  > st
    23171 
    23172  > st
    23173 
    23174  > st
    23175 
    23176  > st
    23177 
    23178  > st
    23179 
    23180  > st
    23181 
    23182  > st
    23183 
    23184  > st
    23185 
    23186  > st
    23187 
    23188  > st
    23189 
    23190  > st
    23191 
    23192  > st
    23193 
    23194  > st
    23195 
    23196  > st
    23197 
    23198  > st
    23199 
    23200  > st
    23201 
    23202  > st
    23203 
    23204  > st
    23205 
    23206  > st
    23207 
    23208  > st
    23209 
    23210  > st
    23211 
    23212  > st
    23213 
    23214  > st
    23215 
    23216  > st
    23217 
    23218  > st
    23219 
    23220  > st
    23221 
    23222  > st
    23223 
    23224  > st
    23225 
    23226  > st
    23227 
    23228  > st
    23229 
    23230  > st
    23231 
    23232  > st
    23233 
    23234  > st
    23235 
    23236  > st
    23237 
    23238  > st
    23239 
    23240  > st
    23241 
    23242  > st
    23243 
    23244  > st
    23245 
    23246  > st
    23247 
    23248  > st
    23249 
    23250  > st
    23251 
    23252  > st
    23253 
    23254  > st
    23255 
    23256  > st
    23257 
    23258  > st
    23259 
    23260  > st
    23261 
    23262  > st
    23263 
    23264  > st
    23265 
    23266  > st
    23267 
    23268  > st
    23269 
    23270  > st
    23271 
    23272  > st
    23273 
    23274  > st
    23275 
    23276  > st
    23277 
    23278  > st
    23279 
    23280  > st
    23281 
    23282  > st
    23283 
    23284  > st
    23285 
    23286  > st
    23287 
    23288  > st
    23289 
    23290  > st
    23291 
    23292  > st
    23293 
    23294  > st
    23295 
    23296  > st
    23297 
    23298  > st
    23299 
    23300  > st
    23301 
    23302  > st
    23303 
    23304  > st
    23305 
    23306  > st
    23307 
    23308  > st
    23309 
    23310  > st
    23311 
    23312  > st
    23313 
    23314  > select clear
    23315 
    23316  > st
    23317 
    23318  > st
    23319 
    23320  > st
    23321 
    23322  > st
    23323 
    23324  > st
    23325 
    23326  > st
    23327 
    23328  > st
    23329 
    23330  > st
    23331 
    23332  > st
    23333 
    23334  > st
    23335 
    23336  > st
    23337 
    23338  > st
    23339 
    23340  > st
    23341 
    23342  > st
    23343 
    23344  > st
    23345 
    23346  > st
    23347 
    23348  > st
    23349 
    23350  > st
    23351 
    23352  > st
    23353 
    23354  > st
    23355 
    23356  > st
    23357 
    23358  > st
    23359 
    23360  > st
    23361 
    23362  > st
    23363 
    23364  > st
    23365 
    23366  > st
    23367 
    23368  > st
    23369 
    23370  > st
    23371 
    23372  > st
    23373 
    23374  > select clear
    23375 
    23376  > st
    23377 
    23378  > st
    23379 
    23380  > st
    23381 
    23382  > st
    23383 
    23384  > st
    23385 
    23386  > select clear
    23387 
    23388  > st
    23389 
    23390  > st
    23391 
    23392  > st
    23393 
    23394  > st
    23395 
    23396  > st
    23397 
    23398  > st
    23399 
    23400  > st
    23401 
    23402  > st
    23403 
    23404  > st
    23405 
    23406  > st
    23407 
    23408  > st
    23409 
    23410  > st
    23411 
    23412  > st
    23413 
    23414  > st
    23415 
    23416  > st
    23417 
    23418  > st
    23419 
    23420  > st
    23421 
    23422  > st
    23423 
    23424  > st
    23425 
    23426  > st
    23427 
    23428  > st
    23429 
    23430  > st
    23431 
    23432  > st
    23433 
    23434  > st
    23435 
    23436  > st
    23437 
    23438  > st
    23439 
    23440  > st
    23441 
    23442  > st
    23443 
    23444  > st
    23445 
    23446  > st
    23447 
    23448  > st
    23449 
    23450  > st
    23451 
    23452  > st
    23453 
    23454  > st
    23455 
    23456  > st
    23457 
    23458  > st
    23459 
    23460  > st
    23461 
    23462  > st
    23463 
    23464  > st
    23465 
    23466  > st
    23467 
    23468  > st
    23469 
    23470  > st
    23471 
    23472  > st
    23473 
    23474  > st
    23475 
    23476  > st
    23477 
    23478  > st
    23479 
    23480  > st
    23481 
    23482  > st
    23483 
    23484  > aw
    23485 
    23486  > isolde sim start sel
    23487 
    23488  > st
    23489 
    23490  > st
    23491 
    23492  > st
    23493 
    23494  > st
    23495 
    23496  > st
    23497 
    23498  > st
    23499 
    23500  > st
    23501 
    23502  > st
    23503 
    23504  > st
    23505 
    23506  > st
    23507 
    23508  > st
    23509 
    23510  > st
    23511 
    23512  > st
    23513 
    23514  > st
    23515 
    23516  > st
    23517 
    23518  > st
    23519 
    23520  > st
    23521 
    23522  > st
    23523 
    23524  > st
    23525 
    23526  > st
    23527 
    23528  > st
    23529 
    23530  > st
    23531 
    23532  > st
    23533 
    23534  > select clear
    23535 
    23536  > st
    23537 
    23538  > st
    23539 
    23540  > st
    23541 
    23542  > st
    23543 
    23544  > st
    23545 
    23546  > st
    23547 
    23548  > st
    23549 
    23550  > st
    23551 
    23552  > st
    23553 
    23554  > st
    23555 
    23556  > st
    23557 
    23558  > st
    23559 
    23560  > st
    23561 
    23562  > st
    23563 
    23564  > st
    23565 
    23566  > st
    23567 
    23568  > st
    23569 
    23570  > select clear
    23571 
    23572  > st
    23573 
    23574  > st
    23575 
    23576  > st
    23577 
    23578  > st
    23579 
    23580  > st
    23581 
    23582  > aw
    23583 
    23584  > isolde sim start sel
    23585 
    23586  > staw
    23587 
    23588  Unknown command: staw
    23589 
    23590  > aw
    23591 
    23592  > isolde sim start sel
    23593 
    23594  > st
    23595 
    23596  > st
    23597 
    23598  > aw
    23599 
    23600  > isolde sim start sel
    23601 
    23602  > st
    23603 
    23604  > st
    23605 
    23606  > st
    23607 
    23608  > st
    23609 
    23610  > st
    23611 
    23612  > st
    23613 
    23614  > st
    23615 
    23616  > st
    23617 
    23618  > select clear
    23619 
    23620  > st
    23621 
    23622  > st
    23623 
    23624  > st
    23625 
    23626  > st
    23627 
    23628  > st
    23629 
    23630  > st
    23631 
    23632  > st
    23633 
    23634  > st
    23635 
    23636  > st
    23637 
    23638  > st
    23639 
    23640  > st
    23641 
    23642  > st
    23643 
    23644  > st
    23645 
    23646  > st
    23647 
    23648  > st
    23649 
    23650  > st
    23651 
    23652  > st
    23653 
    23654  > st
    23655 
    23656  > st
    23657 
    23658  > st
    23659 
    23660  > st
    23661 
    23662  > st
    23663 
    23664  > st
    23665 
    23666  > st
    23667 
    23668  > st
    23669 
    23670  > st
    23671 
    23672  > st
    23673 
    23674  > st
    23675 
    23676  > st
    23677 
    23678  > st
    23679 
    23680  > st
    23681 
    23682  > st
    23683 
    23684  > st
    23685 
    23686  > st
    23687 
    23688  > st
    23689 
    23690  > st
    23691 
    23692  > st
    23693 
    23694  > st
    23695 
    23696  > st
    23697 
    23698  > st
    23699 
    23700  > st
    23701 
    23702  > st
    23703 
    23704  > st
    23705 
    23706  > st
    23707 
    23708  > st
    23709 
    23710  > st
    23711 
    23712  > st
    23713 
    23714  > st
    23715 
    23716  > st
    23717 
    23718  > st
    23719 
    23720  > st
    23721 
    23722  > st
    23723 
    23724  > st
    23725 
    23726  > st
    23727 
    23728  > st
    23729 
    23730  > st
    23731 
    23732  > st
    23733 
    23734  > st
    23735 
    23736  > st
    23737 
    23738  > awsf
    23739 
    23740  > awsf
    23741 
    23742  > select clear
    23743 
    23744  > st
    23745 
    23746  > st
    23747 
    23748  > st
    23749 
    23750  > st
    23751 
    23752  > st
    23753 
    23754  > st
    23755 
    23756  > st
    23757 
    23758  > st
    23759 
    23760  > st
    23761 
    23762  > select clear
    23763 
    23764  > st
    23765 
    23766  > st
    23767 
    23768  > st
    23769 
    23770  > st
    23771 
    23772  > st
    23773 
    23774  > st
    23775 
    23776  > st
    23777 
    23778  > st
    23779 
    23780  > aw
    23781 
    23782  > isolde sim start sel
    23783 
    23784  > st
    23785 
    23786  > st
    23787 
    23788  > st
    23789 
    23790  > st
    23791 
    23792  > st
    23793 
    23794  > aw
    23795 
    23796  > isolde sim start sel
    23797 
    23798  > st
    23799 
    23800  > st
    23801 
    23802  > st
    23803 
    23804  > st
    23805 
    23806  > st
    23807 
    23808  > st
    23809 
    23810  > st
    23811 
    23812  > st
    23813 
    23814  > st
    23815 
    23816  > st
    23817 
    23818  > st
    23819 
    23820  > select clear
    23821 
    23822  > st
    23823 
    23824  > st
    23825 
    23826  > st
    23827 
    23828  > st
    23829 
    23830  > st
    23831 
    23832  > st
    23833 
    23834  > st
    23835 
    23836  > st
    23837 
    23838  > st
    23839 
    23840  > st
    23841 
    23842  > st
    23843 
    23844  > st
    23845 
    23846  > st
    23847 
    23848  > st
    23849 
    23850  > st
    23851 
    23852  > st
    23853 
    23854  > st
    23855 
    23856  > st
    23857 
    23858  > st
    23859 
    23860  > st
    23861 
    23862  > st
    23863 
    23864  > st
    23865 
    23866  > st
    23867 
    23868  > st
    23869 
    23870  > st
    23871 
    23872  > st
    23873 
    23874  > st
    23875 
    23876  > st
    23877 
    23878  > st
    23879 
    23880  > st
    23881 
    23882  > st
    23883 
    23884  > st
    23885 
    23886  > st
    23887 
    23888  > st
    23889 
    23890  > select clear
    23891 
    23892  > st
    23893 
    23894  > st
    23895 
    23896  > aw
    23897 
    23898  > isolde sim start sel
    23899 
    23900  > st
    23901 
    23902  > st
    23903 
    23904  > st
    23905 
    23906  > st
    23907 
    23908  > st
    23909 
    23910  > st
    23911 
    23912  > aw
    23913 
    23914  > isolde sim start sel
    23915 
    23916  > st
    23917 
    23918  > st
    23919 
    23920  > st
    23921 
    23922  > st
    23923 
    23924  > aw
    23925 
    23926  > isolde sim start sel
    23927 
    23928  > st
    23929 
    23930  > st
    23931 
    23932  > st
    23933 
    23934  > st
    23935 
    23936  > st
    23937 
    23938  > st
    23939 
    23940  > st
    23941 
    23942  > st
    23943 
    23944  > st
    23945 
    23946  > st
    23947 
    23948  > st
    23949 
    23950  > st
    23951 
    23952  > st
    23953 
    23954  > st
    23955 
    23956  > st
    23957 
    23958  > st
    23959 
    23960  > st
    23961 
    23962  > st
    23963 
    23964  > st
    23965 
    23966  > st
    23967 
    23968  > st
    23969 
    23970  > st
    23971 
    23972  > st
    23973 
    23974  > st
    23975 
    23976  > st
    23977 
    23978  > st
    23979 
    23980  > st
    23981 
    23982  > st
    23983 
    23984  > st
    23985 
    23986  > st
    23987 
    23988  > st
    23989 
    23990  > st
    23991 
    23992  > st
    23993 
    23994  > st
    23995 
    23996  > st
    23997 
    23998  > st
    23999 
    24000  > st
    24001 
    24002  > st
    24003 
    24004  > st
    24005 
    24006  > st
    24007 
    24008  > st
    24009 
    24010  > st
    24011 
    24012  > st
    24013 
    24014  > st
    24015 
    24016  > st
    24017 
    24018  > select clear
    24019 
    24020  > st
    24021 
    24022  > st
    24023 
    24024  > st
    24025 
    24026  > aw
    24027 
    24028  > isolde sim start sel
    24029 
    24030  > st
    24031 
    24032  > st
    24033 
    24034  > aw
    24035 
    24036  > isolde sim start sel
    24037 
    24038  > st
    24039 
    24040  > st
    24041 
    24042  > st
    24043 
    24044  > st
    24045 
    24046  > st
    24047 
    24048  > st
    24049 
    24050  > st
    24051 
    24052  > st
    24053 
    24054  > st
    24055 
    24056  > st
    24057 
    24058  > st
    24059 
    24060  > st
    24061 
    24062  > st
    24063 
    24064  > st
    24065 
    24066  > st
    24067 
    24068  > st
    24069 
    24070  > st
    24071 
    24072  > st
    24073 
    24074  > st
    24075 
    24076  > st
    24077 
    24078  > st
    24079 
    24080  > st
    24081 
    24082  > st
    24083 
    24084  > st
    24085 
    24086  > st
    24087 
    24088  > select clear
    24089 
    24090  > st
    24091 
    24092  > st
    24093 
    24094  > select clear
    24095 
    24096  > st
    24097 
    24098  > st
    24099 
    24100  > st
    24101 
    24102  > select clear
    24103 
    24104  > st
    24105 
    24106  > st
    24107 
    24108  > st
    24109 
    24110  > st
    24111 
    24112  > st
    24113 
    24114  > st
    24115 
    24116  > st
    24117 
    24118  > st
    24119 
    24120  > st
    24121 
    24122  > st
    24123 
    24124  > st
    24125 
    24126  > st
    24127 
    24128  > st
    24129 
    24130  > st
    24131 
    24132  > st
    24133 
    24134  > st
    24135 
    24136  > st
    24137 
    24138  > st
    24139 
    24140  > st
    24141 
    24142  > st
    24143 
    24144  > st
    24145 
    24146  > st
    24147 
    24148  > st
    24149 
    24150  > st
    24151 
    24152  > st
    24153 
    24154  > st
    24155 
    24156  > st
    24157 
    24158  > st
    24159 
    24160  > st
    24161 
    24162  > st
    24163 
    24164  > aw
    24165 
    24166  > isolde sim start sel
    24167 
    24168  > st
    24169 
    24170  > st
    24171 
    24172  > select clear
    24173 
    24174  > st
    24175 
    24176  > st
    24177 
    24178  > st
    24179 
    24180  > st
    24181 
    24182  > aw
    24183 
    24184  > isolde sim start sel
    24185 
    24186  > st
    24187 
    24188  > st
    24189 
    24190  > st
    24191 
    24192  > st
    24193 
    24194  > st
    24195 
    24196  > st
    24197 
    24198  > st
    24199 
    24200  > st
    24201 
    24202  > st
    24203 
    24204  > st
    24205 
    24206  > st
    24207 
    24208  > st
    24209 
    24210  > st
    24211 
    24212  > st
    24213 
    24214  > st
    24215 
    24216  > select clear
    24217 
    24218  > st
    24219 
    24220  > st
    24221 
    24222  > st
    24223 
    24224  > st
    24225 
    24226  > st
    24227 
    24228  > st
    24229 
    24230  > st
    24231 
    24232  > st
    24233 
    24234  > st
    24235 
    24236  > st
    24237 
    24238  > st
    24239 
    24240  > st
    24241 
    24242  > st
    24243 
    24244  > st
    24245 
    24246  > st
    24247 
    24248  > st
    24249 
    24250  > st
    24251 
    24252  > st
    24253 
    24254  > st
    24255 
    24256  > st
    24257 
    24258  > st
    24259 
    24260  > st
    24261 
    24262  > st
    24263 
    24264  > st
    24265 
    24266  > st
    24267 
    24268  > st
    24269 
    24270  > st
    24271 
    24272  > st
    24273 
    24274  > st
    24275 
    24276  > st
    24277 
    24278  > st
    24279 
    24280  > st
    24281 
    24282  > st
    24283 
    24284  > st
    24285 
    24286  > st
    24287 
    24288  > aw
    24289 
    24290  > isolde sim start sel
    24291 
    24292  > st
    24293 
    24294  > st
    24295 
    24296  > st
    24297 
    24298  > st
    24299 
    24300  > st
    24301 
    24302  > st
    24303 
    24304  > st
    24305 
    24306  > st
    24307 
    24308  > awsf
    24309 
    24310  > awsf
    24311 
    24312  > st
    24313 
    24314  > aw
    24315 
    24316  > isolde sim start sel
    24317 
    24318  > st
    24319 
    24320  > st
    24321 
    24322  > st
    24323 
    24324  > st
    24325 
    24326  > st
    24327 
    24328  > st
    24329 
    24330  > st
    24331 
    24332  > st
    24333 
    24334  > st
    24335 
    24336  > st
    24337 
    24338  > st
    24339 
    24340  > save working.cxs
    24341 
    24342  Taking snapshot of stepper: Model 1a
    24343  opened ChimeraX session
    24344 
    24345  > isolde start
    24346 
    24347  > set selectionWidth 4
    24348 
    24349  Done loading forcefield
    24350 
    24351  > st
    24352 
    24353  > st
    24354 
    24355  > st
    24356 
    24357  > st
    24358 
    24359  > st
    24360 
    24361  > st
    24362 
    24363  > st
    24364 
    24365  > st
    24366 
    24367  > st
    24368 
    24369  > st
    24370 
    24371  > st
    24372 
    24373  > st
    24374 
    24375  > aw
    24376 
    24377  > isolde sim start sel
    24378 
    24379  > st
    24380 
    24381  > st
    24382 
    24383  > st
    24384 
    24385  > st
    24386 
    24387  > st
    24388 
    24389  > st
    24390 
    24391  > st
    24392 
    24393  > st
    24394 
    24395  > st
    24396 
    24397  > st
    24398 
    24399  > st
    24400 
    24401  > st
    24402 
    24403  > st
    24404 
    24405  > st
    24406 
    24407  > st
    24408 
    24409  > st
    24410 
    24411  > st
    24412 
    24413  > st
    24414 
    24415  > st
    24416 
    24417  > st
    24418 
    24419  > st
    24420 
    24421  > st
    24422 
    24423  > aw
    24424 
    24425  > isolde sim start sel
    24426 
    24427  > aw
    24428 
    24429  > isolde sim start sel
    24430 
    24431  > st
    24432 
    24433  > st
    24434 
    24435  > st
    24436 
    24437  > st
    24438 
    24439  > awsf
    24440 
    24441  > awsf
    24442 
    24443  > select clear
    24444 
    24445  > st
    24446 
    24447  > st
    24448 
    24449  > aw
    24450 
    24451  > isolde sim start sel
    24452 
    24453  > st
    24454 
    24455  > st
    24456 
    24457  > st
    24458 
    24459  > st
    24460 
    24461  > st
    24462 
    24463  > awsf
    24464 
    24465  > awsf
    24466 
    24467  > select clear
    24468 
    24469  > st
    24470 
    24471  > st
    24472 
    24473  > st
    24474 
    24475  > st
    24476 
    24477  > st
    24478 
    24479  > st
    24480 
    24481  > st
    24482 
    24483  > st
    24484 
    24485  > st
    24486 
    24487  > st
    24488 
    24489  > st
    24490 
    24491  > st
    24492 
    24493  > st
    24494 
    24495  > st
    24496 
    24497  > st
    24498 
    24499  > st
    24500 
    24501  > st
    24502 
    24503  > select clear
    24504 
    24505  > st
    24506 
    24507  > st
    24508 
    24509  > st
    24510 
    24511  > st
    24512 
    24513  > st
    24514 
    24515  > st
    24516 
    24517  > aw
    24518 
    24519  No existing atoms found within the given distance cutoff of the target
    24520  position. You may repeat with a larger cutoff or explicitly specify the
    24521  B-factor and chain ID, but keep in mind that placing waters outside of
    24522  H-bonding distance to the model is generally inadvisable.
    24523 
    24524  > st
    24525 
    24526  > st
    24527 
    24528  > aw
    24529 
    24530  > isolde sim start sel
    24531 
    24532  > st
    24533 
    24534  > st
    24535 
    24536  > st
    24537 
    24538  > st
    24539 
    24540  > st
    24541 
    24542  > st
    24543 
    24544  > select clear
    24545 
    24546  > st
    24547 
    24548  > st
    24549 
    24550  > st
    24551 
    24552  > st
    24553 
    24554  > st
    24555 
    24556  > st
    24557 
    24558  > st
    24559 
    24560  > st
    24561 
    24562  > st
    24563 
    24564  > st
    24565 
    24566  > st
    24567 
    24568  > st
    24569 
    24570  > st
    24571 
    24572  > st
    24573 
    24574  > st
    24575 
    24576  > st
    24577 
    24578  > st
    24579 
    24580  > st
    24581 
    24582  > st
    24583 
    24584  > st
    24585 
    24586  > select clear
    24587 
    24588  > st
    24589 
    24590  > st
    24591 
    24592  > st
    24593 
    24594  > st
    24595 
    24596  > awsf
    24597 
    24598  > awsf
    24599 
    24600  > select clear
    24601 
    24602  > st
    24603 
    24604  > st
    24605 
    24606  > st
    24607 
    24608  > aw
    24609 
    24610  > isolde sim start sel
    24611 
    24612  > st
    24613 
    24614  > st
    24615 
    24616  > st
    24617 
    24618  > st
    24619 
    24620  > st
    24621 
    24622  > st
    24623 
    24624  > aw
    24625 
    24626  > isolde sim start sel
    24627 
    24628  > st
    24629 
    24630  > aw
    24631 
    24632  > isolde sim start sel
    24633 
    24634  > st
    24635 
    24636  > st
    24637 
    24638  > st
    24639 
    24640  > st
    24641 
    24642  > st
    24643 
    24644  > st
    24645 
    24646  > st
    24647 
    24648  > st
    24649 
    24650  > st
    24651 
    24652  > st
    24653 
    24654  > st
    24655 
    24656  > st
    24657 
    24658  > st
    24659 
    24660  > st
    24661 
    24662  > st
    24663 
    24664  > st
    24665 
    24666  > st
    24667 
    24668  > st
    24669 
    24670  > st
    24671 
    24672  > st
    24673 
    24674  > aw
    24675 
    24676  > isolde sim start sel
    24677 
    24678  > st
    24679 
    24680  > st
    24681 
    24682  > st
    24683 
    24684  > select clear
    24685 
    24686  > st
    24687 
    24688  > st
    24689 
    24690  > st
    24691 
    24692  > st
    24693 
    24694  > st
    24695 
    24696  > st
    24697 
    24698  > st
    24699 
    24700  > st
    24701 
    24702  > st
    24703 
    24704  > st
    24705 
    24706  > st
    24707 
    24708  > st
    24709 
    24710  > st
    24711 
    24712  > st
    24713 
    24714  > st
    24715 
    24716  > st
    24717 
    24718  > st
    24719 
    24720  > st
    24721 
    24722  > st
    24723 
    24724  > st
    24725 
    24726  > st
    24727 
    24728  > st
    24729 
    24730  > select clear
    24731 
    24732  > st
    24733 
    24734  > st
    24735 
    24736  > st
    24737 
    24738  > select clear
    24739 
    24740  > st
    24741 
    24742  > st
    24743 
    24744  > aw
    24745 
    24746  > isolde sim start sel
    24747 
    24748  > st
    24749 
    24750  > st
    24751 
    24752  > st
    24753 
    24754  > aw
    24755 
    24756  > isolde sim start sel
    24757 
    24758  > st
    24759 
    24760  > st
    24761 
    24762  > st
    24763 
    24764  > st
    24765 
    24766  > st
    24767 
    24768  > st
    24769 
    24770  > aw
    24771 
    24772  > isolde sim start sel
    24773 
    24774  > st
    24775 
    24776  > st
    24777 
    24778  > select clear
    24779 
    24780  > st
    24781 
    24782  > st
    24783 
    24784  > aw
    24785 
    24786  > isolde sim start sel
    24787 
    24788  > st
    24789 
    24790  > st
    24791 
    24792  > st
    24793 
    24794  > st
    24795 
    24796  > st
    24797 
    24798  > st
    24799 
    24800  > st
    24801 
    24802  > st
    24803 
    24804  > st
    24805 
    24806  > st
    24807 
    24808  > st
    24809 
    24810  > st
    24811 
    24812  > st
    24813 
    24814  > st
    24815 
    24816  > st
    24817 
    24818  > select clear
    24819 
    24820  > st
    24821 
    24822  > st
    24823 
    24824  > st
    24825 
    24826  > st
    24827 
    24828  > st
    24829 
    24830  > select clear
    24831 
    24832  > st
    24833 
    24834  > st
    24835 
    24836  > st
    24837 
    24838  > st
    24839 
    24840  > st
    24841 
    24842  > st
    24843 
    24844  > st
    24845 
    24846  > st
    24847 
    24848  > st
    24849 
    24850  > st
    24851 
    24852  > st
    24853 
    24854  > st
    24855 
    24856  > st
    24857 
    24858  > st
    24859 
    24860  > st
    24861 
    24862  > st
    24863 
    24864  > st
    24865 
    24866  > st
    24867 
    24868  > st
    24869 
    24870  > st
    24871 
    24872  > st
    24873 
    24874  > st
    24875 
    24876  > aw
    24877 
    24878  > isolde sim start sel
    24879 
    24880  > st
    24881 
    24882  > st
    24883 
    24884  > aw
    24885 
    24886  > isolde sim start sel
    24887 
    24888  > st
    24889 
    24890  > aw
    24891 
    24892  > isolde sim start sel
    24893 
    24894  > st
    24895 
    24896  > st
    24897 
    24898  > select clear
    24899 
    24900  > st
    24901 
    24902  > st
    24903 
    24904  > st
    24905 
    24906  > awsf
    24907 
    24908  > awsf
    24909 
    24910  > st
    24911 
    24912  > st
    24913 
    24914  > st
    24915 
    24916  > st
    24917 
    24918  > st
    24919 
    24920  > aw
    24921 
    24922  > isolde sim start sel
    24923 
    24924  > st
    24925 
    24926  > st
    24927 
    24928  > st
    24929 
    24930  > st
    24931 
    24932  > st
    24933 
    24934  > st
    24935 
    24936  > st
    24937 
    24938  > st
    24939 
    24940  > st
    24941 
    24942  > st
    24943 
    24944  > st
    24945 
    24946  > st
    24947 
    24948  > st
    24949 
    24950  > st
    24951 
    24952  > st
    24953 
    24954  > st
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    25028  > isolde sim start sel
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    25053 
    25054  > select clear
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    25100  > select clear
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    25141 
    25142  > aw
    25143 
    25144  > isolde sim start sel
    25145 
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    25149 
    25150  > isolde sim start sel
    25151 
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    25153 
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    25155 
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    25157 
    25158  > select clear
    25159 
    25160  > aw
    25161 
    25162  > isolde sim start sel
    25163 
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    25177 
    25178  > aw
    25179 
    25180  > isolde sim start sel
    25181 
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    25185 
    25186  > aw
    25187 
    25188  > isolde sim start sel
    25189 
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    25191 
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    25193 
    25194  > aw
    25195 
    25196  > isolde sim start sel
    25197 
    25198  > st
    25199 
    25200  > st
    25201 
    25202  > select clear
    25203 
    25204  > select clear
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    25206  > st
    25207 
    25208  > st
    25209 
    25210  > st
    25211 
    25212  > st
    25213 
    25214  > select clear
    25215 
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    25299 
    25300  > st
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    25302  > aw
    25303 
    25304  > isolde sim start sel
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    25322  > isolde sim start sel
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    25334  > aw
    25335 
    25336  > isolde sim start sel
    25337 
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    25339 
    25340  > isolde sim start sel
    25341 
    25342  > st
    25343 
    25344  > st
    25345 
    25346  > select clear
    25347 
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    25356  > aw
    25357 
    25358  > isolde sim start sel
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    25364  > st
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    25379 
    25380  > isolde sim start sel
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    25460  > st
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    25464  > st
    25465 
    25466  > select clear
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    25469 
    25470  > st
    25471 
    25472  > aw
    25473 
    25474  > isolde sim start sel
    25475 
    25476  > st
    25477 
    25478  > select clear
    25479 
    25480  > st
    25481 
    25482  > st
    25483 
    25484  > select clear
    25485 
    25486  > select clear
    25487 
    25488  > aw
    25489 
    25490  > isolde sim start sel
    25491 
    25492  > st
    25493 
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    25497 
    25498  > aw
    25499 
    25500  > isolde sim start sel
    25501 
    25502  > st
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    25506  > st
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    25509 
    25510  > st
    25511 
    25512  > aw
    25513 
    25514  > isolde sim start sel
    25515 
    25516  > st
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    25521 
    25522  > aw
    25523 
    25524  > isolde sim start sel
    25525 
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    25548  > st
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    25551 
    25552  > st
    25553 
    25554  > st
    25555 
    25556  > select clear
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    25570  > st
    25571 
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    25576  > st
    25577 
    25578  > select clear
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    25597 
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    25599 
    25600  > st
    25601 
    25602  > select clear
    25603 
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    25609 
    25610  > st
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    25614  > aw
    25615 
    25616  > isolde sim start sel
    25617 
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    25621 
    25622  > aw
    25623 
    25624  > isolde sim start sel
    25625 
    25626  > aw
    25627 
    25628  > isolde sim start sel
    25629 
    25630  > select up
    25631 
    25632  3 atoms, 2 bonds, 1 residue, 1 model selected
    25633 
    25634  > delete sel
    25635 
    25636  > st
    25637 
    25638  > st
    25639 
    25640  > st
    25641 
    25642  > st
    25643 
    25644  > awsf
    25645 
    25646  > awsf
    25647 
    25648  > st
    25649 
    25650  > st
    25651 
    25652  > st
    25653 
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    25663 
    25664  > aw
    25665 
    25666  > isolde sim start sel
    25667 
    25668  > st
    25669 
    25670  > st
    25671 
    25672  > st
    25673 
    25674  > st
    25675 
    25676  > st
    25677 
    25678  > select clear
    25679 
    25680  > st
    25681 
    25682  > st
    25683 
    25684  > st
    25685 
    25686  > select clear
    25687 
    25688  > st
    25689 
    25690  > st
    25691 
    25692  > st
    25693 
    25694  > st
    25695 
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    25697 
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    25699 
    25700  > st
    25701 
    25702  > st
    25703 
    25704  > st
    25705 
    25706  > st
    25707 
    25708  > st
    25709 
    25710  > st
    25711 
    25712  > st
    25713 
    25714  > st
    25715 
    25716  > st
    25717 
    25718  > st
    25719 
    25720  > st
    25721 
    25722  > st
    25723 
    25724  > select clear
    25725 
    25726  > st
    25727 
    25728  > st
    25729 
    25730  > st
    25731 
    25732  > st
    25733 
    25734  > st
    25735 
    25736  > st
    25737 
    25738  > st
    25739 
    25740  > st
    25741 
    25742  > st
    25743 
    25744  > st
    25745 
    25746  > st
    25747 
    25748  > st
    25749 
    25750  > st
    25751 
    25752  > st
    25753 
    25754  > st
    25755 
    25756  > st
    25757 
    25758  > st
    25759 
    25760  > st
    25761 
    25762  > st
    25763 
    25764  > st
    25765 
    25766  > aw
    25767 
    25768  No existing atoms found within the given distance cutoff of the target
    25769  position. You may repeat with a larger cutoff or explicitly specify the
    25770  B-factor and chain ID, but keep in mind that placing waters outside of
    25771  H-bonding distance to the model is generally inadvisable.
    25772 
    25773  > awst
    25774 
    25775  Unknown command: awst
    25776 
    25777  > st
    25778 
    25779  > st
    25780 
    25781  > st
    25782 
    25783  > awsf
    25784 
    25785  No existing atoms found within the given distance cutoff of the target
    25786  position. You may repeat with a larger cutoff or explicitly specify the
    25787  B-factor and chain ID, but keep in mind that placing waters outside of
    25788  H-bonding distance to the model is generally inadvisable.
    25789 
    25790  > awsf
    25791 
    25792  No existing atoms found within the given distance cutoff of the target
    25793  position. You may repeat with a larger cutoff or explicitly specify the
    25794  B-factor and chain ID, but keep in mind that placing waters outside of
    25795  H-bonding distance to the model is generally inadvisable.
    25796 
    25797  > awsf
    25798 
    25799  > awsf
    25800 
    25801  > st
    25802 
    25803  > st
    25804 
    25805  > select clear
    25806 
    25807  > st
    25808 
    25809  > awsf
    25810 
    25811  > awsf
    25812 
    25813  > st
    25814 
    25815  > st
    25816 
    25817  > select clear
    25818 
    25819  > st
    25820 
    25821  > st
    25822 
    25823  > select clear
    25824 
    25825  > st
    25826 
    25827  > aw
    25828 
    25829  > isolde sim start sel
    25830 
    25831  > aw
    25832 
    25833  > isolde sim start sel
    25834 
    25835  > aw
    25836 
    25837  > isolde sim start sel
    25838 
    25839  > st
    25840 
    25841  > st
    25842 
    25843  > st
    25844 
    25845  > st
    25846 
    25847  > st
    25848 
    25849  > st
    25850 
    25851  > st
    25852 
    25853  > select clear
    25854 
    25855  > st
    25856 
    25857  > st
    25858 
    25859  > st
    25860 
    25861  > aw
    25862 
    25863  > isolde sim start sel
    25864 
    25865  > st
    25866 
    25867  > aw
    25868 
    25869  > isolde sim start sel
    25870 
    25871  > aw
    25872 
    25873  > isolde sim start sel
    25874 
    25875  > select clear
    25876 
    25877  > st
    25878 
    25879  > st
    25880 
    25881  > st
    25882 
    25883  > st
    25884 
    25885  > st
    25886 
    25887  > st
    25888 
    25889  > st
    25890 
    25891  > st
    25892 
    25893  > st
    25894 
    25895  > st
    25896 
    25897  > st
    25898 
    25899  > st
    25900 
    25901  > st
    25902 
    25903  > st
    25904 
    25905  > st
    25906 
    25907  > st
    25908 
    25909  > st
    25910 
    25911  > st
    25912 
    25913  > st
    25914 
    25915  > st
    25916 
    25917  > st
    25918 
    25919  > st
    25920 
    25921  > st
    25922 
    25923  > st
    25924 
    25925  > aw
    25926 
    25927  > isolde sim start sel
    25928 
    25929  > st
    25930 
    25931  > select clear
    25932 
    25933  > st
    25934 
    25935  > st
    25936 
    25937  > aw
    25938 
    25939  > isolde sim start sel
    25940 
    25941  > select clear
    25942 
    25943  > st
    25944 
    25945  > st
    25946 
    25947  > st
    25948 
    25949  > select clear
    25950 
    25951  > st
    25952 
    25953  > st
    25954 
    25955  > st
    25956 
    25957  > st
    25958 
    25959  > st
    25960 
    25961  > st
    25962 
    25963  > st
    25964 
    25965  > st
    25966 
    25967  > st
    25968 
    25969  > st
    25970 
    25971  > st
    25972 
    25973  > st
    25974 
    25975  > st
    25976 
    25977  > st
    25978 
    25979  > select clear
    25980 
    25981  > st
    25982 
    25983  > st
    25984 
    25985  > st
    25986 
    25987  > st
    25988 
    25989  > st
    25990 
    25991  > st
    25992 
    25993  > st
    25994 
    25995  > select clear
    25996 
    25997  > st
    25998 
    25999  > st
    26000 
    26001  > st
    26002 
    26003  > st
    26004 
    26005  > st
    26006 
    26007  > st
    26008 
    26009  > st
    26010 
    26011  > st
    26012 
    26013  > st
    26014 
    26015  > st
    26016 
    26017  > st
    26018 
    26019  > aw
    26020 
    26021  > isolde sim start sel
    26022 
    26023  > st
    26024 
    26025  > st
    26026 
    26027  > st
    26028 
    26029  > st
    26030 
    26031  > st
    26032 
    26033  > st
    26034 
    26035  > st
    26036 
    26037  > st
    26038 
    26039  > st
    26040 
    26041  > st
    26042 
    26043  > st
    26044 
    26045  > st
    26046 
    26047  > st
    26048 
    26049  > st
    26050 
    26051  > st
    26052 
    26053  > st
    26054 
    26055  > st
    26056 
    26057  > st
    26058 
    26059  > st
    26060 
    26061  > st
    26062 
    26063  > st
    26064 
    26065  > st
    26066 
    26067  > st
    26068 
    26069  > st
    26070 
    26071  > st
    26072 
    26073  > st
    26074 
    26075  > st
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    26077  > st
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    26115  > st
    26116 
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    26118 
    26119  > st
    26120 
    26121  > st
    26122 
    26123  > select clear
    26124 
    26125  > st
    26126 
    26127  > st
    26128 
    26129  > st
    26130 
    26131  > st
    26132 
    26133  > st
    26134 
    26135  > aw
    26136 
    26137  > isolde sim start sel
    26138 
    26139  > st
    26140 
    26141  > st
    26142 
    26143  > st
    26144 
    26145  > st
    26146 
    26147  > st
    26148 
    26149  > aw
    26150 
    26151  > isolde sim start sel
    26152 
    26153  > st
    26154 
    26155  > st
    26156 
    26157  > st
    26158 
    26159  > st
    26160 
    26161  > st
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    26163  > st
    26164 
    26165  > select clear
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    26167  > st
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    26169  > st
    26170 
    26171  > st
    26172 
    26173  > select clear
    26174 
    26175  > st
    26176 
    26177  > st
    26178 
    26179  > st
    26180 
    26181  > select up
    26182 
    26183  14 atoms, 14 bonds, 1 residue, 1 model selected
    26184 
    26185  > select up
    26186 
    26187  364 atoms, 368 bonds, 29 residues, 1 model selected
    26188 
    26189  > select clear
    26190 
    26191  > select clear
    26192 
    26193  > st
    26194 
    26195  > st
    26196 
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    26198 
    26199  > st
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    26205  > st
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    26207  > st
    26208 
    26209  > st
    26210 
    26211  > st
    26212 
    26213  > select clear
    26214 
    26215  > st
    26216 
    26217  > st
    26218 
    26219  > aw
    26220 
    26221  > isolde sim start sel
    26222 
    26223  > st
    26224 
    26225  > st
    26226 
    26227  > st
    26228 
    26229  > st
    26230 
    26231  > st
    26232 
    26233  > save working.cxs
    26234 
    26235  Taking snapshot of stepper: Model 1a
    26236 
    26237  > view /ap:30
    26238 
    26239  > st
    26240 
    26241  > st
    26242 
    26243  > st
    26244 
    26245  > st
    26246 
    26247  > st
    26248 
    26249  > st
    26250 
    26251  > select clear
    26252 
    26253  > st
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    26278 
    26279  > st
    26280 
    26281  > st
    26282 
    26283  > select clear
    26284 
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    26295  > st
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    26297  > st
    26298 
    26299  > st
    26300 
    26301  > st
    26302 
    26303  > select clear
    26304 
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    26306 
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    26311  > st
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    26357  > st
    26358 
    26359  > st
    26360 
    26361  > st
    26362 
    26363  > st
    26364 
    26365  > select clear
    26366 
    26367  > st
    26368 
    26369  > st
    26370 
    26371  > st
    26372 
    26373  > st
    26374 
    26375  > select clear
    26376 
    26377  > st
    26378 
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    26399  > st
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    26404 
    26405  > st
    26406 
    26407  > st
    26408 
    26409  > select clear
    26410 
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    26415  > st
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    26418 
    26419  > st
    26420 
    26421  > select clear
    26422 
    26423  > st
    26424 
    26425  > aw
    26426 
    26427  > isolde sim start sel
    26428 
    26429  > select clear
    26430 
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    26445  > select clear
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    26490 
    26491  > isolde sim start sel
    26492 
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    26560 
    26561  > st
    26562 
    26563  > st
    26564 
    26565  > select clear
    26566 
    26567  > st
    26568 
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    26570 
    26571  > st
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    26592 
    26593  > select clear
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    26650 
    26651  > st
    26652 
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    26654 
    26655  > st
    26656 
    26657  > aw
    26658 
    26659  > isolde sim start sel
    26660 
    26661  > st
    26662 
    26663  > st
    26664 
    26665  > st
    26666 
    26667  > st
    26668 
    26669  > st
    26670 
    26671  > st
    26672 
    26673  > st
    26674 
    26675  > st
    26676 
    26677  > st
    26678 
    26679  > select clear
    26680 
    26681  > st
    26682 
    26683  > st
    26684 
    26685  > st
    26686 
    26687  > st
    26688 
    26689  > st
    26690 
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    26692 
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    26700 
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    26702 
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    26704 
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    26706 
    26707  > st
    26708 
    26709  > st
    26710 
    26711  > st
    26712 
    26713  > st
    26714 
    26715  > select clear
    26716 
    26717  > st
    26718 
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    26720 
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    26722 
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    26724 
    26725  > st
    26726 
    26727  > select clear
    26728 
    26729  > st
    26730 
    26731  > st
    26732 
    26733  > st
    26734 
    26735  > st
    26736 
    26737  > st
    26738 
    26739  > st
    26740 
    26741  > st
    26742 
    26743  > st
    26744 
    26745  > aw
    26746 
    26747  > isolde sim start sel
    26748 
    26749  > select up
    26750 
    26751  3 atoms, 2 bonds, 1 residue, 1 model selected
    26752 
    26753  > delete sel
    26754 
    26755  > st
    26756 
    26757  > view /ap:30
    26758 
    26759  > isolde add ligand MQ8
    26760 
    26761  > isolde ignore ~sel
    26762 
    26763  ISOLDE: currently ignoring 5721 residues in model 8.2
    26764 
    26765  > color sel purple
    26766 
    26767  > color sel byhetero
    26768 
    26769  > select /a*:30
    26770 
    26771  320 atoms, 320 bonds, 16 residues, 1 model selected
    26772 
    26773  > select up
    26774 
    26775  125 atoms, 126 bonds, 1 residue, 1 model selected
    26776 
    26777  > isolde ~ignore sel
    26778 
    26779  ISOLDE: currently ignoring 5721 residues in model 8.2
    26780 
    26781  > select up
    26782 
    26783  125 atoms, 126 bonds, 1 residue, 1 model selected
    26784 
    26785  > isolde ignore sel
    26786 
    26787  ISOLDE: currently ignoring 5721 residues in model 8.2
    26788 
    26789  > select up
    26790 
    26791  125 atoms, 126 bonds, 1 residue, 1 model selected
    26792 
    26793  > select clear
    26794 
    26795  > isolde ~ignore
    26796 
    26797  > select up
    26798 
    26799  125 atoms, 126 bonds, 1 residue, 1 model selected
    26800 
    26801  > isolde ignore sel
    26802 
    26803  ISOLDE: currently ignoring 1 residues in model 8.2
    26804 
    26805  > select up
    26806 
    26807  125 atoms, 126 bonds, 1 residue, 1 model selected
    26808 
    26809  > select clear
    26810 
    26811  > select clear
    26812 
    26813  > select up
    26814 
    26815  270 atoms, 272 bonds, 3 residues, 1 model selected
    26816 
    26817  > clipper isolate sel contextDistance 0
    26818 
    26819  > clipper isolate sel contextDistance 0 maskRadius 7
    26820 
    26821  > clipper isolate sel contextDistance 0 maskRadius 5
    26822 
    26823  > clipper isolate sel contextDistance 0 maskRadius 6
    26824 
    26825  > select sel&~H
    26826 
    26827  117 atoms, 272 bonds, 3 residues, 2 models selected
    26828 
    26829  > save alt_mq8.pdb #8 selectedOnly true
    26830 
    26831  > select up
    26832 
    26833  125 atoms, 126 bonds, 1 residue, 1 model selected
    26834 
    26835  > delete sel
    26836 
    26837  > isolde ~ignore
    26838 
    26839  > select :CDL
    26840 
    26841  1280 atoms, 1275 bonds, 5 residues, 1 model selected
    26842 
    26843  > select clear
    26844 
    26845  > select /a*,b*
    26846 
    26847  37197 atoms, 37702 bonds, 1867 residues, 1 model selected
    26848 
    26849  > select /a*,b*&protein
    26850 
    26851  25462 atoms, 25870 bonds, 1614 residues, 1 model selected
    26852 
    26853  > select :CDL
    26854 
    26855  1280 atoms, 1275 bonds, 5 residues, 1 model selected
    26856 
    26857  > open
    26858  >
    26859  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/alt_mq8.pdb
    26860 
    26861  Summary of feedback from opening
    26862  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/alt_mq8.pdb
    26863  ---
    26864  warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A
    26865  2
    26866  TRP A 5 1 4
    26867  Start residue of secondary structure not found: HELIX 2 2 PRO A 10 PHE A
    26868  36 1
    26869  27
    26870  Start residue of secondary structure not found: HELIX 3 3 ALA A 40 TYR A
    26871  46 1
    26872  7
    26873  Start residue of secondary structure not found: HELIX 4 4 HIS A 2 TRP A 5
    26874  1 4
    26875  Start residue of secondary structure not found: HELIX 5 5 PRO A 10 GLN A
    26876  35 1
    26877  26
    26878  248 messages similar to the above omitted
    26879  Cannot find LINK/SSBOND residue CYS (95 )
    26880  Cannot find LINK/SSBOND residue CYS (98 )
    26881  Cannot find LINK/SSBOND residue CYS (146 )
    26882  Cannot find LINK/SSBOND residue CYS (149 )
    26883  Cannot find LINK/SSBOND residue CYS (216 )
    26884  25 messages similar to the above omitted
    26885 
    26886 
    26887  > view #1
    26888 
    26889  > select #1
    26890 
    26891  117 atoms, 119 bonds, 3 residues, 1 model selected
    26892 
    26893  > close #1
    26894 
    26895  > st
    26896 
    26897  > st
    26898 
    26899  > st
    26900 
    26901  > st
    26902 
    26903  > st
    26904 
    26905  > st
    26906 
    26907  > st
    26908 
    26909  > select clear
    26910 
    26911  > st
    26912 
    26913  > st
    26914 
    26915  > st
    26916 
    26917  > st
    26918 
    26919  > st
    26920 
    26921  > st
    26922 
    26923  > st
    26924 
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    26926 
    26927  > st
    26928 
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    26930 
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    26932 
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    26934 
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    26940 
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    26950 
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    26952 
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    26954 
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    26960 
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    26964 
    26965  > st
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    26970 
    26971  > st
    26972 
    26973  > st
    26974 
    26975  > st
    26976 
    26977  > st
    26978 
    26979  > select clear
    26980 
    26981  > st
    26982 
    26983  > st
    26984 
    26985  > select clear
    26986 
    26987  > st
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    26990 
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    27000 
    27001  > st
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    27005  > st
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    27007  > st
    27008 
    27009  > select clear
    27010 
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    27021  > st
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    27023  > st
    27024 
    27025  > st
    27026 
    27027  > st
    27028 
    27029  > st
    27030 
    27031  > select clear
    27032 
    27033  > st
    27034 
    27035  > st
    27036 
    27037  > st
    27038 
    27039  > st
    27040 
    27041  > st
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    27045  > st
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    27063  > st
    27064 
    27065  > st
    27066 
    27067  > st
    27068 
    27069  > st
    27070 
    27071  > st
    27072 
    27073  > st
    27074 
    27075  > select clear
    27076 
    27077  > st
    27078 
    27079  > st
    27080 
    27081  > st
    27082 
    27083  > st
    27084 
    27085  > st
    27086 
    27087  > st
    27088 
    27089  > st
    27090 
    27091  > st
    27092 
    27093  > select clear
    27094 
    27095  > st
    27096 
    27097  > st
    27098 
    27099  > st
    27100 
    27101  > st
    27102 
    27103  > st
    27104 
    27105  > st
    27106 
    27107  > st
    27108 
    27109  > st
    27110 
    27111  > st
    27112 
    27113  > st
    27114 
    27115  > select clear
    27116 
    27117  > select clear
    27118 
    27119  > st
    27120 
    27121  > st
    27122 
    27123  > st
    27124 
    27125  > st
    27126 
    27127  > st
    27128 
    27129  > st
    27130 
    27131  > st
    27132 
    27133  > st
    27134 
    27135  > select clear
    27136 
    27137  > st
    27138 
    27139  > st
    27140 
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    27163  > st
    27164 
    27165  > select clear
    27166 
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    27200 
    27201  > select clear
    27202 
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    27211  > st
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    27214 
    27215  > st
    27216 
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    27218 
    27219  > select clear
    27220 
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    27222 
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    27224 
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    27229  > st
    27230 
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    27232 
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    27234 
    27235  > st
    27236 
    27237  > select clear
    27238 
    27239  > st
    27240 
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    27242 
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    27294 
    27295  > st
    27296 
    27297  > st
    27298 
    27299  > st
    27300 
    27301  > select clear
    27302 
    27303  > st
    27304 
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    27306 
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    27310 
    27311  > st
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    27337  > st
    27338 
    27339  > st
    27340 
    27341  > st
    27342 
    27343  > st
    27344 
    27345  > select clear
    27346 
    27347  > st
    27348 
    27349  > st
    27350 
    27351  > st
    27352 
    27353  > st
    27354 
    27355  > st
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    27358 
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    27364 
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    27366 
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    27368 
    27369  > st
    27370 
    27371  > st
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    27376 
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    27380 
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    27383  > st
    27384 
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    27386 
    27387  > st
    27388 
    27389  > st
    27390 
    27391  > st
    27392 
    27393  > st
    27394 
    27395  > st
    27396 
    27397  > st
    27398 
    27399  > st
    27400 
    27401  > st
    27402 
    27403  > st
    27404 
    27405  > st
    27406 
    27407  > st
    27408 
    27409  > st
    27410 
    27411  > st
    27412 
    27413  > st
    27414 
    27415  > st
    27416 
    27417  > st
    27418 
    27419  > st
    27420 
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    27422 
    27423  > st
    27424 
    27425  > st
    27426 
    27427  > st
    27428 
    27429  > st
    27430 
    27431  > st
    27432 
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    27434 
    27435  > st
    27436 
    27437  > st
    27438 
    27439  > st
    27440 
    27441  > st
    27442 
    27443  > st
    27444 
    27445  > st
    27446 
    27447  > st
    27448 
    27449  > st
    27450 
    27451  > st
    27452 
    27453  > st
    27454 
    27455  > st
    27456 
    27457  > st
    27458 
    27459  > st
    27460 
    27461  > select clear
    27462 
    27463  > st
    27464 
    27465  > st
    27466 
    27467  > st
    27468 
    27469  > st
    27470 
    27471  > st
    27472 
    27473  > aw
    27474 
    27475  > isolde sim start sel
    27476 
    27477  > st
    27478 
    27479  > st
    27480 
    27481  > st
    27482 
    27483  > st
    27484 
    27485  > st
    27486 
    27487  > st
    27488 
    27489  > select clear
    27490 
    27491  > st
    27492 
    27493  > st
    27494 
    27495  > st
    27496 
    27497  > st
    27498 
    27499  > st
    27500 
    27501  > st
    27502 
    27503  > st
    27504 
    27505  > st
    27506 
    27507  > st
    27508 
    27509  > select clear
    27510 
    27511  > st
    27512 
    27513  > st
    27514 
    27515  > st
    27516 
    27517  > st
    27518 
    27519  > st
    27520 
    27521  > st
    27522 
    27523  > st
    27524 
    27525  > st
    27526 
    27527  > st
    27528 
    27529  > st
    27530 
    27531  > st
    27532 
    27533  > st
    27534 
    27535  > select clear
    27536 
    27537  > st
    27538 
    27539  > st
    27540 
    27541  > st
    27542 
    27543  > st
    27544 
    27545  > st
    27546 
    27547  > st
    27548 
    27549  > st
    27550 
    27551  > st
    27552 
    27553  > st
    27554 
    27555  > st
    27556 
    27557  > st
    27558 
    27559  > st
    27560 
    27561  > st
    27562 
    27563  > st
    27564 
    27565  > st
    27566 
    27567  > st
    27568 
    27569  > st
    27570 
    27571  > st
    27572 
    27573  > st
    27574 
    27575  > st
    27576 
    27577  > st
    27578 
    27579  > st
    27580 
    27581  > st
    27582 
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    27584 
    27585  > st
    27586 
    27587  > st
    27588 
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    27590 
    27591  > st
    27592 
    27593  > st
    27594 
    27595  > st
    27596 
    27597  > st
    27598 
    27599  > st
    27600 
    27601  > st
    27602 
    27603  > st
    27604 
    27605  > st
    27606 
    27607  > st
    27608 
    27609  > st
    27610 
    27611  > st
    27612 
    27613  > st
    27614 
    27615  > st
    27616 
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    27618 
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    27620 
    27621  > st
    27622 
    27623  > st
    27624 
    27625  > st
    27626 
    27627  > st
    27628 
    27629  > st
    27630 
    27631  > st
    27632 
    27633  > st
    27634 
    27635  > st
    27636 
    27637  > st
    27638 
    27639  > st
    27640 
    27641  > st
    27642 
    27643  > st
    27644 
    27645  > st
    27646 
    27647  > st
    27648 
    27649  > st
    27650 
    27651  > st
    27652 
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    27654 
    27655  > st
    27656 
    27657  > st
    27658 
    27659  > st
    27660 
    27661  > st
    27662 
    27663  > st
    27664 
    27665  > delete sel
    27666 
    27667  > st
    27668 
    27669  > st
    27670 
    27671  > st
    27672 
    27673  > st
    27674 
    27675  > select clear
    27676 
    27677  > st
    27678 
    27679  > st
    27680 
    27681  > st
    27682 
    27683  > st
    27684 
    27685  > st
    27686 
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    27688 
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    27690 
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    27692 
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    27694 
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    27696 
    27697  > st
    27698 
    27699  > st
    27700 
    27701  > st
    27702 
    27703  > st
    27704 
    27705  > st
    27706 
    27707  > st
    27708 
    27709  > st
    27710 
    27711  > st
    27712 
    27713  > st
    27714 
    27715  > st
    27716 
    27717  > st
    27718 
    27719  > st
    27720 
    27721  > st
    27722 
    27723  > st
    27724 
    27725  > save working.cxs
    27726 
    27727  Taking snapshot of stepper: Model 1a
    27728 
    27729  > ui tool show Shell
    27730 
    27731  /opt/UCSF/ChimeraX/lib/python3.7/site-
    27732  packages/IPython/core/history.py:226:
    27733  UserWarning: IPython History requires SQLite, your history will not be
    27734  saved
    27735  warn("IPython History requires SQLite, your history will not be saved")
    27736 
    27737  > save working.cxs
    27738 
    27739  Taking snapshot of stepper: Model 1a
    27740  Restoring stepper: Model 1a
    27741  opened ChimeraX session
    27742 
    27743  > select clear
    27744 
    27745  > aw
    27746 
    27747  > isolde sim start sel
    27748 
    27749  > isolde jumpto
    27750 
    27751  > select clear
    27752 
    27753  > isolde jumpto
    27754 
    27755  > select clear
    27756 
    27757  > select clear
    27758 
    27759  > aw
    27760 
    27761  > isolde sim start sel
    27762 
    27763  > isolde jumpto
    27764 
    27765  > select clear
    27766 
    27767  > select /AA-AD:1
    27768 
    27769  80 atoms, 76 bonds, 4 residues, 1 model selected
    27770 
    27771  > select clear
    27772 
    27773  Traceback (most recent call last):
    27774  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27775  packages/chimerax/isolde/isolde.py", line 2708, in
    27776  _start_sim_or_toggle_pause
    27777  self.start_sim()
    27778  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27779  packages/chimerax/isolde/isolde.py", line 2728, in start_sim
    27780  self.params, self.sim_params, excluded_residues = self.ignored_residues)
    27781  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27782  packages/chimerax/isolde/openmm/openmm_interface.py", line 580, in
    27783  __init__
    27784  self._prepare_validation_managers(mobile_atoms)
    27785  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27786  packages/chimerax/isolde/openmm/openmm_interface.py", line 753, in
    27787  _prepare_validation_managers
    27788  rota_a.restrict_to_selected_residues(mobile_res)
    27789  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27790  packages/chimerax/isolde/validation/rota_annotation.py", line 129, in
    27791  restrict_to_selected_residues
    27792  self.update_graphics()
    27793  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27794  packages/chimerax/isolde/validation/rota_annotation.py", line 191, in
    27795  update_graphics
    27796  non_favored_only = self._hide_favored)
    27797  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27798  packages/chimerax/isolde/molobject.py", line 1660, in
    27799  validate_scale_and_color_rotamers
    27800  non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
    27801  pointer(color_out))
    27802  IndexError: _Map_base::at
    27803 
    27804  IndexError: _Map_base::at
    27805 
    27806  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27807  packages/chimerax/isolde/molobject.py", line 1660, in
    27808  validate_scale_and_color_rotamers
    27809  non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
    27810  pointer(color_out))
    27811 
    27812  See log for complete Python traceback.
    27813 
    27814 
    27815  > save working_fme.cxs
    27816 
    27817  Taking snapshot of stepper: Model 1a
    27818  opened ChimeraX session
    27819 
    27820  > isolde start
    27821 
    27822  > set selectionWidth 4
    27823 
    27824  Done loading forcefield
    27825 
    27826  > select clear
    27827 
    27828  > select clear
    27829 
    27830  > st
    27831 
    27832  > isolde jumpto
    27833 
    27834  > ui tool show Shell
    27835 
    27836  /opt/UCSF/ChimeraX/lib/python3.7/site-
    27837  packages/IPython/core/history.py:226:
    27838  UserWarning: IPython History requires SQLite, your history will not be
    27839  saved
    27840  warn("IPython History requires SQLite, your history will not be saved")
    27841 
    27842  > isolde jumpto
    27843 
    27844  > aw
    27845 
    27846  > isolde sim start sel
    27847 
    27848  > select up
    27849 
    27850  3 atoms, 2 bonds, 1 residue, 1 model selected
    27851 
    27852  > delete sel
    27853 
    27854  > st
    27855 
    27856  > isolde jumpto
    27857 
    27858  > select clear
    27859 
    27860  > isolde jumpto
    27861 
    27862  > isolde jumpto
    27863 
    27864  > select clear
    27865 
    27866  > isolde jumpto
    27867 
    27868  > isolde jumpto
    27869 
    27870  > isolde jumpto
    27871 
    27872  > aw
    27873 
    27874  > isolde sim start sel
    27875 
    27876  > isolde jumpto
    27877 
    27878  > select clear
    27879 
    27880  > isolde jumpto
    27881 
    27882  > select clear
    27883 
    27884  > select clear
    27885 
    27886  > isolde jumpto
    27887 
    27888  > select clear
    27889 
    27890  > aw
    27891 
    27892  > isolde sim start sel
    27893 
    27894  > isolde jumpto
    27895 
    27896  > select clear
    27897 
    27898  > select clear
    27899 
    27900  > isolde jumpto
    27901 
    27902  > select clear
    27903 
    27904  > isolde jumpto
    27905 
    27906  > awsf
    27907 
    27908  > select clear
    27909 
    27910  > isolde jumpto
    27911 
    27912  > isolde jumpto
    27913 
    27914  > isolde jumpto
    27915 
    27916  > select clear
    27917 
    27918  > isolde jumpto
    27919 
    27920  > select clear
    27921 
    27922  > isolde jumpto
    27923 
    27924  > isolde jumpto
    27925 
    27926  > select clear
    27927 
    27928  > aw
    27929 
    27930  > isolde sim start sel
    27931 
    27932  > isolde jumpto
    27933 
    27934  > isolde jumpto
    27935 
    27936  > isolde jumpto
    27937 
    27938  > isolde jumpto
    27939 
    27940  > isolde jumpto
    27941 
    27942  > isolde jumpto
    27943 
    27944  > isolde jumpto
    27945 
    27946  > isolde jumpto
    27947 
    27948  > isolde jumpto
    27949 
    27950  > isolde jumpto
    27951 
    27952  > isolde jumpto
    27953 
    27954  > isolde jumpto
    27955 
    27956  > isolde jumpto
    27957 
    27958  > isolde jumpto
    27959 
    27960  > isolde jumpto
    27961 
    27962  > isolde jumpto
    27963 
    27964  > isolde jumpto
    27965 
    27966  > isolde jumpto
    27967 
    27968  > isolde jumpto
    27969 
    27970  > isolde jumpto
    27971 
    27972  > isolde jumpto
    27973 
    27974  > isolde jumpto
    27975 
    27976  > isolde jumpto
    27977 
    27978  > isolde jumpto
    27979 
    27980  > isolde jumpto
    27981 
    27982  > isolde jumpto
    27983 
    27984  > isolde jumpto
    27985 
    27986  > isolde jumpto
    27987 
    27988  > isolde jumpto
    27989 
    27990  > isolde jumpto
    27991 
    27992  > isolde jumpto
    27993 
    27994  > select clear
    27995 
    27996  > isolde jumpto
    27997 
    27998  > isolde jumpto
    27999 
    28000  > isolde jumpto
    28001 
    28002  > isolde jumpto
    28003 
    28004  Traceback (most recent call last):
    28005  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    28006  packages/chimerax/isolde/isolde.py", line 2708, in
    28007  _start_sim_or_toggle_pause
    28008  self.start_sim()
    28009  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    28010  packages/chimerax/isolde/isolde.py", line 2725, in start_sim
    28011  main_sel = self._last_main_sel = self._get_main_sim_selection()
    28012  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    28013  packages/chimerax/isolde/isolde.py", line 2908, in _get_main_sim_selection
    28014  raise TypeError('You must select at least one atom from the current '
    28015  TypeError: You must select at least one atom from the current working
    28016  model
    28017  prior to starting a simulation!
    28018 
    28019  TypeError: You must select at least one atom from the current working
    28020  model
    28021  prior to starting a simulation!
    28022 
    28023  File "/home/tic20/.local/share/ChimeraX/1.1/site-
    28024  packages/chimerax/isolde/isolde.py", line 2908, in _get_main_sim_selection
    28025  raise TypeError('You must select at least one atom from the current '
    28026 
    28027  See log for complete Python traceback.
    28028 
    28029 
    28030  > isolde jumpto
    28031 
    28032  > select clear
    28033 
    28034  > aw
    28035 
    28036  > isolde sim start sel
    28037 
    28038  > isolde jumpto
    28039 
    28040  > isolde jumpto
    28041 
    28042  > select clear
    28043 
    28044  > isolde jumpto
    28045 
    28046  > select clear
    28047 
    28048  > isolde jumpto
    28049 
    28050  > isolde jumpto
    28051 
    28052  > isolde jumpto
    28053 
    28054  > isolde jumpto
    28055 
    28056  > select clear
    28057 
    28058  > isolde jumpto
    28059 
    28060  > isolde jumpto
    28061 
    28062  > isolde jumpto
    28063 
    28064  > isolde jumpto
    28065 
    28066  > save working_fme.cxs
    28067 
    28068  Taking snapshot of stepper: Model 1a
    28069 
    28070  > select /A*,a*:1
    28071 
    28072  800 atoms, 760 bonds, 40 residues, 1 model selected
    28073 
    28074  > select clear
    28075 
    28076  > save working_fme.cxs
    28077 
    28078  Taking snapshot of stepper: Model 1a
    28079  opened ChimeraX session
    28080 
    28081  > isolde start
    28082 
    28083  > set selectionWidth 4
    28084 
    28085  Done loading forcefield
    28086 
    28087  > select clear
    28088 
    28089  > ui tool show Shell
    28090 
    28091  /opt/UCSF/ChimeraX/lib/python3.7/site-
    28092  packages/IPython/core/history.py:226:
    28093  UserWarning: IPython History requires SQLite, your history will not be
    28094  saved
    28095  warn("IPython History requires SQLite, your history will not be saved")
    28096 
    28097  > select ~protein&~:HOH
    28098 
    28099  34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected
    28100 
    28101  > select clear
    28102 
    28103  > aw
    28104 
    28105  > isolde sim start sel
    28106 
    28107  > select clear
    28108 
    28109  > select clear
    28110 
    28111  > aw
    28112 
    28113  > isolde sim start sel
    28114 
    28115  > delete sel
    28116 
    28117  > select clear
    28118 
    28119  > select clear
    28120 
    28121  > select clear
    28122 
    28123  > select clear
    28124 
    28125  > select clear
    28126 
    28127  > select clear
    28128 
    28129  > select clear
    28130 
    28131  > select clear
    28132 
    28133  > select clear
    28134 
    28135  > select clear
    28136 
    28137  > select clear
    28138 
    28139  > select clear
    28140 
    28141  > select clear
    28142 
    28143  > select clear
    28144 
    28145  > select clear
    28146 
    28147  > select clear
    28148 
    28149  > select clear
    28150 
    28151  > select clear
    28152 
    28153  > select clear
    28154 
    28155  > select clear
    28156 
    28157  > select clear
    28158 
    28159  > select clear
    28160 
    28161  > select clear
    28162 
    28163  > select clear
    28164 
    28165  > select clear
    28166 
    28167  > select clear
    28168 
    28169  > select clear
    28170 
    28171  > select clear
    28172 
    28173  > select clear
    28174 
    28175  > select clear
    28176 
    28177  > select clear
    28178 
    28179  > select clear
    28180 
    28181  > select clear
    28182 
    28183  > select clear
    28184 
    28185  > select clear
    28186 
    28187  > select clear
    28188 
    28189  > select clear
    28190 
    28191  > select clear
    28192 
    28193  > select clear
    28194 
    28195  > select clear
    28196 
    28197  > select up
    28198 
    28199  138 atoms, 139 bonds, 1 residue, 1 model selected
    28200 
    28201  > show sel
    28202 
    28203  > awsf
    28204 
    28205  > awsf
    28206 
    28207  > aw
    28208 
    28209  > isolde sim start sel
    28210 
    28211  > select clear
    28212 
    28213  > select clear
    28214 
    28215  > select clear
    28216 
    28217  > select clear
    28218 
    28219  > select clear
    28220 
    28221  > select clear
    28222 
    28223  > select clear
    28224 
    28225  > select clear
    28226 
    28227  > select clear
    28228 
    28229  > select clear
    28230 
    28231  > select clear
    28232 
    28233  > select clear
    28234 
    28235  > select clear
    28236 
    28237  > select clear
    28238 
    28239  > select clear
    28240 
    28241  > select clear
    28242 
    28243  > select clear
    28244 
    28245  > select clear
    28246 
    28247  > select clear
    28248 
    28249  > select clear
    28250 
    28251  > select clear
    28252 
    28253  > select clear
    28254 
    28255  > select clear
    28256 
    28257  > select clear
    28258 
    28259  > select up
    28260 
    28261  140 atoms, 148 bonds, 1 residue, 1 model selected
    28262 
    28263  > select clear
    28264 
    28265  > select clear
    28266 
    28267  > select clear
    28268 
    28269  > select clear
    28270 
    28271  > select clear
    28272 
    28273  > select clear
    28274 
    28275  > select ~protein&~:HOH
    28276 
    28277  34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 22 models selected
    28278 
    28279  > clipper isolate sel contextDistance 0
    28280 
    28281  > hide #!8.1 models
    28282 
    28283  > ~cartoon
    28284 
    28285  > cartoon
    28286 
    28287  > show #!8.1 models
    28288 
    28289  > save working.cxs
    28290 
    28291  Taking snapshot of stepper: Model 1a
    28292 
    28293  > isolde add ligand MQ9
    28294 
    28295  > ui mousemode right "translate selected atoms"
    28296 
    28297  > select up
    28298 
    28299  138 atoms, 139 bonds, 1 residue, 1 model selected
    28300 
    28301  > isolde ignore ~sel
    28302 
    28303  ISOLDE: currently ignoring 5734 residues in model 8.2
    28304 
    28305  > isolde ~ignore
    28306 
    28307  > select up
    28308 
    28309  138 atoms, 139 bonds, 1 residue, 1 model selected
    28310 
    28311  > select clear
    28312 
    28313  > select up
    28314 
    28315  138 atoms, 139 bonds, 1 residue, 1 model selected
    28316 
    28317  > delete sel
    28318 
    28319  > select clear
    28320 
    28321  > select clear
    28322 
    28323  > select clear
    28324 
    28325  > select clear
    28326 
    28327  > select clear
    28328 
    28329  > select clear
    28330 
    28331  > awsf
    28332 
    28333  > awsf
    28334 
    28335  > select clear
    28336 
    28337  > select clear
    28338 
    28339  > select clear
    28340 
    28341  > select up
    28342 
    28343  256 atoms, 255 bonds, 1 residue, 1 model selected
    28344 
    28345  > select clear
    28346 
    28347  > select up
    28348 
    28349  256 atoms, 255 bonds, 1 residue, 1 model selected
    28350 
    28351  > select clear
    28352 
    28353  > select clear
    28354 
    28355  > aw
    28356 
    28357  > isolde sim start sel
    28358 
    28359  > aw
    28360 
    28361  > isolde sim start sel
    28362 
    28363  > aw
    28364 
    28365  > isolde sim start sel
    28366 
    28367  > select clear
    28368 
    28369  > aw
    28370 
    28371  > isolde sim start sel
    28372 
    28373  > select clear
    28374 
    28375  > select clear
    28376 
    28377  > select clear
    28378 
    28379  > clipper set contourSensitivity 0.25
    28380 
    28381  > aw
    28382 
    28383  > isolde sim start sel
    28384 
    28385  > aw
    28386 
    28387  > isolde sim start sel
    28388 
    28389  > aw
    28390 
    28391  > isolde sim start sel
    28392 
    28393  > select clear
    28394 
    28395  > select clear
    28396 
    28397  > aw
    28398 
    28399  > isolde sim start sel
    28400 
    28401  > aw
    28402 
    28403  > isolde sim start sel
    28404 
    28405  > awsf
    28406 
    28407  > awsf
    28408 
    28409  > aw
    28410 
    28411  > isolde sim start sel
    28412 
    28413  > select clear
    28414 
    28415  > aw
    28416 
    28417  > isolde sim start sel
    28418 
    28419  > select clear
    28420 
    28421  > aw
    28422 
    28423  > isolde sim start sel
    28424 
    28425  > select clear
    28426 
    28427  > aw
    28428 
    28429  > isolde sim start sel
    28430 
    28431  > select clear
    28432 
    28433  > isolde add ligand LMT
    28434 
    28435  > ui mousemode right "translate selected atoms"
    28436 
    28437  > awsf
    28438 
    28439  > awsf
    28440 
    28441  > awsf
    28442 
    28443  > select clear
    28444 
    28445  > select up
    28446 
    28447  6 atoms, 4 bonds, 2 residues, 1 model selected
    28448 
    28449  > delete sel
    28450 
    28451  > select clear
    28452 
    28453  > save working.cxs
    28454 
    28455  Taking snapshot of stepper: Model 1a
    28456 
    28457  > select clear
    28458 
    28459  > save working.cxs
    28460 
    28461  Taking snapshot of stepper: Model 1a
    28462 
    28463  > save working.cxs
    28464 
    28465  Taking snapshot of stepper: Model 1a
    28466 
    28467  > open ../jsg.pdb
    28468 
    28469  Summary of feedback from opening ../jsg.pdb
    28470  ---
    28471  warnings | Start residue of secondary structure not found: HELIX 1 1 THR A
    28472  43
    28473  GLY A 51 1 9
    28474  Start residue of secondary structure not found: HELIX 2 2 PRO A 71 ALA A
    28475  76 1
    28476  6
    28477  Start residue of secondary structure not found: HELIX 3 3 SER A 94 VAL A
    28478  102 1
    28479  9
    28480  Start residue of secondary structure not found: HELIX 4 4 ARG A 114 PHE A
    28481  125
    28482  1 12
    28483  Start residue of secondary structure not found: HELIX 5 5 ARG A 144 LEU A
    28484  152
    28485  1 9
    28486  60 messages similar to the above omitted
    28487 
    28488 
    28489  > select #1
    28490 
    28491  200 atoms, 206 bonds, 1 residue, 1 model selected
    28492 
    28493  > close #1
    28494 
    28495  > open ../jsg.pdb
    28496 
    28497  Summary of feedback from opening ../jsg.pdb
    28498  ---
    28499  warnings | Start residue of secondary structure not found: HELIX 1 1 THR A
    28500  43
    28501  GLY A 51 1 9
    28502  Start residue of secondary structure not found: HELIX 2 2 PRO A 71 ALA A
    28503  76 1
    28504  6
    28505  Start residue of secondary structure not found: HELIX 3 3 SER A 94 VAL A
    28506  102 1
    28507  9
    28508  Start residue of secondary structure not found: HELIX 4 4 ARG A 114 PHE A
    28509  125
    28510  1 12
    28511  Start residue of secondary structure not found: HELIX 5 5 ARG A 144 LEU A
    28512  152
    28513  1 9
    28514  60 messages similar to the above omitted
    28515 
    28516 
    28517  > select #1
    28518 
    28519  200 atoms, 206 bonds, 1 residue, 1 model selected
    28520 
    28521  > ui mousemode right "translate selected atoms"
    28522 
    28523  > close #1
    28524 
    28525  > select clear
    28526 
    28527  > select clear
    28528 
    28529  > select clear
    28530 
    28531  > isolde add ligand GAL
    28532 
    28533  Deleted the following atoms from residue GAL L837: O1, HO1
    28534 
    28535  > show sel
    28536 
    28537  > ui mousemode right "translate selected atoms"
    28538 
    28539  > delete sel
    28540 
    28541  > isolde add ligand GLC
    28542 
    28543  Deleted the following atoms from residue GLC L837: HO1, O1
    28544 
    28545  > show sel
    28546 
    28547  > delete sel
    28548 
    28549  > isolde add ligand NAG
    28550 
    28551  Deleted the following atoms from residue NAG L837: O1, HO1
    28552 
    28553  > show sel
    28554 
    28555  > delete sel
    28556 
    28557  > select clear
    28558 
    28559  > aw
    28560 
    28561  > isolde sim start sel
    28562 
    28563  > select up
    28564 
    28565  133 atoms, 132 bonds, 1 residue, 1 model selected
    28566 
    28567  > select clear
    28568 
    28569  > select up
    28570 
    28571  141 atoms, 141 bonds, 1 residue, 1 model selected
    28572 
    28573  > select up
    28574 
    28575  141 atoms, 141 bonds, 1 residue, 1 model selected
    28576 
    28577  > awsf
    28578 
    28579  > awsf
    28580 
    28581  > ui mousemode right "mark point"
    28582 
    28583  > marker #1 position 206,174.5,206.2 color yellow radius 1
    28584 
    28585  > marker #1 position 208.1,175.1,203.3 color yellow radius 1
    28586 
    28587  > marker #1 position 210.5,177.7,202.2 color yellow radius 1
    28588 
    28589  > marker #1 position 209.7,176.4,199 color yellow radius 1
    28590 
    28591  > marker #1 position 213.2,175.9,196.8 color yellow radius 1
    28592 
    28593  > delete sel
    28594 
    28595  > marker #1 position 211.3,175.1,196.4 color yellow radius 1
    28596 
    28597  > marker #1 position 214.6,172.1,194.3 color yellow radius 1
    28598 
    28599  > delete sel
    28600 
    28601  > marker #1 position 213.4,173.4,193.2 color yellow radius 1
    28602 
    28603  > marker #1 position 216.9,174.5,192.6 color yellow radius 1
    28604 
    28605  > delete sel
    28606 
    28607  > marker #1 position 215.5,174.8,190.6 color yellow radius 1
    28608 
    28609  > marker #1 position 214.8,175.9,188.4 color yellow radius 1
    28610 
    28611  > view /aj:12
    28612 
    28613  > marker #1 position 198.9,164,186.4 color yellow radius 1
    28614 
    28615  > marker #1 position 199.1,162.2,189.3 color yellow radius 1
    28616 
    28617  > marker #1 position 197.6,159.5,191.3 color yellow radius 1
    28618 
    28619  > marker #1 position 197.1,156.2,191.5 color yellow radius 1
    28620 
    28621  > marker #1 position 196.1,153.9,193.2 color yellow radius 1
    28622 
    28623  > marker #1 position 195,153.8,196.9 color yellow radius 1
    28624 
    28625  > marker #1 position 195.7,152.3,200.4 color yellow radius 1
    28626 
    28627  > marker #1 position 195.6,150.6,201.3 color yellow radius 1
    28628 
    28629  > marker #1 position 193.5,148.1,198.7 color yellow radius 1
    28630 
    28631  > marker #1 position 194.5,149.2,200.1 color yellow radius 1
    28632 
    28633  > marker #1 position 193.2,148,196.4 color yellow radius 1
    28634 
    28635  > marker #1 position 197.7,166.8,183.9 color yellow radius 1
    28636 
    28637  > select /a*:12
    28638 
    28639  384 atoms, 368 bonds, 16 residues, 1 model selected
    28640 
    28641  > open
    28642  >
    28643  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/class4b_r_2.35A_postprocess_masked.mrc
    28644 
    28645  Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400,
    28646  pixel
    28647  0.999, shown at level 0.0164, step 2, values float32
    28648 
    28649  > volume #8.1.1.1 level 0.03142
    28650 
    28651  > volume #8.1.1.1 level 0.02833
    28652 
    28653  > volume zone #2 nearAtoms #1 range 5
    28654 
    28655  > volume #2 step 1
    28656 
    28657  > volume #2 level 0.03435
    28658 
    28659  > volume #2 level 0.02539
    28660 
    28661  > volume zone #2 nearAtoms #1 range 4
    28662 
    28663  > volume #2 level 0.0224
    28664 
    28665  > save unknown_density_tubes.mrc #2
    28666 
    28667  > usage volume zone
    28668 
    28669  volume zone volumes nearAtoms an atoms specifier [range a number]
    28670  [bondPointSpacing a number] [minimalBounds true or false] [newMap true or
    28671  false] [invert true or false] [subregion map region] [step map step]
    28672  [modelId
    28673  modelId]
    28674  — Zero map values beyond a distance range from atoms
    28675  modelId: a model id
    28676 
    28677  > volume zone #2 nearAtoms #1 range 4 minimalBounds true
    28678 
    28679  > select #2
    28680 
    28681  4 models selected
    28682 
    28683  > volume sel showOutlineBox true
    28684 
    28685  > save unknown_density_tubes.mrc #2
    28686 
    28687  > open unknown_density_tubes.mrc
    28688 
    28689  Opened unknown_density_tubes.mrc, grid size 32,39,32, pixel
    28690  0.999,0.999,0.999,
    28691  shown at level 0.0972, step 1, values float32
    28692 
    28693  > hide #!2 models
    28694 
    28695  > volume #3 level 0.05529
    28696 
    28697  > volume #3 level 0.05219
    28698 
    28699  > volume #3 level 0.02932
    28700 
    28701  > volume #3 level 0.04173
    28702 
    28703  > close #3
    28704 
    28705  > show #!2 models
    28706 
    28707  > save unknown_density_tubes.ccp4 #2
    28708 
    28709  No known data format for file suffix '.ccp4'
    28710 
    28711  > save unknown_density_tubes.map #2
    28712 
    28713  No known data format for file suffix '.map'
    28714 
    28715  > surface unzone #2
    28716 
    28717  > volume zone #2 nearAtoms #1 range 4
    28718 
    28719  > surface unzone #2
    28720 
    28721  > volume zone #2 nearAtoms #1 range 4 minimalBounds true newMap true
    28722 
    28723  > hide #!3 models
    28724 
    28725  > show #!3 models
    28726 
    28727  > surface unzone #3
    28728 
    28729  > save unknown_density_tubes.mrc #3
    28730 
    28731  > open unknown_density_tubes.mrc
    28732 
    28733  Opened unknown_density_tubes.mrc, grid size 32,39,32, pixel
    28734  0.999,0.999,0.999,
    28735  shown at level 0.0254, step 1, values float32
    28736 
    28737  > hide #!3 models
    28738 
    28739  > close #1#2-4
    28740 
    28741  > select clear
    28742 
    28743  > select clear
    28744 
    28745  > aw
    28746 
    28747  > isolde sim start sel
    28748 
    28749  > select up
    28750 
    28751  3 atoms, 2 bonds, 1 residue, 1 model selected
    28752 
    28753  > delete sel
    28754 
    28755  > select clear
    28756 
    28757  > aw
    28758 
    28759  > isolde sim start sel
    28760 
    28761  > select up
    28762 
    28763  3 atoms, 2 bonds, 1 residue, 1 model selected
    28764 
    28765  > delete sel
    28766 
    28767  > aw
    28768 
    28769  > isolde sim start sel
    28770 
    28771  > select clear
    28772 
    28773  > select up
    28774 
    28775  81 atoms, 82 bonds, 1 residue, 1 model selected
    28776 
    28777  > delete sel
    28778 
    28779  > select clear
    28780 
    28781  > select clear
    28782 
    28783  > select clear
    28784 
    28785  > select clear
    28786 
    28787  > save working.cxs
    28788 
    28789  Taking snapshot of stepper: Model 1a
    28790  Restoring stepper: Model 1a
    28791  opened ChimeraX session
    28792 
    28793  > volume unzone
    28794 
    28795  Missing or invalid "volumes" argument: empty atom specifier
    28796 
    28797  > volume unzone #8
    28798 
    28799  > close #8.1
    28800 
    28801  > open
    28802  >
    28803  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/class4b_r_2.35A_postprocess_masked.mrc
    28804 
    28805  Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400,
    28806  pixel
    28807  0.999, shown at level 0.0164, step 2, values float32
    28808 
    28809  > volume gaussian #1 bfactor 50
    28810 
    28811  > clipper associate #1,2 toModel #8
    28812 
    28813  > clipper set contourSensitivity 0.25
    28814 
    28815  > select ~protein&~:HOH
    28816 
    28817  34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected
    28818 
    28819  > select clear
    28820 
    28821  > select clear
    28822 
    28823  > save working.cxs
    28824 
    28825  Taking snapshot of stepper: Model 1a
    28826 
    28827  > save working.cxs
    28828 
    28829  Taking snapshot of stepper: Model 1a
    28830 
    28831  > select clear
    28832 
    28833  > select up
    28834 
    28835  124 atoms, 122 bonds, 2 residues, 1 model selected
    28836 
    28837  > delete sel
    28838 
    28839  > isolde add ligand CDL
    28840 
    28841  place_ligand() was called with use_md_template=True, but no suitable
    28842  template
    28843  was found. This command has been ignored.
    28844 
    28845  > select up
    28846 
    28847  256 atoms, 255 bonds, 1 residue, 1 model selected
    28848 
    28849  > ui mousemode right "translate selected atoms"
    28850 
    28851  > select up
    28852 
    28853  256 atoms, 255 bonds, 1 residue, 1 model selected
    28854 
    28855  > isolde ignore ~sel
    28856 
    28857  ISOLDE: currently ignoring 5754 residues in model 8.2
    28858 
    28859  > isolde ~ignore
    28860 
    28861  > select up
    28862 
    28863  256 atoms, 255 bonds, 1 residue, 1 model selected
    28864 
    28865  > select clear
    28866 
    28867  > select up
    28868 
    28869  256 atoms, 255 bonds, 1 residue, 1 model selected
    28870 
    28871  > select clear
    28872 
    28873  > isolde ~ignore
    28874 
    28875  > select clear
    28876 
    28877  > select clear
    28878 
    28879  > select clear
    28880 
    28881  > select up
    28882 
    28883  49 atoms, 50 bonds, 2 residues, 1 model selected
    28884 
    28885  > select clear
    28886 
    28887  > save working.cxs
    28888 
    28889  Taking snapshot of stepper: Model 1a
    28890 
    28891  > select #1
    28892 
    28893  Nothing selected
    28894 
    28895  > select #8
    28896 
    28897  114704 atoms, 116622 bonds, 15 pseudobonds, 5755 residues, 23 models
    28898  selected
    28899 
    28900  > select clear
    28901 
    28902  > volume zone #8.1.1.1 nearAtoms #8 range 2.5 newMap true
    28903 
    28904  > volume subtract #8.1.1.1 #1
    28905 
    28906  > close #1
    28907 
    28908  > show #!8.1.1.1 models
    28909 
    28910  > isolde add ligand LMT
    28911 
    28912  > ui mousemode right "translate selected atoms"
    28913 
    28914  > isolde ignore ~sel
    28915 
    28916  ISOLDE: currently ignoring 5755 residues in model 8.2
    28917 
    28918  > isolde ~ignore
    28919 
    28920  > hide #!2 models
    28921 
    28922  > ui mousemode right "mark point"
    28923 
    28924  > marker #1 position 243.7,161,187.6 color yellow radius 1
    28925 
    28926  > ui mousemode right "resize markers"
    28927 
    28928  > marker change #1:24 radius 3.127
    28929 
    28930  > show #!2 models
    28931 
    28932  > hide #!2 models
    28933 
    28934  > isolde add ligand LMT
    28935 
    28936  > ui mousemode right "translate selected atoms"
    28937 
    28938  > select up
    28939 
    28940  14 atoms, 13 bonds, 1 residue, 1 model selected
    28941 
    28942  > select up
    28943 
    28944  50 atoms, 49 bonds, 4 residues, 1 model selected
    28945 
    28946  > isolde ignore sel
    28947 
    28948  ISOLDE: currently ignoring 4 residues in model 8.2
    28949 
    28950  > isolde ~ignore
    28951 
    28952  > select clear
    28953 
    28954  > select up
    28955 
    28956  81 atoms, 82 bonds, 1 residue, 1 model selected
    28957 
    28958  > delete sel
    28959 
    28960  > ui mousemode right "mark point"
    28961 
    28962  > marker #1 position 204.4,140.7,186.9 color yellow radius 3.127
    28963 
    28964  > color sel red
    28965 
    28966  > select clear
    28967 
    28968  > show #!2 models
    28969 
    28970  > hide #!2 models
    28971 
    28972  > show #!2 models
    28973 
    28974  > hide #1 models
    28975 
    28976  > sequence chain /C
    28977 
    28978  Chains must have same sequence
    28979 
    28980  > sequence chain #8/C
    28981 
    28982  Chains must have same sequence
    28983 
    28984  > select #8/C
    28985 
    28986  5225 atoms, 5244 bonds, 4 pseudobonds, 395 residues, 2 models selected
    28987 
    28988  > hide #!2 models
    28989 
    28990  > select clear
    28991 
    28992  > select clear
    28993 
    28994  > delete sel
    28995 
    28996  > save working.cxs
    28997 
    28998  Taking snapshot of stepper: Model 1a
    28999 
    29000  > select up
    29001 
    29002  216 atoms, 217 bonds, 12 residues, 1 model selected
    29003 
    29004  > select clear
    29005 
    29006  > select clear
    29007 
    29008  > save working.cxs
    29009 
    29010  Taking snapshot of stepper: Model 1a
    29011 
    29012  > save model1a_fully_rebuilt.cif #8
    29013 
    29014  Not saving entity_poly_seq for non-authoritative sequences
    29015 
    29016  > save working.cxs
    29017 
    29018  Taking snapshot of stepper: Model 1a
    29019  opened ChimeraX session
    29020 
    29021  > select #1/A*:BCL
    29022 
    29023  Nothing selected
    29024 
    29025  > select #8/A*:BCL
    29026 
    29027  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    29028 
    29029  > select clear
    29030 
    29031  > isolde start
    29032 
    29033  > set selectionWidth 4
    29034 
    29035  Done loading forcefield
    29036 
    29037  > select #8/A*:BCL
    29038 
    29039  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    29040 
    29041  > select clear
    29042 
    29043  > awsf
    29044 
    29045  > awsf
    29046 
    29047  > awsf
    29048 
    29049  > awsf
    29050 
    29051  > open
    29052  >
    29053  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/model1a_fully_rebuilt.cif
    29054 
    29055  Summary of feedback from opening
    29056  /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/model1a_fully_rebuilt.cif
    29057  ---
    29058  warnings | Unknown polymer entity '1' near line 610
    29059  Unknown polymer entity '2' near line 2941
    29060  Unknown polymer entity '3' near line 6564
    29061  Unknown polymer entity '4' near line 29734
    29062  Unknown polymer entity '5' near line 30743
    29063  5 messages similar to the above omitted
    29064  Unable to fetch template for 'LMX': might have incorrect bonds
    29065  Unknown polymer entity '11' near line 71410
    29066  Unknown polymer entity '12' near line 78114
    29067  Unknown polymer entity '13' near line 89914
    29068  Unknown polymer entity '14' near line 95896
    29069  Atom C1 is not in the residue template for GPC /AA:201
    29070  Atom C1 is not in the residue template for GPC /AB:201
    29071  Atom C1 is not in the residue template for GPC /AC:201
    29072  Atom C1 is not in the residue template for GPC /AD:201
    29073  Atom C1 is not in the residue template for GPC /AE:201
    29074  19 messages similar to the above omitted
    29075  Atom H is not in the residue template for GLY /BQ:5
    29076  Atom H is not in the residue template for GLY /BR:5
    29077  Atom H is not in the residue template for GLY /BS:5
    29078  Atom H is not in the residue template for GLY /BT:5
    29079  Atom H is not in the residue template for GLY /C:13
    29080  Atom O2 is not in the residue template for GUX /C:1001
    29081  Atom H6 is not in the residue template for P5S /H1:1001
    29082  Atom H11 is not in the residue template for BPH /L:606
    29083  Atom H11 is not in the residue template for BPH /M:605
    29084  Atom C1 is not in the residue template for RCC /M:701
    29085  Atom O2 is not in the residue template for GUX /M:1001
    29086  Atom HN2 is not in the residue template for ARG /ak:71
    29087  Atom C1 is not in the residue template for GPC /ba:100
    29088  Atom C1 is not in the residue template for GPC /bb:100
    29089  Atom C26 is not in the residue template for PEX /bb:203
    29090  Atom C26 is not in the residue template for PEX /bb:204
    29091  Atom C1 is not in the residue template for GPC /bc:100
    29092  Atom C1 is not in the residue template for GPC /bd:100
    29093  Atom C26 is not in the residue template for PEX /bd:211
    29094  Atom C26 is not in the residue template for PEX /bd:209
    29095  Atom C1 is not in the residue template for GPC /be:100
    29096  Atom C26 is not in the residue template for PEX /be:205
    29097  Atom C1 is not in the residue template for GPC /bf:100
    29098  Atom C26 is not in the residue template for PEX /bf:212
    29099  Atom C1 is not in the residue template for GPC /bg:100
    29100  Atom C1 is not in the residue template for GPC /bh:100
    29101  Atom C26 is not in the residue template for PEX /bh:209
    29102  Atom C26 is not in the residue template for PEX /bh:207
    29103  Atom C1 is not in the residue template for GPC /bi:100
    29104  Atom C1 is not in the residue template for GPC /bj:100
    29105  Atom C26 is not in the residue template for PEX /bj:210
    29106  Atom C26 is not in the residue template for PEX /bj:208
    29107  Atom C1 is not in the residue template for GPC /bk:100
    29108  Atom C1 is not in the residue template for GPC /bl:100
    29109  Atom C26 is not in the residue template for PEX /bl:204
    29110  Atom C26 is not in the residue template for PEX /bl:206
    29111  Atom C1 is not in the residue template for GPC /bm:100
    29112  Atom C1 is not in the residue template for GPC /bn:100
    29113  Atom C26 is not in the residue template for PEX /bn:209
    29114  Atom C26 is not in the residue template for PEX /bn:207
    29115  Atom C1 is not in the residue template for GPC /bo:100
    29116  Atom C26 is not in the residue template for PEX /bp:206
    29117  Atom C1 is not in the residue template for GPC /bp:100
    29118  Atom C26 is not in the residue template for PEX /bp:204
    29119  Atom O2 is not in the residue template for GUX /M:1001
    29120  Atom O2 is not in the residue template for GUX /C:1001
    29121  Missing or incomplete entity_poly_seq table. Inferred polymer
    29122  connectivity.
    29123 
    29124  Chain information for model1a_fully_rebuilt.cif #3
    29125  ---
    29126  Chain | Description
    29127  AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?
    29128  AC AD | ?
    29129  BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk
    29130  bl
    29131  bm bo bp | ?
    29132  BB BD BE BI BQ BR BS BT BV BW bn | ?
    29133  C | ?
    29134  C1 | ?
    29135  H1 | ?
    29136  H2 | ?
    29137  L | ?
    29138  M | ?
    29139  aa ab ad ae af ag ah ai aj al am ao | ?
    29140  ac | ?
    29141  ak an | ?
    29142  ap | ?
    29143 
    29144 
    29145  > hide #1*protein
    29146 
    29147  Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    29148  'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
    29149 
    29150  > hide #1&protein
    29151 
    29152  > hide #3&protein
    29153 
    29154  > close #1#2
    29155 
    29156  > matchmaker #3/AC to #8/AB
    29157 
    29158  Parameters
    29159  ---
    29160  Chain pairing | bb
    29161  Alignment algorithm | Needleman-Wunsch
    29162  Similarity matrix | BLOSUM-62
    29163  SS fraction | 0.3
    29164  Gap open (HH/SS/other) | 18/18/6
    29165  Gap extend | 1
    29166  SS matrix |  |  | H | S | O
    29167  ---|---|---|---
    29168  H | 6 | -9 | -6
    29169  S |  | 6 | -6
    29170  O |  |  | 4
    29171  Iteration cutoff | 2
    29172 
    29173  Matchmaker Model 1a, chain AB (#8.2) with model1a_fully_rebuilt.cif, chain
    29174  AC
    29175  (#3), sequence alignment score = 261.6
    29176  RMSD between 48 pruned atom pairs is 0.331 angstroms; (across all 48
    29177  pairs:
    29178  0.331)
    29179 
    29180 
    29181  > color #3 tan
    29182 
    29183  > color byhetero
    29184 
    29185  > hide #!3 models
    29186 
    29187  > awsf
    29188 
    29189  > awsf
    29190 
    29191  > select clear
    29192 
    29193  > show #!3 models
    29194 
    29195  > matchmaker #3/AG to #8/AF
    29196 
    29197  Parameters
    29198  ---
    29199  Chain pairing | bb
    29200  Alignment algorithm | Needleman-Wunsch
    29201  Similarity matrix | BLOSUM-62
    29202  SS fraction | 0.3
    29203  Gap open (HH/SS/other) | 18/18/6
    29204  Gap extend | 1
    29205  SS matrix |  |  | H | S | O
    29206  ---|---|---|---
    29207  H | 6 | -9 | -6
    29208  S |  | 6 | -6
    29209  O |  |  | 4
    29210  Iteration cutoff | 2
    29211 
    29212  Matchmaker Model 1a, chain AF (#8.2) with model1a_fully_rebuilt.cif, chain
    29213  AG
    29214  (#3), sequence alignment score = 262.1
    29215  RMSD between 49 pruned atom pairs is 0.317 angstroms; (across all 49
    29216  pairs:
    29217  0.317)
    29218 
    29219 
    29220  > hide #!3 models
    29221 
    29222  > select clear
    29223 
    29224  > aw
    29225 
    29226  > isolde sim start sel
    29227 
    29228  > awsf
    29229 
    29230  > awsf
    29231 
    29232  > awsf
    29233 
    29234  > awsf
    29235 
    29236  > show #!3 models
    29237 
    29238  > matchmaker #3/AM to #1/AL
    29239 
    29240  No 'to' model specified
    29241 
    29242  > hide #!3 models
    29243 
    29244  > awsf
    29245 
    29246  > awsf
    29247 
    29248  > awsf
    29249 
    29250  > awsf
    29251 
    29252  > show #!3 models
    29253 
    29254  > matchmaker #3/AP to #1/AO
    29255 
    29256  No 'to' model specified
    29257 
    29258  > matchmaker #3/AP to #8/AO
    29259 
    29260  Parameters
    29261  ---
    29262  Chain pairing | bb
    29263  Alignment algorithm | Needleman-Wunsch
    29264  Similarity matrix | BLOSUM-62
    29265  SS fraction | 0.3
    29266  Gap open (HH/SS/other) | 18/18/6
    29267  Gap extend | 1
    29268  SS matrix |  |  | H | S | O
    29269  ---|---|---|---
    29270  H | 6 | -9 | -6
    29271  S |  | 6 | -6
    29272  O |  |  | 4
    29273  Iteration cutoff | 2
    29274 
    29275  Matchmaker Model 1a, chain AO (#8.2) with model1a_fully_rebuilt.cif, chain
    29276  AP
    29277  (#3), sequence alignment score = 271.3
    29278  RMSD between 49 pruned atom pairs is 0.357 angstroms; (across all 49
    29279  pairs:
    29280  0.357)
    29281 
    29282 
    29283  > hide #!3 models
    29284 
    29285  > awsf
    29286 
    29287  > awsf
    29288 
    29289  > awsf
    29290 
    29291  > select clear
    29292 
    29293  > show #!3 models
    29294 
    29295  > hide #!3 models
    29296 
    29297  > awsf
    29298 
    29299  > awsf
    29300 
    29301  > select clear
    29302 
    29303  > awsf
    29304 
    29305  > awsf
    29306 
    29307  > show #!3 models
    29308 
    29309  > hide #!3 models
    29310 
    29311  > awsf
    29312 
    29313  > awsf
    29314 
    29315  > awsf
    29316 
    29317  > awsf
    29318 
    29319  > select clear
    29320 
    29321  > save working.cxs
    29322 
    29323  Taking snapshot of stepper: Model 1a
    29324 
    29325  > select #8/A*:BCL
    29326 
    29327  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    29328 
    29329  > select clear
    29330 
    29331  > select #8/A*:BCL
    29332 
    29333  6720 atoms, 7104 bonds, 48 residues, 1 model selected
    29334 
    29335  > save working.cxs
    29336 
    29337  Taking snapshot of stepper: Model 1a
    29338  opened ChimeraX session
    29339 
    29340  > isolde start
    29341 
    29342  > set selectionWidth 4
    29343 
    29344  Done loading forcefield
    29345 
    29346  > view /M:609
    29347 
    29348  No objects specified.
    29349 
    29350  > view /M:608
    29351 
    29352  > select clear
    29353 
    29354  > select clear
    29355 
    29356  > select clear
    29357 
    29358  > close #1
    29359 
    29360  > select up
    29361 
    29362  138 atoms, 139 bonds, 1 residue, 1 model selected
    29363 
    29364  > isolde replace ligand sel MQ8
    29365 
    29366  Deleted the following atoms from residue MQ9 M608: H48, C47, H512, C49,
    29367  H501,
    29368  C50, H471, H503, H511, C48, H513, H502, C51, H472
    29369 
    29370  124 atoms were automatically renamed to match the template: O1->O4,
    29371  C1->C4,
    29372  C2->C5, C6->C3, C7->C11, C5->C2, C8->C12, C9->C13, H8->H121, C10->C14,
    29373  C11->C15, C12->C16, C13->C17, C14->C18, H13->H171, C15->C19, C16->C20,
    29374  C17->C21, C18->C22, C19->C23, H18->H221, C20->C24, C21->C25, C22->C26,
    29375  C23->C27, C24->C28, H23->H271, C25->C29, C26->C30, C27->C31, C28->C32,
    29376  C29->C33, H28->H321, C30->C34, C31->C35, C32->C36, C33->C37, C34->C38,
    29377  H33->H371, C35->C39, C36->C40, C37->C41, C38->C42, C39->C43, H38->H421,
    29378  C40->C45, C41->C44, C42->C46, C43->C47, C44->C48, H43->H471, C45->C49,
    29379  C46->C50, C5M->C2M, C4->C1, C3->C10, C3A->C9, C3B->C8, C3C->C7, C3D->C6,
    29380  O4->O1, H3A->H91, H3B->H81, H3C->H71, H3D->H61, H111->H151, H112->H152,
    29381  H121->H161, H122->H162, H161->H201, H162->H202, H171->H211, H172->H212,
    29382  H211->H251, H212->H252, H221->H261, H222->H262, H261->H301, H262->H302,
    29383  H271->H311, H272->H312, H311->H351, H312->H352, H321->H361, H322->H362,
    29384  H361->H401, H362->H402, H371->H411, H372->H412, H411->H441, H412->H442,
    29385  H421->H461, H422->H462, H71->H111, H72->H112, H461->H501, H462->H502,
    29386  H101->H141, H102->H142, H103->H143, H151->H191, H152->H192, H153->H193,
    29387  H201->H241, H202->H242, H203->H243, H251->H291, H252->H292, H253->H293,
    29388  H301->H341, H302->H342, H303->H343, H351->H391, H352->H392, H353->H393,
    29389  H401->H451, H402->H452, H403->H453, H451->H491, H452->H492, H453->H493,
    29390  H5M1->H2M1, H5M2->H2M2, H5M3->H2M3
    29391 
    29392  > show sel
    29393 
    29394  > select :CDL
    29395 
    29396  1536 atoms, 1530 bonds, 6 residues, 1 model selected
    29397 
    29398  > select clear
    29399 
    29400  > save working.cxs
    29401 
    29402  Taking snapshot of stepper: Model 1a
    29403 
    29404  > view /M:608
    29405 
    29406  > select up
    29407 
    29408  125 atoms, 126 bonds, 1 residue, 1 model selected
    29409 
    29410  > save working.cxs
    29411 
    29412  Taking snapshot of stepper: Model 1a
    29413 
    29414  > view /M:701
    29415 
    29416  > select /M:701
    29417 
    29418  100 atoms, 99 bonds, 1 residue, 1 model selected
    29419 
    29420  > movie record
    29421 
    29422  > movie stop
    29423 
    29424  > movie encode RCC.mp4
    29425 
    29426  Movie saved to RCC.mp4
    29427 
    29428 
    29429  > windowsize size
    29430 
    29431  Expected an integer >= 1 or a keyword
    29432 
    29433  > windowsize
    29434 
    29435  window size 1136 934
    29436 
    29437  > windowsize
    29438 
    29439  window size 1136 934
    29440 
    29441  > show sel
    29442 
    29443  > select clear
    29444 
    29445  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    29446  bonded heavy atom.
    29447 
    29448  Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    29449  bonded heavy atom.
    29450 
    29451  > isolde replace ligand sel CRT
    29452 
    29453  Timed out trying to match residue RCC to template CRT. Match may not be
    29454  ideal.
    29455 
    29456  Deleted the following atoms from residue RCC M701: H27B, C27, O45, H24B,
    29457  H43C,
    29458  C24, O42, H38A, H23A, C39, H28B, C29, C26, O44, H38C, H27A, H24A, C23,
    29459  H43B,
    29460  C38, H28A, C28, HC25, C25, C43, H38B, H23B, C40, HC29, H43A
    29461 
    29462  68 atoms were automatically renamed to match the template: O32->O1,
    29463  C41->C1M,
    29464  C2->C4, C3->C5, C4->C6, C5->C7, HC3->H5, HC4->H6, C30->C2, C31->C3,
    29465  C33->C8,
    29466  C6->C9, C7->C10, C8->C11, C9->C12, HC6->H9, HC7->H10, HC8->H11, C10->C14,
    29467  C11->C15, C12->C16, C13->C17, C34->C13, HC10->H14, HC11->H15, HC12->H16,
    29468  C35->C18, C14->C19, C15->C20, C16->C21, C17->C22, C18->C23, HC14->H19,
    29469  HC15->H20, HC16->H21, HC17->H22, C36->C24, C19->C25, C20->C26, C21->C27,
    29470  C22->C28, HC19->H25, HC20->H26, HC21->H27, C37->C29, HC2A->H41, HC2B->H42,
    29471  H30A->H21A, H30B->H22A, H30C->H23, H31B->H32A, H31C->H33, H33A->H81,
    29472  H33B->H82, H33C->H83, HC34->H131, H35A->H181, H35B->H182, H35C->H183,
    29473  H36A->H241, H36B->H242, H36C->H243, H37A->H291, H37B->H292, H37C->H293,
    29474  H41A->H1M1, H41B->H1M2, H41C->H1M3
    29475 
    29476  > select up
    29477 
    29478  153 atoms, 152 bonds, 2 residues, 1 model selected
    29479 
    29480  > isolde ignore sel
    29481 
    29482  ISOLDE: currently ignoring 2 residues in model 8.2
    29483 
    29484  > isolde ~ignore
    29485 
    29486  > save working.cxs
    29487 
    29488  Taking snapshot of stepper: Model 1a
    29489 
    29490  > select up
    29491 
    29492  3 atoms, 2 bonds, 1 residue, 1 model selected
    29493 
    29494  > delete sel
    29495 
    29496  > save working.cxs
    29497 
    29498  Taking snapshot of stepper: Model 1a
    29499 
    29500  > view /ah:11
    29501 
    29502  > select /ag:12
    29503 
    29504  24 atoms, 23 bonds, 1 residue, 1 model selected
    29505 
    29506  > select /ah,ag:12
    29507 
    29508  48 atoms, 46 bonds, 2 residues, 1 model selected
    29509 
    29510  > view /M:36
    29511 
    29512  > ui tool show Shell
    29513 
    29514  /opt/UCSF/ChimeraX/lib/python3.7/site-
    29515  packages/IPython/core/history.py:226:
    29516  UserWarning: IPython History requires SQLite, your history will not be
    29517  saved
    29518  warn("IPython History requires SQLite, your history will not be saved")
    29519 
    29520  > save model_1a_working.cif #1
    29521 
    29522  no structures to save
    29523 
    29524  > save working.cxs
    29525 
    29526  Taking snapshot of stepper: Model 1a
    29527  opened ChimeraX session
    29528 
    29529  > ui tool show Shell
    29530 
    29531  /opt/UCSF/ChimeraX/lib/python3.7/site-
    29532  packages/IPython/core/history.py:226:
    29533  UserWarning: IPython History requires SQLite, your history will not be
    29534  saved
    29535  warn("IPython History requires SQLite, your history will not be saved")
    29536 
    29537  > select /M:MAN
    29538 
    29539  20 atoms, 20 bonds, 1 residue, 1 model selected
    29540 
    29541  > view sel
    29542 
    29543  > select up
    29544 
    29545  49 atoms, 50 bonds, 2 residues, 1 model selected
    29546 
    29547  > hide #!8.1 models
    29548 
    29549  > set bgColor black
    29550 
    29551  > hide :HOH
    29552 
    29553  > select up
    29554 
    29555  59 atoms, 60 bonds, 3 residues, 1 model selected
    29556 
    29557  > hide protein&~sel
    29558 
    29559  > select /M:1000@O5
    29560 
    29561  1 atom, 1 residue, 1 model selected
    29562 
    29563  > select up
    29564 
    29565  3 atoms, 1 bond, 2 residues, 1 model selected
    29566 
    29567  > select up
    29568 
    29569  49 atoms, 50 bonds, 2 residues, 1 model selected
    29570 
    29571  > save duplicated_sugars.jpg
    29572 
    29573 
    29574 
    29575 
    29576  OpenGL version: 3.3.0 NVIDIA 455.32.00
    29577  OpenGL renderer: TITAN Xp/PCIe/SSE2
    29578  OpenGL vendor: NVIDIA Corporation
    29579  Manufacturer: Dell Inc.
    29580  Model: Precision T5600
    29581  OS: CentOS Linux 7 Core
    29582  Architecture: 64bit ELF
    29583  CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
    29584  Cache Size: 20480 KB
    29585  Memory:
    29586                        total        used        free      shared
    29587  buff/cache   available
    29588          Mem:            62G        8.7G         40G        311M
    29589  13G         53G
    29590          Swap:          4.9G          0B        4.9G
    29591 
    29592  Graphics:
    29593          03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
    29594  [TITAN Xp] [10de:1b02] (rev a1)
    29595          Subsystem: NVIDIA Corporation Device [10de:11df]
    29596          Kernel driver in use: nvidia
    29597  PyQt version: 5.12.3
    29598  Compiled Qt version: 5.12.4
    29599  Runtime Qt version: 5.12.9
    29600  Installed Packages:
    29601      alabaster: 0.7.12
    29602      appdirs: 1.4.4
    29603      Babel: 2.8.0
    29604      backcall: 0.2.0
    29605      blockdiag: 2.0.1
    29606      certifi: 2020.6.20
    29607      chardet: 3.0.4
    29608      ChimeraX-AddH: 2.1.1
    29609      ChimeraX-AlignmentAlgorithms: 2.0
    29610      ChimeraX-AlignmentHdrs: 3.2
    29611      ChimeraX-AlignmentMatrices: 2.0
    29612      ChimeraX-Alignments: 2.1
    29613      ChimeraX-Arrays: 1.0
    29614      ChimeraX-Async: 0.1
    29615      ChimeraX-Atomic: 1.6.1
    29616      ChimeraX-AtomSearch: 2.0
    29617      ChimeraX-AxesPlanes: 2.0
    29618      ChimeraX-BasicActions: 1.1
    29619      ChimeraX-BILD: 1.0
    29620      ChimeraX-BlastProtein: 1.0.1
    29621      ChimeraX-BondRot: 2.0
    29622      ChimeraX-BugReporter: 1.0
    29623      ChimeraX-BuildStructure: 2.0
    29624      ChimeraX-Bumps: 1.0
    29625      ChimeraX-BundleBuilder: 1.0
    29626      ChimeraX-ButtonPanel: 1.0
    29627      ChimeraX-CageBuilder: 1.0
    29628      ChimeraX-CellPack: 1.0
    29629      ChimeraX-Centroids: 1.1
    29630      ChimeraX-ChemGroup: 2.0
    29631      ChimeraX-Clashes: 2.0
    29632      ChimeraX-Clipper: 0.15.0
    29633      ChimeraX-ColorActions: 1.0
    29634      ChimeraX-ColorGlobe: 1.0
    29635      ChimeraX-CommandLine: 1.1.3
    29636      ChimeraX-ConnectStructure: 2.0
    29637      ChimeraX-Contacts: 1.0
    29638      ChimeraX-Core: 1.1
    29639      ChimeraX-CoreFormats: 1.0
    29640      ChimeraX-coulombic: 1.0.1
    29641      ChimeraX-Crosslinks: 1.0
    29642      ChimeraX-Crystal: 1.0
    29643      ChimeraX-DataFormats: 1.0
    29644      ChimeraX-Dicom: 1.0
    29645      ChimeraX-DistMonitor: 1.1
    29646      ChimeraX-DistUI: 1.0
    29647      ChimeraX-Dssp: 2.0
    29648      ChimeraX-EMDB-SFF: 1.0
    29649      ChimeraX-ExperimentalCommands: 1.0
    29650      ChimeraX-FileHistory: 1.0
    29651      ChimeraX-FunctionKey: 1.0
    29652      ChimeraX-Geometry: 1.1
    29653      ChimeraX-gltf: 1.0
    29654      ChimeraX-Graphics: 1.0
    29655      ChimeraX-Hbonds: 2.0
    29656      ChimeraX-Help: 1.0
    29657      ChimeraX-HKCage: 1.3
    29658      ChimeraX-IHM: 1.0
    29659      ChimeraX-ImageFormats: 1.0
    29660      ChimeraX-IMOD: 1.0
    29661      ChimeraX-IO: 1.0
    29662      ChimeraX-ISOLDE: 1.1.0
    29663      ChimeraX-Label: 1.0
    29664      ChimeraX-LinuxSupport: 1.0
    29665      ChimeraX-ListInfo: 1.0
    29666      ChimeraX-Log: 1.1.1
    29667      ChimeraX-LookingGlass: 1.1
    29668      ChimeraX-Map: 1.0.1
    29669      ChimeraX-MapData: 2.0
    29670      ChimeraX-MapEraser: 1.0
    29671      ChimeraX-MapFilter: 2.0
    29672      ChimeraX-MapFit: 2.0
    29673      ChimeraX-MapSeries: 2.0
    29674      ChimeraX-Markers: 1.0
    29675      ChimeraX-Mask: 1.0
    29676      ChimeraX-MatchMaker: 1.1
    29677      ChimeraX-MDcrds: 2.0
    29678      ChimeraX-MedicalToolbar: 1.0.1
    29679      ChimeraX-Meeting: 1.0
    29680      ChimeraX-MLP: 1.0
    29681      ChimeraX-mmCIF: 2.2
    29682      ChimeraX-MMTF: 2.0
    29683      ChimeraX-Modeller: 1.0
    29684      ChimeraX-ModelPanel: 1.0
    29685      ChimeraX-ModelSeries: 1.0
    29686      ChimeraX-Mol2: 2.0
    29687      ChimeraX-Morph: 1.0
    29688      ChimeraX-MouseModes: 1.0
    29689      ChimeraX-Movie: 1.0
    29690      ChimeraX-Neuron: 1.0
    29691      ChimeraX-Nucleotides: 2.0
    29692      ChimeraX-OpenCommand: 1.2.1
    29693      ChimeraX-PDB: 2.1
    29694      ChimeraX-PDBBio: 1.0
    29695      ChimeraX-Phenix: 0.1
    29696      ChimeraX-PickBlobs: 1.0
    29697      ChimeraX-Positions: 1.0
    29698      ChimeraX-PresetMgr: 1.0
    29699      ChimeraX-PubChem: 2.0
    29700      ChimeraX-Read-Pbonds: 1.0
    29701      ChimeraX-Registration: 1.1
    29702      ChimeraX-RemoteControl: 1.0
    29703      ChimeraX-ResidueFit: 1.0
    29704      ChimeraX-RestServer: 1.0
    29705      ChimeraX-RNALayout: 1.0
    29706      ChimeraX-RotamerLibMgr: 2.0
    29707      ChimeraX-RotamerLibsDunbrack: 2.0
    29708      ChimeraX-RotamerLibsDynameomics: 2.0
    29709      ChimeraX-RotamerLibsRichardson: 2.0
    29710      ChimeraX-SaveCommand: 1.2
    29711      ChimeraX-SchemeMgr: 1.0
    29712      ChimeraX-SDF: 2.0
    29713      ChimeraX-Segger: 1.0
    29714      ChimeraX-Segment: 1.0
    29715      ChimeraX-SeqView: 2.2
    29716      ChimeraX-Shape: 1.0.1
    29717      ChimeraX-Shell: 1.0
    29718      ChimeraX-Shortcuts: 1.0
    29719      ChimeraX-ShowAttr: 1.0
    29720      ChimeraX-ShowSequences: 1.0
    29721      ChimeraX-SideView: 1.0
    29722      ChimeraX-Smiles: 2.0
    29723      ChimeraX-SmoothLines: 1.0
    29724      ChimeraX-SpaceNavigator: 1.0
    29725      ChimeraX-StdCommands: 1.0.4
    29726      ChimeraX-STL: 1.0
    29727      ChimeraX-Storm: 1.0
    29728      ChimeraX-Struts: 1.0
    29729      ChimeraX-Surface: 1.0
    29730      ChimeraX-SwapAA: 2.0
    29731      ChimeraX-SwapRes: 2.0
    29732      ChimeraX-TapeMeasure: 1.0
    29733      ChimeraX-Test: 1.0
    29734      ChimeraX-Toolbar: 1.0
    29735      ChimeraX-ToolshedUtils: 1.0
    29736      ChimeraX-Tug: 1.0
    29737      ChimeraX-UI: 1.2.3
    29738      ChimeraX-uniprot: 2.0
    29739      ChimeraX-ViewDockX: 1.0
    29740      ChimeraX-Vive: 1.1
    29741      ChimeraX-VolumeMenu: 1.0
    29742      ChimeraX-VTK: 1.0
    29743      ChimeraX-WavefrontOBJ: 1.0
    29744      ChimeraX-WebCam: 1.0
    29745      ChimeraX-WebServices: 1.0
    29746      ChimeraX-Zone: 1.0
    29747      colorama: 0.4.3
    29748      comtypes: 1.1.7
    29749      cxservices: 1.0
    29750      cycler: 0.10.0
    29751      Cython: 0.29.20
    29752      decorator: 4.4.2
    29753      distlib: 0.3.1
    29754      distro: 1.5.0
    29755      docutils: 0.16
    29756      filelock: 3.0.12
    29757      funcparserlib: 0.3.6
    29758      grako: 3.16.5
    29759      graphviz: 0.14.1
    29760      h5py: 2.10.0
    29761      html2text: 2020.1.16
    29762      idna: 2.10
    29763      ihm: 0.16
    29764      imagecodecs: 2020.5.30
    29765      imagecodecs-lite: 2020.1.31
    29766      imagesize: 1.2.0
    29767      ipykernel: 5.3.0
    29768      ipython: 7.15.0
    29769      ipython-genutils: 0.2.0
    29770      jedi: 0.17.2
    29771      Jinja2: 2.11.2
    29772      jupyter-client: 6.1.3
    29773      jupyter-core: 4.6.3
    29774      kiwisolver: 1.2.0
    29775      line-profiler: 2.1.2
    29776      lxml: 4.5.1
    29777      MarkupSafe: 1.1.1
    29778      matplotlib: 3.2.1
    29779      msgpack: 1.0.0
    29780      netifaces: 0.10.9
    29781      networkx: 2.4
    29782      numexpr: 2.7.1
    29783      numpy: 1.18.5
    29784      numpydoc: 1.0.0
    29785      objgraph: 3.4.1
    29786      openvr: 1.12.501
    29787      packaging: 20.4
    29788      ParmEd: 3.2.0
    29789      parso: 0.7.1
    29790      pexpect: 4.8.0
    29791      pickleshare: 0.7.5
    29792      Pillow: 7.1.2
    29793      pip: 20.2.2
    29794      pkginfo: 1.5.0.1
    29795      prompt-toolkit: 3.0.7
    29796      psutil: 5.7.0
    29797      ptyprocess: 0.6.0
    29798      pycollada: 0.7.1
    29799      pydicom: 2.0.0
    29800      Pygments: 2.6.1
    29801      PyOpenGL: 3.1.5
    29802      PyOpenGL-accelerate: 3.1.5
    29803      pyparsing: 2.4.7
    29804      PyQt5-commercial: 5.12.3
    29805      PyQt5-sip: 4.19.19
    29806      PyQtWebEngine-commercial: 5.12.1
    29807      python-dateutil: 2.8.1
    29808      pytz: 2020.1
    29809      pyzmq: 19.0.2
    29810      qtconsole: 4.7.4
    29811      QtPy: 1.9.0
    29812      RandomWords: 0.3.0
    29813      requests: 2.24.0
    29814      scipy: 1.4.1
    29815      Send2Trash: 1.5.0
    29816      SEQCROW: 0.20
    29817      setuptools: 49.4.0
    29818      sfftk-rw: 0.6.6.dev0
    29819      six: 1.15.0
    29820      snowballstemmer: 2.0.0
    29821      sortedcontainers: 2.2.2
    29822      Sphinx: 3.1.1
    29823      sphinxcontrib-applehelp: 1.0.2
    29824      sphinxcontrib-blockdiag: 2.0.0
    29825      sphinxcontrib-devhelp: 1.0.2
    29826      sphinxcontrib-htmlhelp: 1.0.3
    29827      sphinxcontrib-jsmath: 1.0.1
    29828      sphinxcontrib-qthelp: 1.0.3
    29829      sphinxcontrib-serializinghtml: 1.1.4
    29830      suds-jurko: 0.6
    29831      tables: 3.6.1
    29832      tifffile: 2020.6.3
    29833      tinyarray: 1.2.2
    29834      tornado: 6.0.4
    29835      traitlets: 5.0.4
    29836      urllib3: 1.25.10
    29837      versioneer: 0.18
    29838      wcwidth: 0.2.5
    29839      webcolors: 1.11.1
    29840      wheel: 0.34.2
    29841  File attachment: duplicated_sugars.jpg
    29842 
    29843  }}}
    29844 
    29845  [attachment:"duplicated_sugars.jpg"]
    29846 
    29847 --
    29848 Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4176>
    29849 ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    29850 ChimeraX Issue Tracker
    29851 }}}