Changes between Initial Version and Version 2 of Ticket #4176


Ignore:
Timestamp:
Jan 27, 2021, 9:45:51 AM (5 years ago)
Author:
Eric Pettersen
Comment:

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  • Ticket #4176

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → mmCIF save/restore produces duplicate residues

  • Ticket #4176 – Description

    initial v2  
    66I have an ISOLDE session containing a very large, complex model. Everything in the session itself is well-behaved, but when I save to mmCIF and reopen five residues are duplicated. One of these is a protein residue (somehow ended up appearing twice in its `Chain` object, no idea how - easy enough to fix). The other four are two pairs of sugars, each internal to an O-linked glycan (like in the attached image). Much less sure how to fix that, other than to delete the duplicate residues in the reopened mmCIF. Any clues?
    77
    8 Log:
    9 UCSF ChimeraX version: 1.1 (2020-09-09) 
    10 © 2016-2020 Regents of the University of California. All rights reserved. 
    11 
    12 > open working.cxs
    13 
    14 restore_snapshot for "RotamerRestraintMgr" returned None 
    15 
    16 Log from Mon Jan 25 22:36:36 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    17 © 2016-2020 Regents of the University of California. All rights reserved. 
    18 
    19 > open working.cxs
    20 
    21 restore_snapshot for "RotamerRestraintMgr" returned None 
    22 
    23 Log from Sat Jan 23 15:29:45 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    24 © 2016-2020 Regents of the University of California. All rights reserved. 
    25 
    26 > open working.cxs
    27 
    28 restore_snapshot for "RotamerRestraintMgr" returned None 
    29 
    30 Log from Wed Jan 20 20:19:45 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    31 © 2016-2020 Regents of the University of California. All rights reserved. 
    32 
    33 > open working.cxs
    34 
    35 restore_snapshot for "RotamerRestraintMgr" returned None 
    36 
    37 Log from Wed Jan 20 18:04:18 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    38 © 2016-2020 Regents of the University of California. All rights reserved. 
    39 
    40 > open working_fme.cxs
    41 
    42 restore_snapshot for "RotamerRestraintMgr" returned None 
    43 
    44 Failed to restore chiral restraints. This is usually not a problem - they will
    45 be automatically regenerated on first simulation. 
    46 
    47 Log from Tue Jan 19 20:41:55 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    48 © 2016-2020 Regents of the University of California. All rights reserved. 
    49 
    50 > open working_fme.cxs
    51 
    52 restore_snapshot for "RotamerRestraintMgr" returned None 
    53 
    54 Failed to restore chiral restraints. This is usually not a problem - they will
    55 be automatically regenerated on first simulation. 
    56 
    57 Log from Tue Jan 19 19:42:56 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    58 © 2016-2020 Regents of the University of California. All rights reserved. 
    59 
    60 > open working.cxs
    61 
    62 restore_snapshot for "RotamerRestraintMgr" returned None 
    63 
    64 Log from Tue Jan 19 15:18:30 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    65 © 2016-2020 Regents of the University of California. All rights reserved. 
    66 
    67 > open working.cxs
    68 
    69 restore_snapshot for "RotamerRestraintMgr" returned None 
    70 
    71 Log from Mon Jan 18 21:58:27 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    72 © 2016-2020 Regents of the University of California. All rights reserved. 
    73 
    74 > open working.cxs
    75 
    76 restore_snapshot for "RotamerRestraintMgr" returned None 
    77 
    78 Log from Thu Jan 14 20:29:04 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    79 © 2016-2020 Regents of the University of California. All rights reserved. 
    80 
    81 > open working.cxs
    82 
    83 restore_snapshot for "RotamerRestraintMgr" returned None 
    84 
    85 Log from Thu Jan 14 18:05:53 2021UCSF ChimeraX version: 1.1 (2020-09-09) 
    86 © 2016-2020 Regents of the University of California. All rights reserved. 
    87 
    88 > open model1a_2020_11_04.cxs
    89 
    90 restore_snapshot for "RotamerRestraintMgr" returned None 
    91 
    92 Log from Wed Nov 4 20:47:05 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    93 © 2016-2020 Regents of the University of California. All rights reserved. 
    94 
    95 > open model1a_2020_11_02.cxs
    96 
    97 restore_snapshot for "RotamerRestraintMgr" returned None 
    98 
    99 Log from Mon Nov 2 17:41:56 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    100 © 2016-2020 Regents of the University of California. All rights reserved. 
    101 
    102 > open working.cxs
    103 
    104 restore_snapshot for "RotamerRestraintMgr" returned None 
    105 
    106 Log from Sat Oct 31 21:36:29 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    107 © 2016-2020 Regents of the University of California. All rights reserved. 
    108 
    109 > open
    110 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/reassigning_ligands.cxs
    111 > format session
    112 
    113 restore_snapshot for "RotamerRestraintMgr" returned None 
    114 
    115 Log from Fri Oct 30 09:34:25 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    116 © 2016-2020 Regents of the University of California. All rights reserved. 
    117 
    118 > open
    119 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/reassigning_ligands.cxs
    120 > format session
    121 
    122 restore_snapshot for "RotamerRestraintMgr" returned None 
    123 
    124 Log from Fri Oct 30 09:16:38 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 Thu Oct 29 16:35:33 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    132 © 2016-2020 Regents of the University of California. All rights reserved. 
    133 
    134 > open working.cxs
    135 
    136 restore_snapshot for "RotamerRestraintMgr" returned None 
    137 
    138 restore_snapshot for "RotamerRestraintMgr" returned None 
    139 
    140 Log from Wed Oct 28 21:12:33 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    141 © 2016-2020 Regents of the University of California. All rights reserved. 
    142 
    143 > open working.cxs
    144 
    145 restore_snapshot for "RotamerRestraintMgr" returned None 
    146 
    147 restore_snapshot for "RotamerRestraintMgr" returned None 
    148 
    149 Log from Tue Oct 27 22:03:57 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    150 © 2016-2020 Regents of the University of California. All rights reserved. 
    151 
    152 > open working.cxs
    153 
    154 restore_snapshot for "RotamerRestraintMgr" returned None 
    155 
    156 Log from Fri Oct 23 21:33:44 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    157 © 2016-2020 Regents of the University of California. All rights reserved. 
    158 
    159 > open working.cxs
    160 
    161 restore_snapshot for "RotamerRestraintMgr" returned None 
    162 
    163 Log from Fri Oct 23 12:38:35 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    164 © 2016-2020 Regents of the University of California. All rights reserved. 
    165 
    166 > open working.cxs
    167 
    168 restore_snapshot for "RotamerRestraintMgr" returned None 
    169 
    170 restore_snapshot for "RotamerRestraintMgr" returned None 
    171 
    172 Log from Thu Oct 22 21:38:47 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    173 © 2016-2020 Regents of the University of California. All rights reserved. 
    174 
    175 > open working_3.cxs
    176 
    177 restore_snapshot for "RotamerRestraintMgr" returned None 
    178 
    179 restore_snapshot for "RotamerRestraintMgr" returned None 
    180 
    181 Log from Thu Oct 22 17:00:13 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    182 © 2016-2020 Regents of the University of California. All rights reserved. 
    183 
    184 > open
    185 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/reopened.cxs
    186 
    187 restore_snapshot for "RotamerRestraintMgr" returned None 
    188 
    189 Log from Thu Oct 22 16:23:14 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    190 © 2016-2020 Regents of the University of California. All rights reserved. 
    191 
    192 > open working_2.cxs
    193 
    194 restore_snapshot for "RotamerRestraintMgr" returned None 
    195 
    196 Log from Thu Oct 22 16:02:14 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    197 © 2016-2020 Regents of the University of California. All rights reserved. 
    198 
    199 > open
    200 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.cxs
    201 
    202 restore_snapshot for "RotamerRestraintMgr" returned None 
    203 
    204 Log from Thu Oct 22 13:56:05 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    205 © 2016-2020 Regents of the University of California. All rights reserved. 
    206 
    207 > open ../old_model_in_map_1b.cxs
    208 
    209 Log from Thu Oct 22 06:57:21 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    210 © 2016-2020 Regents of the University of California. All rights reserved. 
    211 
    212 > open model1b_working.cxs
    213 
    214 restore_snapshot for "RotamerRestraintMgr" returned None 
    215 
    216 Log from Wed Oct 21 20:17:18 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    217 © 2016-2020 Regents of the University of California. All rights reserved. 
    218 
    219 > open model1b_working.cxs
    220 
    221 restore_snapshot for "RotamerRestraintMgr" returned None 
    222 
    223 Log from Wed Oct 21 20:13:59 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    224 © 2016-2020 Regents of the University of California. All rights reserved. 
    225 
    226 > open
    227 > /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/model1b_working.cxs
    228 
    229 restore_snapshot for "RotamerRestraintMgr" returned None 
    230 
    231 Log from Wed Oct 21 19:55:36 2020UCSF ChimeraX version: 1.1 (2020-09-09) 
    232 © 2016-2020 Regents of the University of California. All rights reserved. 
    233 How to cite UCSF ChimeraX 
    234 
    235 > open /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/rc-
    236 > dlh1-model1b_rearranged.pdb format pdb
    237 
    238 Chain information for rc-dlh1-model1b_rearranged.pdb #1 
    239 --- 
    240 Chain | Description 
    241 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    242 description available 
    243 Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available 
    244 Ag | No description available 
    245 B | No description available 
    246 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 Bb
    247 Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available 
    248 C | No description available 
    249 C1 | No description available 
    250 H1 | No description available 
    251 H2 | No description available 
    252 L | No description available 
    253 M | No description available 
    254  
    255 
    256 > open
    257 > /run/media/tic20/storage/structure_dump/pu_qian/2020_10_new_maps/class1b_26A.mrc
    258 
    259 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    260 0.0224, step 2, values float32 
    261 
    262 > clipper associate #2 toModel #1
    263 
    264 Chain information for rc-dlh1-model1b_rearranged.pdb 
    265 --- 
    266 Chain | Description 
    267 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 1.2/AK
    268 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 1.2/AV
    269 1.2/AW 1.2/AX | No description available 
    270 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 1.2/Al
    271 1.2/Am 1.2/An 1.2/Ao 1.2/Ap | No description available 
    272 1.2/Ag | No description available 
    273 1.2/B | No description available 
    274 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 1.2/BK
    275 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 1.2/BV
    276 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 1.2/Bi
    277 1.2/Bj 1.2/Bk 1.2/Bl 1.2/Bm 1.2/Bn 1.2/Bo 1.2/Bp | No description available 
    278 1.2/C | No description available 
    279 1.2/C1 | No description available 
    280 1.2/H1 | No description available 
    281 1.2/H2 | No description available 
    282 1.2/L | No description available 
    283 1.2/M | No description available 
    284  
    285 
    286 > delete :GPC@HO45
    287 
    288 > ui tool show Shell
    289 
    290 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    291 UserWarning: IPython History requires SQLite, your history will not be saved 
    292 warn("IPython History requires SQLite, your history will not be saved") 
    293 
    294 > select ~protein
    295 
    296 10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 8 models selected 
    297 
    298 > ui tool show ISOLDE
    299 
    300 > set selectionWidth 4
    301 
    302 Done loading forcefield 
    303 
    304 > select ~protein
    305 
    306 10060 atoms, 10377 bonds, 352 pseudobonds, 135 residues, 13 models selected 
    307 
    308 > addh
    309 
    310 Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb
    311 #1.2 
    312 --- 
    313 warning | Skipped 8 atom(s) with bad connectivities; see log for details 
    314 notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2)
    315 chain AA; guessing termini instead 
    316 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AB;
    317 guessing termini instead 
    318 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AC;
    319 guessing termini instead 
    320 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AD;
    321 guessing termini instead 
    322 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#1.2) chain AE;
    323 guessing termini instead 
    324 82 messages similar to the above omitted 
    325 Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
    326 HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
    327 HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
    328 HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
    329 HIS 2, /Aa MET 1, /Ab MET 1, /Ac MET 1, /Ad MET 1, /Ae MET 1, /Af MET 1, /Ag
    330 MET 1, /Ah MET 1, /Ai MET 1, /Aj MET 1, /Ak MET 1, /Al MET 1, /Am MET 1, /An
    331 MET 1, /Ao MET 1, /Ap MET 1, /B PRO 25, /BA MET 1, /BB MET 1, /BC MET 1, /BD
    332 MET 1, /BE MET 1, /BF MET 1, /BG MET 1, /BH MET 1, /BI MET 1, /BJ MET 1, /BK
    333 MET 1, /BL MET 1, /BM MET 1, /BN MET 1, /BO MET 1, /BP MET 1, /BQ MET 1, /BR
    334 MET 1, /BS MET 1, /BT MET 1, /BU MET 1, /BV MET 1, /BW MET 1, /BX MET 1, /Ba
    335 MET 1, /Bb MET 1, /Bc MET 1, /Bd MET 1, /Be MET 1, /Bf MET 1, /Bg MET 1, /Bh
    336 MET 1, /Bi MET 1, /Bj MET 1, /Bk MET 1, /Bl MET 1, /Bm MET 1, /Bn MET 1, /Bo
    337 MET 1, /Bp MET 1, /C ALA 15, /H1 MET 1, /H2 SER 1, /L ALA 1, /M MET 1 
    338 Chain-initial residues that are not actual N termini: /C1 GLN 1, /H2 ARG 38 
    339 Chain-final residues that are actual C termini: /BA PHE 38, /BB PHE 38, /BC
    340 PHE 38, /BD PHE 38, /BE PHE 38, /BF PHE 38, /BG PHE 38, /BH PHE 38, /BI PHE
    341 38, /BJ PHE 38, /BK PHE 38, /BL PHE 38, /BM PHE 38, /BN PHE 38, /BO PHE 38,
    342 /BP PHE 38, /BQ PHE 38, /BR PHE 38, /BS PHE 38, /BT PHE 38, /BU PHE 38, /BV
    343 PHE 38, /BW PHE 38, /BX PHE 38, /Ba PHE 38, /Bb PHE 38, /Bc PHE 38, /Bd PHE
    344 38, /Be PHE 38, /Bf PHE 38, /Bg PHE 38, /Bh PHE 38, /Bi PHE 38, /Bj PHE 38,
    345 /Bk PHE 38, /Bl PHE 38, /Bm PHE 38, /Bn PHE 38, /Bo PHE 38, /Bp PHE 38 
    346 Chain-final residues that are not actual C termini: /AA PRO 48, /AB PRO 48,
    347 /AC PRO 48, /AD PRO 48, /AE PRO 48, /AF PRO 48, /AG PRO 48, /AH PRO 48, /AI
    348 PRO 48, /AJ PRO 48, /AK PRO 48, /AL PRO 48, /AM PRO 48, /AN PRO 48, /AO PRO
    349 48, /AP PRO 48, /AQ PRO 48, /AR PRO 48, /AS PRO 48, /AT PRO 48, /AU PRO 48,
    350 /AV PRO 48, /AW PRO 48, /AX PRO 48, /Aa ALA 60, /Ab ALA 60, /Ac ALA 60, /Ad
    351 ALA 60, /Ae ALA 60, /Af ALA 60, /Ag LEU 67, /Ah ALA 60, /Ai ALA 60, /Aj ALA
    352 60, /Ak ALA 60, /Al ALA 60, /Am ALA 60, /An ALA 60, /Ao ALA 60, /Ap ALA 60, /B
    353 ILE 123, /C ILE 313, /C1 LEU 92, /H1 HIS 67, /H2 ILE 181, /H2 ARG 36, /L TRP
    354 272, /M TYR 324 
    355 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    356 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    357  
    358 Skipping possible acceptor with bad geometry: /C ARG 302 OXT 
    359 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT 
    360  
    361 Skipping possible acceptor with bad geometry: /C ARG 302 OXT 
    362 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 OXT 
    363  
    364 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    365 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    366  
    367 Skipping possible acceptor with bad geometry: /C ARG 302 O 
    368 Wrong number of grandchild atoms for phi/psi acceptor /C ARG 302 O 
    369  
    370 3 messages similar to the above omitted 
    371 4746 hydrogen bonds 
    372 Adding 'H' to /H2 ARG 38 
    373 /AA PRO 48 is not terminus, removing H atom from 'C' 
    374 /AB PRO 48 is not terminus, removing H atom from 'C' 
    375 /AC PRO 48 is not terminus, removing H atom from 'C' 
    376 /AD PRO 48 is not terminus, removing H atom from 'C' 
    377 /AE PRO 48 is not terminus, removing H atom from 'C' 
    378 42 messages similar to the above omitted 
    379 44090 hydrogens added 
    380  
    381 
    382 > save model1b_working.cxs
    383 
    384 opened ChimeraX session 
    385 
    386 > select up
    387 
    388 101 atoms, 100 bonds, 1 residue, 1 model selected 
    389 
    390 > show sel
    391 
    392 > select clear
    393 
    394 > style sel ball
    395 
    396 Changed 100 atom styles 
    397 
    398 > select :GPC
    399 
    400 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    401 
    402 > show sel
    403 
    404 > select :GPC@HC19
    405 
    406 40 atoms, 40 residues, 1 model selected 
    407 
    408 > select :GPC
    409 
    410 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    411 
    412 > delete sel
    413 
    414 MD template USER_BCL for residue BCL L604 contains extra atoms that are not in
    415 a coordinate template, and are not directly connected to existing atoms. Since
    416 MD templates do not explicitly provide geometry,these atoms will not be built. 
    417 
    418 > select sel&@CBD
    419 
    420 1 atom, 1 residue, 1 model selected 
    421 
    422 > style sel sphere
    423 
    424 Changed 1 atom style 
    425 
    426 > style sel stick
    427 
    428 Changed 1 atom style 
    429 
    430 > select up
    431 
    432 139 atoms, 147 bonds, 1 residue, 1 model selected 
    433 Deleted the following atoms from residue BCL L604: HHC1, HHD1 
    434 Deleted the following atoms from residue BCL L602: HHD2, HHC2, HHD1, HHC1 
    435 Deleted the following atoms from residue BPH L606: H12, H92, HHD1, H41, H93,
    436 H91, H52, H11, HHD2, H43, H61, H51, H62, H42, H71, H72 
    437 
    438 > save model1b_working.cxs
    439 
    440 opened ChimeraX session 
    441 Deleted the following atoms from residue MQ8 M405: H272, H9, H502, H122, C49,
    442 C46, H172, H503, C50, H461, H471, H222, H11, H422, H492, H6, H472, C48, H462,
    443 H7, H501, C47, H8, H491, H372, H322 
    444 Deleted the following atoms from residue BCL M601: HHD2, HHD1 
    445 Deleted the following atoms from residue BCL M603: HHD1, HHD2, HHC1, HHC2 
    446 Deleted the following atoms from residue BPH M605: H11, H62, H72, H42, H12,
    447 H91, H52, H71, HHD2, H93, H51, H92, HHD1, H61, H43, H41 
    448 Residue RCC M701 has only 0 connected atoms in common with template GPC. At
    449 least 3 matching atoms are needed. 
    450 
    451 > save model1b_working.cxs
    452 
    453 > delete sel
    454 
    455 > save model1b_working.cxs
    456 
    457 opened ChimeraX session 
    458 
    459 > open
    460 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb
    461 
    462 Summary of feedback from opening
    463 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/RealSpaceRefine_44/working_noh_real_space_refined.pdb 
    464 --- 
    465 warnings | Ignored bad PDB record found on line 317 
    466 LINK NE2 HIS AA 29 MG BCL AA 57 
    467  
    468 Ignored bad PDB record found on line 318 
    469 LINK NE2 HIS AB 29 MG BCL AB 57 
    470  
    471 Ignored bad PDB record found on line 319 
    472 LINK NE2 HIS AC 29 MG BCL AC 57 
    473  
    474 Ignored bad PDB record found on line 320 
    475 LINK NE2 HIS AD 29 MG BCL AD 57 
    476  
    477 Ignored bad PDB record found on line 321 
    478 LINK NE2 HIS AE 29 MG BCL AE 57 
    479  
    480 75 messages similar to the above omitted 
    481 Start residue of secondary structure not found: HELIX 1 1 PROAA 10 PHEAA 36 1
    482 26 
    483 Start residue of secondary structure not found: HELIX 2 2 ALAAA 40 LYSAA 45 1
    484 5 
    485 Start residue of secondary structure not found: HELIX 3 3 ARGAB 3 TRPAB 5 1 2 
    486 Start residue of secondary structure not found: HELIX 4 4 PROAB 10 GLNAB 35 1
    487 25 
    488 Start residue of secondary structure not found: HELIX 5 5 ALAAB 40 LEUAB 42 1
    489 2 
    490 207 messages similar to the above omitted 
    491  
    492 Chain information for working_noh_real_space_refined.pdb #2 
    493 --- 
    494 Chain | Description 
    495 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    496 description available 
    497 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 bh
    498 bi bj bk bl bm bo bp | No description available 
    499 BB BD BE BI BV BW bn | No description available 
    500 C | No description available 
    501 H1 | No description available 
    502 H2 | No description available 
    503 L | No description available 
    504 M | No description available 
    505 UA | No description available 
    506 UB | No description available 
    507 UC | No description available 
    508 aa | No description available 
    509 ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available 
    510  
    511 
    512 > matchmaker #2 to #1
    513 
    514 Parameters 
    515 --- 
    516 Chain pairing | bb 
    517 Alignment algorithm | Needleman-Wunsch 
    518 Similarity matrix | BLOSUM-62 
    519 SS fraction | 0.3 
    520 Gap open (HH/SS/other) | 18/18/6 
    521 Gap extend | 1 
    522 SS matrix |  |  | H | S | O 
    523 ---|---|---|--- 
    524 H | 6 | -9 | -6 
    525 S |  | 6 | -6 
    526 O |  |  | 4 
    527 Iteration cutoff | 2 
    528  
    529 Matchmaker rc-dlh1-model1b_rearranged.pdb, chain M (#1.2) with
    530 working_noh_real_space_refined.pdb, chain M (#2), sequence alignment score =
    531 1582 
    532 RMSD between 295 pruned atom pairs is 0.684 angstroms; (across all 324 pairs:
    533 1.723) 
    534  
    535 
    536 > delete #2/UA,UB,UC
    537 
    538 > open
    539 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    540 
    541 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    542 0.0224, step 2, values float32 
    543 
    544 > clipper associate #3 toModel #2
    545 
    546 Chain information for working_noh_real_space_refined.pdb 
    547 --- 
    548 Chain | Description 
    549 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 2.2/AK
    550 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 2.2/AV
    551 2.2/AW 2.2/AX | No description available 
    552 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 2.2/BO
    553 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 2.2/bd
    554 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 2.2/bp |
    555 No description available 
    556 2.2/BB 2.2/BD 2.2/BE 2.2/BI 2.2/BV 2.2/BW 2.2/bn | No description available 
    557 2.2/C | No description available 
    558 2.2/H1 | No description available 
    559 2.2/H2 | No description available 
    560 2.2/L | No description available 
    561 2.2/M | No description available 
    562 2.2/aa | No description available 
    563 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 2.2/al
    564 2.2/am 2.2/an 2.2/ao 2.2/ap | No description available 
    565  
    566 
    567 > select #2:GPC
    568 
    569 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    570 
    571 > select #2:RCC
    572 
    573 Nothing selected 
    574 
    575 > select #1:RCC
    576 
    577 100 atoms, 99 bonds, 1 residue, 1 model selected 
    578 
    579 > select #2:GPC
    580 
    581 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    582 
    583 > select #1:GPC
    584 
    585 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    586 
    587 > select #2:GPC
    588 
    589 1800 atoms, 1760 bonds, 40 residues, 1 model selected 
    590 
    591 > delete sel
    592 
    593 > ui tool show Shell
    594 
    595 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    596 UserWarning: IPython History requires SQLite, your history will not be saved 
    597 warn("IPython History requires SQLite, your history will not be saved") 
    598 
    599 > delete #2:GP1
    600 
    601 > select #1:RCC
    602 
    603 100 atoms, 99 bonds, 1 residue, 1 model selected 
    604 
    605 > select #1:RCC,GCC
    606 
    607 100 atoms, 99 bonds, 1 residue, 1 model selected 
    608 
    609 > select #1:RCC,GPC
    610 
    611 4100 atoms, 4059 bonds, 41 residues, 1 model selected 
    612 
    613 > close #1
    614 
    615 > addh
    616 
    617 Summary of feedback from adding hydrogens to
    618 working_noh_real_space_refined.pdb #2.2 
    619 --- 
    620 notes | No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2)
    621 chain AA; guessing termini instead 
    622 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    623 AB; guessing termini instead 
    624 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    625 AC; guessing termini instead 
    626 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    627 AD; guessing termini instead 
    628 No usable SEQRES records for working_noh_real_space_refined.pdb (#2.2) chain
    629 AE; guessing termini instead 
    630 80 messages similar to the above omitted 
    631 Chain-initial residues that are actual N termini: /AA HIS 2, /AB HIS 2, /AC
    632 HIS 2, /AD HIS 2, /AE HIS 2, /AF HIS 2, /AG HIS 2, /AH HIS 2, /AI HIS 2, /AJ
    633 HIS 2, /AK HIS 2, /AL HIS 2, /AM HIS 2, /AN HIS 2, /AO HIS 2, /AP HIS 2, /AQ
    634 HIS 2, /AR HIS 2, /AS HIS 2, /AT HIS 2, /AU HIS 2, /AV HIS 2, /AW HIS 2, /AX
    635 HIS 2, /BA GLY 6, /BB GLY 5, /BC GLY 6, /BD GLY 5, /BE GLY 5, /BF GLY 6, /BG
    636 GLY 6, /BH GLY 6, /BI GLY 5, /BJ GLY 6, /BK GLY 6, /BL GLY 6, /BM GLY 6, /BN
    637 GLY 6, /BO GLY 6, /BP GLY 6, /BQ GLY 6, /BR GLY 6, /BS GLY 6, /BT GLY 6, /BU
    638 GLY 6, /BV GLY 5, /BW GLY 5, /BX GLY 6, /C ALA 15, /H1 MET 1, /H2 SER 1, /L
    639 ALA 1, /M MET 1, /aa HIS 2, /ab MET 1, /ac MET 1, /ad MET 1, /ae MET 1, /af
    640 MET 1, /ag MET 1, /ah MET 1, /ai MET 1, /aj MET 1, /ak MET 1, /al MET 1, /am
    641 MET 1, /an MET 1, /ao MET 1, /ap MET 1, /ba GLY 6, /bb GLY 6, /bc GLY 6, /bd
    642 GLY 6, /be GLY 6, /bf GLY 6, /bg GLY 6, /bh GLY 6, /bi GLY 6, /bj GLY 6, /bk
    643 GLY 6, /bl GLY 6, /bm GLY 6, /bn GLY 5, /bo GLY 6, /bp GLY 6 
    644 Chain-initial residues that are not actual N termini: 
    645 Chain-final residues that are actual C termini: /BA PHE 44, /BB PHE 44, /BC
    646 PHE 44, /BD PHE 44, /BE PHE 44, /BF PHE 44, /BG PHE 44, /BH PHE 44, /BI PHE
    647 44, /BJ PHE 44, /BK PHE 44, /BL PHE 44, /BM PHE 44, /BN PHE 44, /BO PHE 44,
    648 /BP PHE 44, /BQ PHE 44, /BR PHE 44, /BS PHE 44, /BT PHE 44, /BU PHE 44, /BV
    649 PHE 44, /BW PHE 44, /BX PHE 44, /C ARG 302, /H2 ILE 181, /L LYS 273, /ba PHE
    650 44, /bb PHE 44, /bc PHE 44, /bd PHE 44, /be PHE 44, /bf PHE 44, /bg PHE 44,
    651 /bh PHE 44, /bi PHE 44, /bj PHE 44, /bk PHE 44, /bl PHE 44, /bm PHE 44, /bn
    652 PHE 44, /bo PHE 44, /bp PHE 44 
    653 Chain-final residues that are not actual C termini: /AA TYR 46, /AB TYR 46,
    654 /AC TYR 46, /AD TYR 46, /AE TYR 46, /AF TYR 46, /AG TYR 46, /AH TYR 46, /AI
    655 TYR 46, /AJ TYR 46, /AK TYR 46, /AL TYR 46, /AM TYR 46, /AN TYR 46, /AO TYR
    656 46, /AP TYR 46, /AQ TYR 46, /AR TYR 46, /AS TYR 46, /AT TYR 46, /AU TYR 46,
    657 /AV TYR 46, /AW TYR 46, /AX TYR 46, /H1 LYS 53, /M TYR 324, /aa ALA 60, /ab
    658 ALA 60, /ac ALA 60, /ad ALA 60, /ae ALA 60, /af ALA 60, /ag ALA 60, /ah ALA
    659 60, /ai ALA 60, /aj ALA 60, /ak ALA 60, /al ALA 60, /am ALA 60, /an ALA 60,
    660 /ao ALA 60, /ap ALA 60 
    661 4864 hydrogen bonds 
    662 /AA TYR 46 is not terminus, removing H atom from 'C' 
    663 /AB TYR 46 is not terminus, removing H atom from 'C' 
    664 /AC TYR 46 is not terminus, removing H atom from 'C' 
    665 /AD TYR 46 is not terminus, removing H atom from 'C' 
    666 /AE TYR 46 is not terminus, removing H atom from 'C' 
    667 37 messages similar to the above omitted 
    668 43714 hydrogens added 
    669  
    670 
    671 > hide HC
    672 
    673 > select ~protein
    674 
    675 16594 atoms, 16919 bonds, 365 pseudobonds, 133 residues, 8 models selected 
    676 
    677 > select clear
    678 
    679 > save old_model_in_map_1b.cxs
    680 
    681 opened ChimeraX session 
    682 
    683 > isolde start
    684 
    685 > set selectionWidth 4
    686 
    687 Done loading forcefield 
    688 
    689 > select :GPC
    690 
    691 4013 atoms, 3973 bonds, 40 residues, 1 model selected 
    692 
    693 > ui tool show Shell
    694 
    695 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    696 UserWarning: IPython History requires SQLite, your history will not be saved 
    697 warn("IPython History requires SQLite, your history will not be saved") 
    698 
    699 > select clear
    700 
    701 > delete sel
    702 
    703 > delete sel
    704 
    705 > delete sel
    706 
    707 > delete sel
    708 
    709 > save ready.cxs
    710 
    711 > select gpc
    712 
    713 Expected an objects specifier or a keyword 
    714 
    715 > select :GPC
    716 
    717 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    718 
    719 > select :GPC
    720 
    721 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    722 
    723 > show sel
    724 
    725 > select clear
    726 
    727 > show sel
    728 
    729 > save ready.cxs
    730 
    731 > volume gaussian #1 bfactor 50
    732 
    733 > volume gaussian #2 bfactor 50
    734 
    735 > clipper associate #1 toModel #2
    736 
    737 > hide HC
    738 
    739 > select #1
    740 
    741 Nothing selected 
    742 
    743 > select #2
    744 
    745 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    746 
    747 > clipper set contourSensitivity 0.25
    748 
    749 > select clear
    750 
    751 > set bgColor white
    752 
    753 > select #1
    754 
    755 Nothing selected 
    756 
    757 > select #2
    758 
    759 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    760 
    761 > select clear
    762 
    763 > select #2
    764 
    765 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    766 
    767 > select #1
    768 
    769 Nothing selected 
    770 
    771 > select #2
    772 
    773 91607 atoms, 93634 bonds, 14 pseudobonds, 4857 residues, 16 models selected 
    774 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    775 more memory-efficient implementation. 
    776 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    777 more memory-efficient implementation. 
    778 
    779 > select clear
    780 
    781 > open
    782 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb
    783 
    784 Summary of feedback from opening
    785 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/assigned_sequence.pdb 
    786 --- 
    787 warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B 5
    788 TYR B 9 1 5 
    789 Start residue of secondary structure not found: HELIX 2 2 ARG B 22 ARG B 52 1
    790 31 
    791 Start residue of secondary structure not found: HELIX 3 3 VAL B 55 ARG B 86 1
    792 32 
    793  
    794 Chain information for assigned_sequence.pdb #1 
    795 --- 
    796 Chain | Description 
    797 Ba | No description available 
    798  
    799 
    800 > open
    801 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb
    802 
    803 Summary of feedback from opening
    804 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/c_extra/sequence_assigned.pdb 
    805 --- 
    806 warnings | Start residue of secondary structure not found: HELIX 1 1 THR C 19
    807 GLY C 21 1 3 
    808 Start residue of secondary structure not found: HELIX 2 2 VAL C 28 VAL C 31 1
    809 4 
    810 Start residue of secondary structure not found: HELIX 3 3 VAL C 32 HIS C 34 1
    811 3 
    812 Start residue of secondary structure not found: HELIX 4 4 GLY C 61 ILE C 64 1
    813 4 
    814 Start residue of secondary structure not found: HELIX 5 5 MET C 71 LYS C 74 1
    815 4 
    816 3 messages similar to the above omitted 
    817  
    818 Chain information for sequence_assigned.pdb #3 
    819 --- 
    820 Chain | Description 
    821 C1 | No description available 
    822  
    823 
    824 > open
    825 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/rc-
    826 > dlh1-model1b_rearranged.pdb
    827 
    828 Chain information for rc-dlh1-model1b_rearranged.pdb #4 
    829 --- 
    830 Chain | Description 
    831 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    832 description available 
    833 Aa Ab Ac Ad Ae Af Ah Ai Aj Ak Al Am An Ao Ap | No description available 
    834 Ag | No description available 
    835 B | No description available 
    836 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 Bb
    837 Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | No description available 
    838 C | No description available 
    839 C1 | No description available 
    840 H1 | No description available 
    841 H2 | No description available 
    842 L | No description available 
    843 M | No description available 
    844  
    845 
    846 > hide #!4 models
    847 
    848 > select #3
    849 
    850 1472 atoms, 1487 bonds, 92 residues, 1 model selected 
    851 
    852 > save working.cxs
    853 
    854 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    855 
    856 > hide #3 models
    857 
    858 > select #1
    859 
    860 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    861 
    862 > select #2/Ba
    863 
    864 100 atoms, 99 bonds, 1 residue, 1 model selected 
    865 
    866 > view sel
    867 
    868 > select #1
    869 
    870 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    871 
    872 > select clear
    873 
    874 > select /AA
    875 
    876 1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected 
    877 
    878 > select /BA
    879 
    880 1151 atoms, 1189 bonds, 4 pseudobonds, 79 residues, 3 models selected 
    881 
    882 > isolde stepto /AA
    883 
    884 Multiple residues selected! Going to the first... 
    885 
    886 > select /AA
    887 
    888 1506 atoms, 1545 bonds, 4 pseudobonds, 96 residues, 3 models selected 
    889 
    890 > select clear
    891 
    892 > select clear
    893 
    894 > select /AA
    895 
    896 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    897 
    898 > select clear
    899 
    900 > sequence chain /AA
    901 
    902 Chains must have same sequence 
    903 
    904 > sequence chain #1/AA
    905 
    906 Chains must have same sequence 
    907 
    908 > sequence chain #2/AA
    909 
    910 Alignment identifier is 2.2/AA 
    911 
    912 > select /AA
    913 
    914 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    915 
    916 > select clear
    917 
    918 > select clear
    919 
    920 > select /AA
    921 
    922 1521 atoms, 1560 bonds, 4 pseudobonds, 97 residues, 3 models selected 
    923 
    924 > select clear
    925 
    926 > select clear
    927 
    928 > show #!4 models
    929 
    930 > select #4/AS
    931 
    932 540 atoms, 558 bonds, 4 pseudobonds, 49 residues, 2 models selected 
    933 
    934 > select clear
    935 
    936 > select #4
    937 
    938 51294 atoms, 53027 bonds, 354 pseudobonds, 5083 residues, 3 models selected 
    939 
    940 > style sel stick
    941 
    942 Changed 51294 atom styles 
    943 
    944 > select clear
    945 
    946 > hide #!4 models
    947 
    948 > select clear
    949 
    950 > isolde stepto /C
    951 
    952 Multiple residues selected! Going to the first... 
    953 
    954 > select /C:15-200
    955 
    956 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    957 
    958 > select clear
    959 
    960 > show #!4 models
    961 
    962 > hide #!4 models
    963 
    964 > show #!4 models
    965 
    966 > hide #!4 models
    967 
    968 > isolde stepto
    969 
    970 > isolde stepto
    971 
    972 > isolde stepto
    973 
    974 > show #!4 models
    975 
    976 > hide #!4 models
    977 
    978 reverting to start 
    979 
    980 > select /C1
    981 
    982 4416 atoms, 4461 bonds, 276 residues, 3 models selected 
    983 
    984 > isolde ignore /C1:30-300
    985 
    986 ISOLDE: currently ignoring 63 residues in model 2.2 
    987 ISOLDE: currently ignoring 63 residues in model 3 
    988 ISOLDE: currently ignoring 63 residues in model 4 
    989 
    990 > select /C:15-200
    991 
    992 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    993 
    994 > select /M:311-400
    995 
    996 359 atoms, 361 bonds, 28 residues, 2 models selected 
    997 
    998 > select clear
    999 
    1000 > isolde ~ignore
    1001 
    1002 > show #!4 models
    1003 
    1004 > hide #!4 models
    1005 
    1006 > save working.cxs
    1007 
    1008 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1009 
    1010 > select /C:15-200
    1011 
    1012 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    1013 
    1014 > select clear
    1015 
    1016 > isolde stepto
    1017 
    1018 > hide #1 models
    1019 
    1020 > isolde ignore /C2
    1021 
    1022 ISOLDE: currently ignoring 99 residues in model 2.2 
    1023 
    1024 > select /H2:120-129
    1025 
    1026 241 atoms, 251 bonds, 20 residues, 2 models selected 
    1027 
    1028 > select clear
    1029 
    1030 > select clear
    1031 
    1032 > isolde ~ignore
    1033 
    1034 > select up
    1035 
    1036 22 atoms, 21 bonds, 1 residue, 1 model selected 
    1037 
    1038 > isolde ignore sel
    1039 
    1040 ISOLDE: currently ignoring 1 residues in model 2.2 
    1041 
    1042 > isolde ~ignore
    1043 
    1044 > select clear
    1045 
    1046 > select up
    1047 
    1048 24 atoms, 23 bonds, 1 residue, 1 model selected 
    1049 
    1050 > isolde ignore sel
    1051 
    1052 ISOLDE: currently ignoring 1 residues in model 2.2 
    1053 
    1054 > isolde ~ignore
    1055 
    1056 > select up
    1057 
    1058 14 atoms, 13 bonds, 1 residue, 1 model selected 
    1059 
    1060 > select up
    1061 
    1062 105 atoms, 108 bonds, 7 residues, 1 model selected 
    1063 
    1064 > isolde ignore sel
    1065 
    1066 ISOLDE: currently ignoring 8 residues in model 2.2 
    1067 
    1068 > select up
    1069 
    1070 10 atoms, 9 bonds, 1 residue, 1 model selected 
    1071 
    1072 > select up
    1073 
    1074 939 atoms, 951 bonds, 60 residues, 1 model selected 
    1075 
    1076 > select clear
    1077 
    1078 > show #!4 models
    1079 
    1080 > select clear
    1081 
    1082 > hide #!4 models
    1083 
    1084 > select clear
    1085 
    1086 > select clear
    1087 
    1088 > select clear
    1089 
    1090 > select clear
    1091 
    1092 > select clear
    1093 
    1094 > save working.cxs
    1095 
    1096 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1097 
    1098 > select /C:15-200
    1099 
    1100 4296 atoms, 4372 bonds, 372 residues, 2 models selected 
    1101 
    1102 > select clear
    1103 
    1104 > isolde stepto /C
    1105 
    1106 Multiple residues selected! Going to the first... 
    1107 
    1108 > select clear
    1109 
    1110 > isolde stepto
    1111 
    1112 > isolde stepto
    1113 
    1114 > isolde stepto
    1115 
    1116 > select clear
    1117 
    1118 > show #!4 models
    1119 
    1120 > hide #!4 models
    1121 
    1122 > isolde stepto
    1123 
    1124 > isolde stepto
    1125 
    1126 > isolde stepto
    1127 
    1128 > show #!4 models
    1129 
    1130 > hide #!4 models
    1131 
    1132 > isolde stepto
    1133 
    1134 > isolde stepto
    1135 
    1136 > isolde stepto
    1137 
    1138 > isolde stepto
    1139 
    1140 > isolde stepto
    1141 
    1142 > isolde stepto
    1143 
    1144 > select clear
    1145 
    1146 > isolde stepto
    1147 
    1148 > isolde stepto
    1149 
    1150 > isolde stepto
    1151 
    1152 > isolde stepto
    1153 
    1154 > isolde stepto
    1155 
    1156 > isolde stepto
    1157 
    1158 > isolde stepto
    1159 
    1160 > isolde stepto
    1161 
    1162 > show #!4 models
    1163 
    1164 > hide #!4 models
    1165 
    1166 > show #!4 models
    1167 
    1168 > hide #!4 models
    1169 
    1170 > select clear
    1171 
    1172 > select up
    1173 
    1174 14 atoms, 14 bonds, 1 residue, 1 model selected 
    1175 
    1176 > select up
    1177 
    1178 450 atoms, 459 bonds, 30 residues, 1 model selected 
    1179 
    1180 > select clear
    1181 
    1182 > select clear
    1183 
    1184 > select /C:64-200
    1185 
    1186 3217 atoms, 3269 bonds, 274 residues, 2 models selected 
    1187 
    1188 > select clear
    1189 
    1190 > select clear
    1191 
    1192 > select clear
    1193 
    1194 > isolde stepto /C:64
    1195 
    1196 Multiple residues selected! Going to the first... 
    1197 
    1198 > isolde stepto
    1199 
    1200 > isolde stepto
    1201 
    1202 > isolde stepto
    1203 
    1204 > isolde stepto
    1205 
    1206 > isolde stepto
    1207 
    1208 > isolde stepto
    1209 
    1210 > isolde stepto
    1211 
    1212 > isolde stepto
    1213 
    1214 > isolde stepto
    1215 
    1216 > isolde stepto
    1217 
    1218 > isolde stepto
    1219 
    1220 > isolde stepto
    1221 
    1222 > isolde stepto
    1223 
    1224 > isolde stepto
    1225 
    1226 > isolde stepto
    1227 
    1228 > isolde stepto
    1229 
    1230 > isolde stepto
    1231 
    1232 > isolde stepto
    1233 
    1234 > isolde stepto
    1235 
    1236 > isolde stepto
    1237 
    1238 > isolde stepto
    1239 
    1240 > select clear
    1241 
    1242 > isolde stepto
    1243 
    1244 > isolde stepto
    1245 
    1246 > isolde stepto
    1247 
    1248 > isolde stepto
    1249 
    1250 > isolde stepto
    1251 
    1252 > isolde stepto
    1253 
    1254 > isolde stepto
    1255 
    1256 > isolde stepto
    1257 
    1258 > isolde stepto
    1259 
    1260 > isolde stepto
    1261 
    1262 > isolde stepto
    1263 
    1264 > isolde stepto
    1265 
    1266 > isolde stepto
    1267 
    1268 > isolde stepto
    1269 
    1270 > select clear
    1271 
    1272 > delete sel
    1273 
    1274 > select /C:99-200
    1275 
    1276 2415 atoms, 2455 bonds, 204 residues, 2 models selected 
    1277 
    1278 > select clear
    1279 
    1280 > select clear
    1281 
    1282 > select clear
    1283 
    1284 > isolde stepto
    1285 
    1286 > isolde stepto
    1287 
    1288 > isolde stepto
    1289 
    1290 > isolde stepto
    1291 
    1292 > isolde stepto
    1293 
    1294 > isolde stepto
    1295 
    1296 > isolde stepto
    1297 
    1298 > isolde stepto
    1299 
    1300 > select clear
    1301 
    1302 > isolde stepto
    1303 
    1304 > isolde stepto
    1305 
    1306 > isolde stepto
    1307 
    1308 > isolde stepto
    1309 
    1310 > isolde stepto
    1311 
    1312 > isolde stepto
    1313 
    1314 > isolde stepto
    1315 
    1316 > isolde stepto
    1317 
    1318 > select clear
    1319 
    1320 > isolde stepto
    1321 
    1322 > isolde stepto
    1323 
    1324 > isolde stepto
    1325 
    1326 > isolde stepto
    1327 
    1328 > isolde stepto
    1329 
    1330 > isolde stepto
    1331 
    1332 > isolde stepto
    1333 
    1334 > isolde stepto
    1335 
    1336 > isolde stepto
    1337 
    1338 > isolde stepto
    1339 
    1340 > isolde stepto
    1341 
    1342 > isolde stepto
    1343 
    1344 > isolde stepto
    1345 
    1346 > isolde stepto
    1347 
    1348 > isolde stepto
    1349 
    1350 > isolde stepto
    1351 
    1352 > isolde stepto
    1353 
    1354 > isolde stepto
    1355 
    1356 > isolde stepto
    1357 
    1358 > isolde stepto
    1359 
    1360 > isolde stepto
    1361 
    1362 > isolde stepto
    1363 
    1364 > isolde stepto
    1365 
    1366 > isolde stepto
    1367 
    1368 > isolde stepto
    1369 
    1370 > isolde stepto
    1371 
    1372 > isolde stepto
    1373 
    1374 > isolde stepto
    1375 
    1376 > isolde stepto
    1377 
    1378 > isolde stepto
    1379 
    1380 > isolde stepto
    1381 
    1382 > isolde stepto
    1383 
    1384 > isolde stepto
    1385 
    1386 > isolde stepto
    1387 
    1388 > isolde stepto
    1389 
    1390 > isolde stepto
    1391 
    1392 > isolde stepto
    1393 
    1394 > isolde stepto
    1395 
    1396 > isolde stepto
    1397 
    1398 > isolde stepto
    1399 
    1400 > isolde stepto
    1401 
    1402 > isolde stepto
    1403 
    1404 > isolde stepto
    1405 
    1406 > isolde stepto
    1407 
    1408 > isolde stepto
    1409 
    1410 > isolde stepto
    1411 
    1412 > isolde stepto
    1413 
    1414 > show #!4 models
    1415 
    1416 > hide #!4 models
    1417 
    1418 > show #!4 models
    1419 
    1420 > hide #!4 models
    1421 
    1422 > isolde stepto
    1423 
    1424 > isolde stepto
    1425 
    1426 > isolde stepto
    1427 
    1428 > isolde stepto
    1429 
    1430 > isolde stepto
    1431 
    1432 > isolde stepto
    1433 
    1434 > isolde stepto
    1435 
    1436 > isolde stepto
    1437 
    1438 > isolde stepto
    1439 
    1440 > isolde stepto
    1441 
    1442 > isolde stepto
    1443 
    1444 > isolde stepto
    1445 
    1446 > show #!4 models
    1447 
    1448 > hide #!4 models
    1449 
    1450 > select /C:179-189
    1451 
    1452 241 atoms, 241 bonds, 22 residues, 2 models selected 
    1453 
    1454 > select #2/C:179-189
    1455 
    1456 162 atoms, 162 bonds, 11 residues, 1 model selected 
    1457 
    1458 > select clear
    1459 
    1460 > isolde stepto
    1461 
    1462 > isolde stepto
    1463 
    1464 > select clear
    1465 
    1466 > isolde stepto
    1467 
    1468 > isolde stepto
    1469 
    1470 > isolde stepto
    1471 
    1472 > isolde stepto
    1473 
    1474 > isolde stepto
    1475 
    1476 > isolde stepto
    1477 
    1478 > isolde stepto
    1479 
    1480 > select clear
    1481 
    1482 > isolde stepto
    1483 
    1484 > isolde stepto
    1485 
    1486 > isolde stepto
    1487 
    1488 > isolde stepto
    1489 
    1490 > isolde stepto
    1491 
    1492 > isolde stepto
    1493 
    1494 > isolde stepto
    1495 
    1496 > isolde stepto
    1497 
    1498 > isolde stepto
    1499 
    1500 > isolde stepto
    1501 
    1502 > isolde stepto
    1503 
    1504 > isolde stepto
    1505 
    1506 > isolde stepto
    1507 
    1508 > isolde stepto
    1509 
    1510 > isolde stepto
    1511 
    1512 > isolde stepto
    1513 
    1514 > isolde stepto
    1515 
    1516 > isolde stepto
    1517 
    1518 > isolde stepto
    1519 
    1520 > isolde stepto
    1521 
    1522 > isolde stepto
    1523 
    1524 > isolde stepto
    1525 
    1526 > isolde stepto
    1527 
    1528 > isolde stepto
    1529 
    1530 > isolde stepto
    1531 
    1532 > isolde stepto
    1533 
    1534 > isolde stepto
    1535 
    1536 > isolde stepto
    1537 
    1538 > save working.cxs
    1539 
    1540 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1541 
    1542 > select /C:200-400
    1543 
    1544 2486 atoms, 2541 bonds, 217 residues, 2 models selected 
    1545 
    1546 > select clear
    1547 
    1548 > select clear
    1549 
    1550 > isolde stepto
    1551 
    1552 > isolde stepto
    1553 
    1554 > isolde stepto
    1555 
    1556 > isolde stepto
    1557 
    1558 > isolde stepto
    1559 
    1560 > isolde stepto
    1561 
    1562 > isolde stepto
    1563 
    1564 > isolde stepto
    1565 
    1566 > isolde stepto
    1567 
    1568 > isolde stepto
    1569 
    1570 > isolde stepto
    1571 
    1572 > isolde stepto
    1573 
    1574 > isolde stepto
    1575 
    1576 > isolde stepto
    1577 
    1578 > isolde stepto
    1579 
    1580 > isolde stepto
    1581 
    1582 > isolde stepto
    1583 
    1584 > isolde stepto
    1585 
    1586 > isolde stepto
    1587 
    1588 > isolde stepto
    1589 
    1590 > isolde stepto
    1591 
    1592 > isolde stepto
    1593 
    1594 > isolde stepto
    1595 
    1596 > isolde stepto
    1597 
    1598 > isolde stepto
    1599 
    1600 > isolde stepto
    1601 
    1602 > isolde stepto
    1603 
    1604 > isolde stepto
    1605 
    1606 > isolde stepto
    1607 
    1608 > isolde stepto
    1609 
    1610 > isolde stepto
    1611 
    1612 > isolde stepto
    1613 
    1614 > isolde stepto
    1615 
    1616 > isolde stepto
    1617 
    1618 > isolde stepto
    1619 
    1620 > isolde stepto
    1621 
    1622 > isolde stepto
    1623 
    1624 > isolde stepto
    1625 
    1626 > isolde stepto
    1627 
    1628 > select clear
    1629 
    1630 > isolde stepto
    1631 
    1632 > isolde stepto
    1633 
    1634 > isolde stepto
    1635 
    1636 > isolde stepto
    1637 
    1638 > isolde stepto
    1639 
    1640 > isolde stepto
    1641 
    1642 > isolde stepto
    1643 
    1644 > isolde stepto
    1645 
    1646 > isolde stepto
    1647 
    1648 > isolde stepto
    1649 
    1650 > isolde stepto
    1651 
    1652 > isolde stepto
    1653 
    1654 > isolde stepto
    1655 
    1656 > isolde stepto
    1657 
    1658 > isolde stepto
    1659 
    1660 > isolde stepto
    1661 
    1662 > isolde stepto
    1663 
    1664 > isolde stepto
    1665 
    1666 > isolde stepto
    1667 
    1668 > isolde stepto
    1669 
    1670 > isolde stepto
    1671 
    1672 > isolde stepto
    1673 
    1674 > isolde stepto
    1675 
    1676 > isolde stepto
    1677 
    1678 > isolde stepto
    1679 
    1680 > isolde stepto
    1681 
    1682 > isolde stepto
    1683 
    1684 > select clear
    1685 
    1686 > isolde stepto
    1687 
    1688 > isolde stepto
    1689 
    1690 > isolde stepto
    1691 
    1692 > isolde stepto
    1693 
    1694 > isolde stepto
    1695 
    1696 > isolde stepto
    1697 
    1698 > isolde stepto
    1699 
    1700 > isolde stepto
    1701 
    1702 > isolde stepto
    1703 
    1704 > isolde stepto
    1705 
    1706 > isolde stepto
    1707 
    1708 > isolde stepto
    1709 
    1710 > isolde stepto
    1711 
    1712 > isolde stepto
    1713 
    1714 > isolde stepto
    1715 
    1716 > isolde stepto
    1717 
    1718 > isolde stepto
    1719 
    1720 > isolde stepto
    1721 
    1722 > isolde stepto
    1723 
    1724 > isolde stepto
    1725 
    1726 > isolde stepto
    1727 
    1728 > isolde stepto
    1729 
    1730 > isolde stepto
    1731 
    1732 > isolde stepto
    1733 
    1734 > show #!4 models
    1735 
    1736 > save working.cxs
    1737 
    1738 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    1739 
    1740 > select #4/C:303-313
    1741 
    1742 83 atoms, 87 bonds, 11 residues, 1 model selected 
    1743 
    1744 > select clear
    1745 
    1746 > hide #!4 models
    1747 
    1748 > select #2/C:303-400
    1749 
    1750 83 atoms, 87 bonds, 11 residues, 1 model selected 
    1751 
    1752 > show sel
    1753 
    1754 > delete sell
    1755 
    1756 Missing or invalid "atoms" argument: invalid atoms specifier 
    1757 
    1758 > delete sel
    1759 
    1760 > addh #4
    1761 
    1762 Summary of feedback from adding hydrogens to rc-dlh1-model1b_rearranged.pdb #4 
    1763 --- 
    1764 warning | Skipped 8 atom(s) with bad connectivities; see log for details 
    1765 notes | No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain
    1766 AA; guessing termini instead 
    1767 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AB;
    1768 guessing termini instead 
    1769 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AC;
    1770 guessing termini instead 
    1771 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AD;
    1772 guessing termini instead 
    1773 No usable SEQRES records for rc-dlh1-model1b_rearranged.pdb (#4) chain AE;
    1774 guessing termini instead 
    1775 82 messages similar to the above omitted 
    1776 Chain-initial residues that are actual N termini: rc-
    1777 dlh1-model1b_rearranged.pdb #4/AA HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AB
    1778 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AC HIS 2, rc-
    1779 dlh1-model1b_rearranged.pdb #4/AD HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AE
    1780 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AF HIS 2, rc-
    1781 dlh1-model1b_rearranged.pdb #4/AG HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AH
    1782 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AI HIS 2, rc-
    1783 dlh1-model1b_rearranged.pdb #4/AJ HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AK
    1784 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AL HIS 2, rc-
    1785 dlh1-model1b_rearranged.pdb #4/AM HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AN
    1786 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AO HIS 2, rc-
    1787 dlh1-model1b_rearranged.pdb #4/AP HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AQ
    1788 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AR HIS 2, rc-
    1789 dlh1-model1b_rearranged.pdb #4/AS HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AT
    1790 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AU HIS 2, rc-
    1791 dlh1-model1b_rearranged.pdb #4/AV HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AW
    1792 HIS 2, rc-dlh1-model1b_rearranged.pdb #4/AX HIS 2, rc-
    1793 dlh1-model1b_rearranged.pdb #4/Aa MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ab
    1794 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ac MET 1, rc-
    1795 dlh1-model1b_rearranged.pdb #4/Ad MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ae
    1796 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Af MET 1, rc-
    1797 dlh1-model1b_rearranged.pdb #4/Ag MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ah
    1798 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ai MET 1, rc-
    1799 dlh1-model1b_rearranged.pdb #4/Aj MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ak
    1800 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Al MET 1, rc-
    1801 dlh1-model1b_rearranged.pdb #4/Am MET 1, rc-dlh1-model1b_rearranged.pdb #4/An
    1802 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ao MET 1, rc-
    1803 dlh1-model1b_rearranged.pdb #4/Ap MET 1, rc-dlh1-model1b_rearranged.pdb #4/B
    1804 PRO 25, rc-dlh1-model1b_rearranged.pdb #4/BA MET 1, rc-
    1805 dlh1-model1b_rearranged.pdb #4/BB MET 1, rc-dlh1-model1b_rearranged.pdb #4/BC
    1806 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BD MET 1, rc-
    1807 dlh1-model1b_rearranged.pdb #4/BE MET 1, rc-dlh1-model1b_rearranged.pdb #4/BF
    1808 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BG MET 1, rc-
    1809 dlh1-model1b_rearranged.pdb #4/BH MET 1, rc-dlh1-model1b_rearranged.pdb #4/BI
    1810 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BJ MET 1, rc-
    1811 dlh1-model1b_rearranged.pdb #4/BK MET 1, rc-dlh1-model1b_rearranged.pdb #4/BL
    1812 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BM MET 1, rc-
    1813 dlh1-model1b_rearranged.pdb #4/BN MET 1, rc-dlh1-model1b_rearranged.pdb #4/BO
    1814 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BP MET 1, rc-
    1815 dlh1-model1b_rearranged.pdb #4/BQ MET 1, rc-dlh1-model1b_rearranged.pdb #4/BR
    1816 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BS MET 1, rc-
    1817 dlh1-model1b_rearranged.pdb #4/BT MET 1, rc-dlh1-model1b_rearranged.pdb #4/BU
    1818 MET 1, rc-dlh1-model1b_rearranged.pdb #4/BV MET 1, rc-
    1819 dlh1-model1b_rearranged.pdb #4/BW MET 1, rc-dlh1-model1b_rearranged.pdb #4/BX
    1820 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Ba MET 1, rc-
    1821 dlh1-model1b_rearranged.pdb #4/Bb MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bc
    1822 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bd MET 1, rc-
    1823 dlh1-model1b_rearranged.pdb #4/Be MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bf
    1824 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bg MET 1, rc-
    1825 dlh1-model1b_rearranged.pdb #4/Bh MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bi
    1826 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bj MET 1, rc-
    1827 dlh1-model1b_rearranged.pdb #4/Bk MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bl
    1828 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bm MET 1, rc-
    1829 dlh1-model1b_rearranged.pdb #4/Bn MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bo
    1830 MET 1, rc-dlh1-model1b_rearranged.pdb #4/Bp MET 1, rc-
    1831 dlh1-model1b_rearranged.pdb #4/C ALA 15, rc-dlh1-model1b_rearranged.pdb #4/H1
    1832 MET 1, rc-dlh1-model1b_rearranged.pdb #4/H2 SER 1, rc-
    1833 dlh1-model1b_rearranged.pdb #4/L ALA 1, rc-dlh1-model1b_rearranged.pdb #4/M
    1834 MET 1 
    1835 Chain-initial residues that are not actual N termini: rc-
    1836 dlh1-model1b_rearranged.pdb #4/C1 GLN 1, rc-dlh1-model1b_rearranged.pdb #4/H2
    1837 ARG 38 
    1838 Chain-final residues that are actual C termini: rc-dlh1-model1b_rearranged.pdb
    1839 #4/BA PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BB PHE 38, rc-
    1840 dlh1-model1b_rearranged.pdb #4/BC PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BD
    1841 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BE PHE 38, rc-
    1842 dlh1-model1b_rearranged.pdb #4/BF PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BG
    1843 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BH PHE 38, rc-
    1844 dlh1-model1b_rearranged.pdb #4/BI PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BJ
    1845 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BK PHE 38, rc-
    1846 dlh1-model1b_rearranged.pdb #4/BL PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BM
    1847 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BN PHE 38, rc-
    1848 dlh1-model1b_rearranged.pdb #4/BO PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BP
    1849 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BQ PHE 38, rc-
    1850 dlh1-model1b_rearranged.pdb #4/BR PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BS
    1851 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BT PHE 38, rc-
    1852 dlh1-model1b_rearranged.pdb #4/BU PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BV
    1853 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/BW PHE 38, rc-
    1854 dlh1-model1b_rearranged.pdb #4/BX PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Ba
    1855 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bb PHE 38, rc-
    1856 dlh1-model1b_rearranged.pdb #4/Bc PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bd
    1857 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Be PHE 38, rc-
    1858 dlh1-model1b_rearranged.pdb #4/Bf PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bg
    1859 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bh PHE 38, rc-
    1860 dlh1-model1b_rearranged.pdb #4/Bi PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bj
    1861 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bk PHE 38, rc-
    1862 dlh1-model1b_rearranged.pdb #4/Bl PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bm
    1863 PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bn PHE 38, rc-
    1864 dlh1-model1b_rearranged.pdb #4/Bo PHE 38, rc-dlh1-model1b_rearranged.pdb #4/Bp
    1865 PHE 38 
    1866 Chain-final residues that are not actual C termini: rc-
    1867 dlh1-model1b_rearranged.pdb #4/AA PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AB
    1868 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48, rc-
    1869 dlh1-model1b_rearranged.pdb #4/AD PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AE
    1870 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AF PRO 48, rc-
    1871 dlh1-model1b_rearranged.pdb #4/AG PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AH
    1872 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AI PRO 48, rc-
    1873 dlh1-model1b_rearranged.pdb #4/AJ PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AK
    1874 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AL PRO 48, rc-
    1875 dlh1-model1b_rearranged.pdb #4/AM PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AN
    1876 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AO PRO 48, rc-
    1877 dlh1-model1b_rearranged.pdb #4/AP PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AQ
    1878 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AR PRO 48, rc-
    1879 dlh1-model1b_rearranged.pdb #4/AS PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AT
    1880 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AU PRO 48, rc-
    1881 dlh1-model1b_rearranged.pdb #4/AV PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AW
    1882 PRO 48, rc-dlh1-model1b_rearranged.pdb #4/AX PRO 48, rc-
    1883 dlh1-model1b_rearranged.pdb #4/Aa ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ab
    1884 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ac ALA 60, rc-
    1885 dlh1-model1b_rearranged.pdb #4/Ad ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ae
    1886 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Af ALA 60, rc-
    1887 dlh1-model1b_rearranged.pdb #4/Ag LEU 67, rc-dlh1-model1b_rearranged.pdb #4/Ah
    1888 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ai ALA 60, rc-
    1889 dlh1-model1b_rearranged.pdb #4/Aj ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ak
    1890 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Al ALA 60, rc-
    1891 dlh1-model1b_rearranged.pdb #4/Am ALA 60, rc-dlh1-model1b_rearranged.pdb #4/An
    1892 ALA 60, rc-dlh1-model1b_rearranged.pdb #4/Ao ALA 60, rc-
    1893 dlh1-model1b_rearranged.pdb #4/Ap ALA 60, rc-dlh1-model1b_rearranged.pdb #4/B
    1894 ILE 123, rc-dlh1-model1b_rearranged.pdb #4/C ILE 313, rc-
    1895 dlh1-model1b_rearranged.pdb #4/C1 LEU 92, rc-dlh1-model1b_rearranged.pdb #4/H1
    1896 HIS 67, rc-dlh1-model1b_rearranged.pdb #4/H2 ILE 181, rc-
    1897 dlh1-model1b_rearranged.pdb #4/H2 ARG 36, rc-dlh1-model1b_rearranged.pdb #4/L
    1898 TRP 272, rc-dlh1-model1b_rearranged.pdb #4/M TYR 324 
    1899 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1900 #4/C ARG 302 O 
    1901 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1902 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1903  
    1904 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1905 #4/C ARG 302 OXT 
    1906 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1907 dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT 
    1908  
    1909 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1910 #4/C ARG 302 OXT 
    1911 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1912 dlh1-model1b_rearranged.pdb #4/C ARG 302 OXT 
    1913  
    1914 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1915 #4/C ARG 302 O 
    1916 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1917 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1918  
    1919 Skipping possible acceptor with bad geometry: rc-dlh1-model1b_rearranged.pdb
    1920 #4/C ARG 302 O 
    1921 Wrong number of grandchild atoms for phi/psi acceptor rc-
    1922 dlh1-model1b_rearranged.pdb #4/C ARG 302 O 
    1923  
    1924 3 messages similar to the above omitted 
    1925 4768 hydrogen bonds 
    1926 Adding 'H' to rc-dlh1-model1b_rearranged.pdb #4/H2 ARG 38 
    1927 rc-dlh1-model1b_rearranged.pdb #4/AA PRO 48 is not terminus, removing H atom
    1928 from 'C' 
    1929 rc-dlh1-model1b_rearranged.pdb #4/AB PRO 48 is not terminus, removing H atom
    1930 from 'C' 
    1931 rc-dlh1-model1b_rearranged.pdb #4/AC PRO 48 is not terminus, removing H atom
    1932 from 'C' 
    1933 rc-dlh1-model1b_rearranged.pdb #4/AD PRO 48 is not terminus, removing H atom
    1934 from 'C' 
    1935 rc-dlh1-model1b_rearranged.pdb #4/AE PRO 48 is not terminus, removing H atom
    1936 from 'C' 
    1937 42 messages similar to the above omitted 
    1938 44090 hydrogens added 
    1939  
    1940 
    1941 > select #2/C:303-400
    1942 
    1943 157 atoms, 161 bonds, 11 residues, 1 model selected 
    1944 
    1945 > select clear
    1946 
    1947 > isolde stepto
    1948 
    1949 > isolde stepto
    1950 
    1951 > isolde stepto
    1952 
    1953 > isolde stepto
    1954 
    1955 > isolde stepto
    1956 
    1957 > isolde stepto
    1958 
    1959 > isolde stepto
    1960 
    1961 > isolde stepto
    1962 
    1963 > isolde stepto
    1964 
    1965 > isolde stepto
    1966 
    1967 > isolde stepto
    1968 
    1969 > isolde stepto
    1970 
    1971 > isolde stepto
    1972 
    1973 > show #!4 models
    1974 
    1975 > hide #!4 models
    1976 
    1977 > select up
    1978 
    1979 12 atoms, 11 bonds, 1 residue, 1 model selected 
    1980 
    1981 > select up
    1982 
    1983 874 atoms, 890 bonds, 53 residues, 1 model selected 
    1984 
    1985 > select #2/H1:3-100
    1986 
    1987 838 atoms, 854 bonds, 51 residues, 1 model selected 
    1988 
    1989 > show #!4 models
    1990 
    1991 > hide #!4 models
    1992 
    1993 > isolde stepto
    1994 
    1995 > isolde stepto
    1996 
    1997 > isolde stepto
    1998 
    1999 > isolde stepto
    2000 
    2001 > isolde stepto
    2002 
    2003 > isolde stepto
    2004 
    2005 > isolde stepto
    2006 
    2007 > isolde stepto
    2008 
    2009 > isolde stepto
    2010 
    2011 > isolde stepto
    2012 
    2013 > isolde stepto
    2014 
    2015 > isolde stepto
    2016 
    2017 > isolde stepto
    2018 
    2019 > isolde stepto
    2020 
    2021 > isolde stepto
    2022 
    2023 > isolde stepto
    2024 
    2025 > isolde stepto
    2026 
    2027 > isolde stepto
    2028 
    2029 > isolde stepto
    2030 
    2031 > isolde stepto
    2032 
    2033 > isolde stepto
    2034 
    2035 > isolde stepto
    2036 
    2037 > isolde stepto
    2038 
    2039 > isolde stepto
    2040 
    2041 > isolde stepto
    2042 
    2043 > isolde stepto
    2044 
    2045 > isolde stepto
    2046 
    2047 > isolde stepto
    2048 
    2049 > isolde stepto
    2050 
    2051 > isolde stepto
    2052 
    2053 > isolde stepto
    2054 
    2055 > isolde stepto
    2056 
    2057 > isolde stepto
    2058 
    2059 > isolde stepto
    2060 
    2061 > isolde stepto
    2062 
    2063 > isolde stepto
    2064 
    2065 > isolde stepto
    2066 
    2067 > isolde stepto
    2068 
    2069 > isolde stepto
    2070 
    2071 > show #!4 models
    2072 
    2073 > hide #!4 models
    2074 
    2075 > select up
    2076 
    2077 38 atoms, 40 bonds, 2 residues, 1 model selected 
    2078 
    2079 > select clear
    2080 
    2081 > select clear
    2082 
    2083 > select #1
    2084 
    2085 1516 atoms, 1537 bonds, 99 residues, 1 model selected 
    2086 
    2087 > select #2
    2088 
    2089 94789 atoms, 96857 bonds, 14 pseudobonds, 5061 residues, 22 models selected 
    2090 
    2091 > style sel sphere
    2092 
    2093 Changed 94789 atom styles 
    2094 
    2095 > select clear
    2096 
    2097 > style #!2.2 stick
    2098 
    2099 Changed 94789 atom styles 
    2100 
    2101 > delete sel
    2102 
    2103 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2104 bonded heavy atom. 
    2105 
    2106 > delete sel
    2107 
    2108 > delete sel
    2109 
    2110 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2111 bonded heavy atom. 
    2112 
    2113 > delete sel
    2114 
    2115 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2116 bonded heavy atom. 
    2117 
    2118 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    2119 bonded heavy atom. 
    2120 
    2121 > select #2/H2
    2122 
    2123 2777 atoms, 2816 bonds, 180 residues, 1 model selected 
    2124 
    2125 > select clear
    2126 
    2127 > isolde jumpto
    2128 
    2129 > select #2/H2:3-100
    2130 
    2131 1476 atoms, 1499 bonds, 97 residues, 1 model selected 
    2132 
    2133 > select clear
    2134 
    2135 > select clear
    2136 
    2137 > isolde stepto
    2138 
    2139 > isolde stepto
    2140 
    2141 > isolde stepto
    2142 
    2143 > isolde stepto
    2144 
    2145 > isolde stepto
    2146 
    2147 > isolde stepto
    2148 
    2149 > isolde stepto
    2150 
    2151 > isolde stepto
    2152 
    2153 > isolde stepto
    2154 
    2155 > isolde stepto
    2156 
    2157 > isolde stepto
    2158 
    2159 > isolde stepto
    2160 
    2161 > isolde stepto
    2162 
    2163 > isolde stepto
    2164 
    2165 > select #2/H2:3-100
    2166 
    2167 1476 atoms, 1499 bonds, 97 residues, 1 model selected 
    2168 
    2169 > select clear
    2170 
    2171 > isolde stepto
    2172 
    2173 > isolde stepto
    2174 
    2175 > isolde stepto
    2176 
    2177 > isolde stepto
    2178 
    2179 > isolde stepto
    2180 
    2181 > isolde stepto
    2182 
    2183 > isolde stepto
    2184 
    2185 > isolde stepto
    2186 
    2187 > isolde stepto
    2188 
    2189 > isolde stepto
    2190 
    2191 > isolde stepto
    2192 
    2193 > isolde stepto
    2194 
    2195 > isolde stepto
    2196 
    2197 > isolde stepto
    2198 
    2199 > isolde stepto
    2200 
    2201 > isolde stepto
    2202 
    2203 > isolde stepto
    2204 
    2205 > isolde stepto
    2206 
    2207 > isolde stepto
    2208 
    2209 > isolde stepto
    2210 
    2211 > isolde stepto
    2212 
    2213 > isolde stepto
    2214 
    2215 > isolde stepto
    2216 
    2217 > isolde stepto
    2218 
    2219 > isolde stepto
    2220 
    2221 > isolde stepto
    2222 
    2223 > isolde stepto
    2224 
    2225 > isolde stepto
    2226 
    2227 > isolde stepto
    2228 
    2229 > isolde stepto
    2230 
    2231 > isolde stepto
    2232 
    2233 > isolde stepto
    2234 
    2235 > isolde stepto
    2236 
    2237 > isolde stepto
    2238 
    2239 > isolde stepto
    2240 
    2241 > isolde stepto
    2242 
    2243 > isolde stepto
    2244 
    2245 > isolde stepto
    2246 
    2247 > isolde stepto
    2248 
    2249 > isolde stepto
    2250 
    2251 > isolde stepto
    2252 
    2253 > isolde stepto
    2254 
    2255 > isolde stepto
    2256 
    2257 > isolde stepto
    2258 
    2259 > isolde stepto
    2260 
    2261 > isolde stepto
    2262 
    2263 > isolde stepto
    2264 
    2265 > isolde stepto
    2266 
    2267 > isolde stepto
    2268 
    2269 > isolde stepto
    2270 
    2271 > isolde stepto
    2272 
    2273 > isolde stepto
    2274 
    2275 > isolde stepto
    2276 
    2277 > isolde stepto
    2278 
    2279 > isolde stepto
    2280 
    2281 > isolde stepto
    2282 
    2283 > isolde stepto
    2284 
    2285 > isolde stepto
    2286 
    2287 > isolde stepto
    2288 
    2289 > isolde stepto
    2290 
    2291 > isolde stepto
    2292 
    2293 > isolde stepto
    2294 
    2295 > isolde stepto
    2296 
    2297 > isolde stepto
    2298 
    2299 > isolde stepto
    2300 
    2301 > isolde stepto
    2302 
    2303 > isolde stepto
    2304 
    2305 > isolde stepto
    2306 
    2307 > isolde stepto
    2308 
    2309 > isolde stepto
    2310 
    2311 > isolde stepto
    2312 
    2313 > isolde stepto
    2314 
    2315 > isolde stepto
    2316 
    2317 > isolde stepto
    2318 
    2319 > isolde stepto
    2320 
    2321 > isolde stepto
    2322 
    2323 > isolde stepto
    2324 
    2325 > isolde stepto
    2326 
    2327 > isolde stepto
    2328 
    2329 > select #2/H1:95-205
    2330 
    2331 Nothing selected 
    2332 
    2333 > select #2/H1:95-205
    2334 
    2335 Nothing selected 
    2336 
    2337 > select #2/H2:95-205
    2338 
    2339 1376 atoms, 1394 bonds, 87 residues, 1 model selected 
    2340 
    2341 > select clear
    2342 
    2343 > isolde stepto
    2344 
    2345 > isolde stepto
    2346 
    2347 > isolde stepto
    2348 
    2349 > isolde stepto
    2350 
    2351 > isolde stepto
    2352 
    2353 > isolde stepto
    2354 
    2355 > isolde stepto
    2356 
    2357 > isolde stepto
    2358 
    2359 > isolde stepto
    2360 
    2361 > isolde stepto
    2362 
    2363 > select clear
    2364 
    2365 > isolde stepto
    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 > isolde stepto
    2396 
    2397 > isolde stepto
    2398 
    2399 > isolde stepto
    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 > save working.cxs
    2520 
    2521 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    2522 
    2523 > isolde stepto
    2524 
    2525 > select #2/L:1-100
    2526 
    2527 1563 atoms, 1592 bonds, 100 residues, 1 model selected 
    2528 
    2529 > select clear
    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 > select clear
    2552 
    2553 > isolde stepto
    2554 
    2555 > isolde stepto
    2556 
    2557 > isolde stepto
    2558 
    2559 > isolde stepto
    2560 
    2561 > isolde stepto
    2562 
    2563 > isolde stepto
    2564 
    2565 > isolde stepto
    2566 
    2567 > isolde stepto
    2568 
    2569 > isolde stepto
    2570 
    2571 > isolde stepto
    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 > isolde stepto
    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 > select clear
    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 > isolde stepto
    2750 
    2751 > isolde stepto
    2752 
    2753 > isolde stepto
    2754 
    2755 > select #2/L:100-300
    2756 
    2757 2756 atoms, 2816 bonds, 174 residues, 1 model selected 
    2758 
    2759 > select clear
    2760 
    2761 > select clear
    2762 
    2763 > isolde stepto
    2764 
    2765 > isolde stepto
    2766 
    2767 > isolde stepto
    2768 
    2769 > select clear
    2770 
    2771 > isolde stepto
    2772 
    2773 > isolde stepto
    2774 
    2775 > isolde stepto
    2776 
    2777 > isolde stepto
    2778 
    2779 > isolde stepto
    2780 
    2781 > isolde stepto
    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 > isolde stepto
    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 > select clear
    2952 
    2953 > isolde stepto
    2954 
    2955 > isolde stepto
    2956 
    2957 > isolde stepto
    2958 
    2959 > isolde stepto
    2960 
    2961 > select clear
    2962 
    2963 > isolde stepto
    2964 
    2965 > isolde stepto
    2966 
    2967 > isolde stepto
    2968 
    2969 > select clear
    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 > isolde stepto
    2986 
    2987 > isolde stepto
    2988 
    2989 > isolde stepto
    2990 
    2991 > isolde stepto
    2992 
    2993 > isolde stepto
    2994 
    2995 > isolde stepto
    2996 
    2997 > isolde stepto
    2998 
    2999 > isolde stepto
    3000 
    3001 > swapaa mousemode sel ILE
    3002 
    3003 > select up
    3004 
    3005 19 atoms, 18 bonds, 1 residue, 1 model selected 
    3006 
    3007 > color sel bychain
    3008 
    3009 > color sel byhetero
    3010 
    3011 > select #2/L:227-400
    3012 
    3013 777 atoms, 798 bonds, 47 residues, 1 model selected 
    3014 
    3015 > hide HC
    3016 
    3017 > select up
    3018 
    3019 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3020 
    3021 > color sel byhetero
    3022 
    3023 > select clear
    3024 
    3025 > color bychain
    3026 
    3027 > color byhetero
    3028 
    3029 > hide HC
    3030 
    3031 > select #2/L:227-400
    3032 
    3033 777 atoms, 798 bonds, 47 residues, 1 model selected 
    3034 
    3035 > select clear
    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 > select clear
    3078 
    3079 > show H&~HC
    3080 
    3081 > select clear
    3082 
    3083 > show H&~HC
    3084 
    3085 > show ~H
    3086 
    3087 > select #2/L:227-400
    3088 
    3089 777 atoms, 798 bonds, 47 residues, 1 model selected 
    3090 
    3091 > select clear
    3092 
    3093 > select clear
    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 > select #2/M
    3150 
    3151 5833 atoms, 5950 bonds, 6 pseudobonds, 330 residues, 2 models selected 
    3152 
    3153 > select #2/M:1-50
    3154 
    3155 763 atoms, 772 bonds, 50 residues, 1 model selected 
    3156 
    3157 > select clear
    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 > isolde stepto
    3182 
    3183 > isolde stepto
    3184 
    3185 > isolde stepto
    3186 
    3187 > select clear
    3188 
    3189 > select clear
    3190 
    3191 > isolde stepto
    3192 
    3193 > isolde stepto
    3194 
    3195 > isolde stepto
    3196 
    3197 > isolde stepto
    3198 
    3199 > isolde stepto
    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 > isolde stepto
    3232 
    3233 > isolde stepto
    3234 
    3235 > isolde stepto
    3236 
    3237 > isolde stepto
    3238 
    3239 > isolde stepto
    3240 
    3241 > isolde stepto
    3242 
    3243 > isolde stepto
    3244 
    3245 > isolde stepto
    3246 
    3247 > isolde stepto
    3248 
    3249 > isolde stepto
    3250 
    3251 > isolde stepto
    3252 
    3253 > isolde stepto
    3254 
    3255 > isolde stepto
    3256 
    3257 > isolde stepto
    3258 
    3259 > isolde stepto
    3260 
    3261 > isolde stepto
    3262 
    3263 > isolde stepto
    3264 
    3265 > isolde stepto
    3266 
    3267 > isolde stepto
    3268 
    3269 > isolde stepto
    3270 
    3271 > isolde stepto
    3272 
    3273 > isolde stepto
    3274 
    3275 > isolde stepto
    3276 
    3277 > select #2/M:58-158
    3278 
    3279 1664 atoms, 1698 bonds, 101 residues, 1 model selected 
    3280 
    3281 > select clear
    3282 
    3283 > select #2/M:58-158
    3284 
    3285 1664 atoms, 1698 bonds, 101 residues, 1 model selected 
    3286 
    3287 > select clear
    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 > select clear
    3306 
    3307 > isolde stepto
    3308 
    3309 > isolde stepto
    3310 
    3311 > isolde stepto
    3312 
    3313 > isolde stepto
    3314 
    3315 > sequence chain #2/M
    3316 
    3317 Alignment identifier is 2.2/M 
    3318 
    3319 > select #2/M:58-158
    3320 
    3321 1665 atoms, 1699 bonds, 101 residues, 1 model selected 
    3322 
    3323 > select clear
    3324 
    3325 > select clear
    3326 
    3327 > isolde stepto
    3328 
    3329 > isolde stepto
    3330 
    3331 > isolde stepto
    3332 
    3333 > isolde stepto
    3334 
    3335 > select clear
    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 > select clear
    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 > isolde stepto
    3380 
    3381 > isolde stepto
    3382 
    3383 > isolde stepto
    3384 
    3385 > isolde stepto
    3386 
    3387 > isolde stepto
    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 > select clear
    3404 
    3405 > isolde stepto
    3406 
    3407 > isolde stepto
    3408 
    3409 > isolde stepto
    3410 
    3411 > isolde stepto
    3412 
    3413 > select clear
    3414 
    3415 > isolde stepto
    3416 
    3417 > isolde stepto
    3418 
    3419 > isolde stepto
    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 > isolde stepto
    3508 
    3509 > isolde stepto
    3510 
    3511 > isolde stepto
    3512 
    3513 > isolde stepto
    3514 
    3515 > isolde stepto
    3516 
    3517 > isolde stepto
    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 > isolde stepto
    3536 
    3537 > isolde stepto
    3538 
    3539 > isolde stepto
    3540 
    3541 > isolde stepto
    3542 
    3543 > isolde stepto
    3544 
    3545 > isolde stepto
    3546 
    3547 > isolde stepto
    3548 
    3549 > isolde stepto
    3550 
    3551 > delete sel
    3552 
    3553 > select #2/M:178-400
    3554 
    3555 2337 atoms, 2378 bonds, 147 residues, 1 model selected 
    3556 
    3557 > select clear
    3558 
    3559 > select clear
    3560 
    3561 > select clear
    3562 
    3563 > isolde stepto
    3564 
    3565 > isolde stepto
    3566 
    3567 > isolde stepto
    3568 
    3569 > isolde stepto
    3570 
    3571 > select clear
    3572 
    3573 > isolde stepto
    3574 
    3575 > isolde stepto
    3576 
    3577 > isolde stepto
    3578 
    3579 > isolde stepto
    3580 
    3581 > isolde stepto
    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 > isolde stepto
    3634 
    3635 > isolde stepto
    3636 
    3637 > select clear
    3638 
    3639 > isolde stepto
    3640 
    3641 > select clear
    3642 
    3643 > isolde stepto
    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 > select clear
    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 > isolde stepto
    3782 
    3783 > isolde stepto
    3784 
    3785 > isolde stepto
    3786 
    3787 > isolde stepto
    3788 
    3789 > isolde stepto
    3790 
    3791 > isolde stepto
    3792 
    3793 > isolde stepto
    3794 
    3795 > isolde stepto
    3796 
    3797 > isolde stepto
    3798 
    3799 > isolde stepto
    3800 
    3801 > isolde stepto
    3802 
    3803 > isolde stepto
    3804 
    3805 > select clear
    3806 
    3807 > isolde stepto
    3808 
    3809 > isolde stepto
    3810 
    3811 > isolde stepto
    3812 
    3813 > select clear
    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 > select clear
    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 > select clear
    3860 
    3861 > isolde stepto
    3862 
    3863 > isolde stepto
    3864 
    3865 > isolde stepto
    3866 
    3867 > isolde stepto
    3868 
    3869 > isolde stepto
    3870 
    3871 > save working.cxs
    3872 
    3873 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    3874 
    3875 > show #!4 models
    3876 
    3877 > hide #!4 models
    3878 
    3879 > swapaa mousemode sel GLY
    3880 
    3881 > select up
    3882 
    3883 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3884 
    3885 > select up
    3886 
    3887 255 atoms, 259 bonds, 18 residues, 1 model selected 
    3888 
    3889 > isolde ignore sel
    3890 
    3891 ISOLDE: currently ignoring 26 residues in model 2.2 
    3892 
    3893 > select clear
    3894 
    3895 > isolde ~ignore
    3896 
    3897 > select up
    3898 
    3899 23 atoms, 21 bonds, 2 residues, 1 model selected 
    3900 
    3901 > select clear
    3902 
    3903 > delete sel
    3904 
    3905 > delete sel
    3906 
    3907 > select clear
    3908 
    3909 > save working.cxs
    3910 
    3911 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    3912 
    3913 > ui tool show "Build Structure"
    3914 
    3915 > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    3916 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3917 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3918 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3919 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3920 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3921 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3922 > rotLib Dunbrack
    3923 
    3924 Chain information for custom built #5 
    3925 --- 
    3926 Chain | Description 
    3927 A | No description available 
    3928  
    3929 
    3930 > build start peptide "custom built" FPSYVVPQNATMPDTAAAPIVTDSITTDSTKTGGTQ
    3931 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3932 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3933 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3934 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3935 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3936 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
    3937 > rotLib Dunbrack
    3938 
    3939 Chain information for custom built #6 
    3940 --- 
    3941 Chain | Description 
    3942 A | No description available 
    3943  
    3944 
    3945 > close #5
    3946 
    3947 > select #6
    3948 
    3949 258 atoms, 263 bonds, 36 residues, 1 model selected 
    3950 
    3951 > show sel&:1
    3952 
    3953 > ui mousemode right "translate selected models"
    3954 
    3955 > ui mousemode right "rotate selected models"
    3956 
    3957 > ui mousemode right "translate selected models"
    3958 
    3959 > ui mousemode right "rotate selected models"
    3960 
    3961 > ui mousemode right "translate selected models"
    3962 
    3963 > hide #6 models
    3964 
    3965 > delete #2/M:332-367
    3966 
    3967 > addh #6
    3968 
    3969 Summary of feedback from adding hydrogens to custom built #6 
    3970 --- 
    3971 notes | No usable SEQRES records for custom built (#6) chain A; guessing
    3972 termini instead 
    3973 Chain-initial residues that are actual N termini: custom built #6/A PHE 1 
    3974 Chain-initial residues that are not actual N termini: 
    3975 Chain-final residues that are actual C termini: custom built #6/A GLN 36 
    3976 Chain-final residues that are not actual C termini: 
    3977 37 hydrogen bonds 
    3978 250 hydrogens added 
    3979  
    3980 
    3981 > isolde ignore #2/C
    3982 
    3983 ISOLDE: currently ignoring 303 residues in model 2.2 
    3984 
    3985 > select #2/M:332-367
    3986 
    3987 506 atoms, 511 bonds, 36 residues, 1 model selected 
    3988 
    3989 > hide HC
    3990 
    3991 > delete #2/M:339-367
    3992 
    3993 > isolde ~ignore
    3994 
    3995 > select clear
    3996 
    3997 > select clear
    3998 
    3999 > select up
    4000 
    4001 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4002 
    4003 > select up
    4004 
    4005 92 atoms, 94 bonds, 6 residues, 1 model selected 
    4006 
    4007 > select clear
    4008 
    4009 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    4010 bonded heavy atom. 
    4011 
    4012 > select up
    4013 
    4014 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4015 
    4016 > delete sel
    4017 
    4018 > save ser_M331_O_glycan.jpg
    4019 
    4020 > open 3e80
    4021 
    4022 3e80 title: 
    4023 Structure of Heparinase II complexed with heparan sulfate degradation
    4024 disaccharide product [more info...] 
    4025  
    4026 Chain information for 3e80 #5 
    4027 --- 
    4028 Chain | Description 
    4029 A B C | Heparinase II protein 
    4030  
    4031 Non-standard residues in 3e80 #5 
    4032 --- 
    4033 GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid 
    4034 GCU — alpha-D-glucopyranuronic acid 
    4035 MAN — alpha-D-mannopyranose 
    4036 NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose 
    4037 PO4 — phosphate ion 
    4038 RAM — alpha-L-rhamnopyranose 
    4039 XYS — alpha-D-xylopyranose 
    4040 ZN — zinc ion 
    4041  
    4042 3e80 mmCIF Assemblies 
    4043 --- 
    4044 1| author_and_software_defined_assembly 
    4045 2| author_and_software_defined_assembly 
    4046 3| author_and_software_defined_assembly 
    4047  
    4048 
    4049 > addh #5
    4050 
    4051 Summary of feedback from adding hydrogens to 3e80 #5 
    4052 --- 
    4053 warning | Not adding hydrogens to 3e80 #5/C LEU 732 CB because it is missing
    4054 heavy-atom bond partners 
    4055 notes | Termini for 3e80 (#5) chain A determined from SEQRES records 
    4056 Termini for 3e80 (#5) chain B determined from SEQRES records 
    4057 Termini for 3e80 (#5) chain C determined from SEQRES records 
    4058 Chain-initial residues that are actual N termini: 
    4059 Chain-initial residues that are not actual N termini: 3e80 #5/A PCA 26, 3e80
    4060 #5/B PCA 26, 3e80 #5/C PCA 26 
    4061 Chain-final residues that are actual C termini: 3e80 #5/A ARG 772, 3e80 #5/B
    4062 ARG 772, 3e80 #5/C ARG 772 
    4063 Chain-final residues that are not actual C termini: 
    4064 Missing OXT added to C-terminal residue 3e80 #5/A ARG 772 
    4065 Missing OXT added to C-terminal residue 3e80 #5/B ARG 772 
    4066 Missing OXT added to C-terminal residue 3e80 #5/C ARG 772 
    4067 3540 hydrogen bonds 
    4068 Adding 'H' to 3e80 #5/A PCA 26 
    4069 Adding 'H' to 3e80 #5/B PCA 26 
    4070 Adding 'H' to 3e80 #5/C PCA 26 
    4071 18911 hydrogens added 
    4072  
    4073 
    4074 > select #5
    4075 
    4076 37630 atoms, 37586 bonds, 17 pseudobonds, 2807 residues, 2 models selected 
    4077 
    4078 > hide #!2 models
    4079 
    4080 > select clear
    4081 
    4082 > select clear
    4083 
    4084 > select #5/B:134|(#5/E:1-4)
    4085 
    4086 90 atoms, 93 bonds, 5 residues, 1 model selected 
    4087 
    4088 > hide #5&~sel
    4089 
    4090 > ~cartoon #5
    4091 
    4092 > show #!2 models
    4093 
    4094 > ui mousemode right "translate selected models"
    4095 
    4096 > ui mousemode right "rotate selected models"
    4097 
    4098 > ui mousemode right "translate selected models"
    4099 
    4100 > ui mousemode right "rotate selected models"
    4101 
    4102 > ui mousemode right "translate selected models"
    4103 
    4104 > select (#5/E:1-4)
    4105 
    4106 77 atoms, 80 bonds, 4 residues, 1 model selected 
    4107 
    4108 > save working.cxs
    4109 
    4110 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4111 Restoring stepper: working_noh_real_space_refined.pdb 
    4112 opened ChimeraX session 
    4113 
    4114 > open
    4115 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb
    4116 
    4117 Summary of feedback from opening
    4118 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb 
    4119 --- 
    4120 warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
    4121 GLY C 21 1 3 
    4122 Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
    4123 1 7 
    4124 Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
    4125 1 3 
    4126 Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
    4127 1 6 
    4128 Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
    4129 1 7 
    4130 Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
    4131 1 3 
    4132 5 messages similar to the above omitted 
    4133 Cannot find LINK/SSBOND residue GCU (2 ) 
    4134 Cannot find LINK/SSBOND residue XYS (3 ) 
    4135 Cannot find LINK/SSBOND residue RAM (4 ) 
    4136 Cannot find LINK/SSBOND residue MAN (1 ) 
    4137 Cannot find LINK/SSBOND residue GCU (2 ) 
    4138 3 messages similar to the above omitted 
    4139  
    4140 Chain information for working.pdb #7 
    4141 --- 
    4142 Chain | Description 
    4143 AA | No description available 
    4144 AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4145 description available 
    4146 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 bh
    4147 bi bj bk bl bm bo bp | No description available 
    4148 BB BD BE BI BV BW bn | No description available 
    4149 C | No description available 
    4150 C1 | No description available 
    4151 C2 | No description available 
    4152 H1 | No description available 
    4153 H2 | No description available 
    4154 L | No description available 
    4155 M | No description available 
    4156 aa | No description available 
    4157 ab ac ad ae af ag ah ai aj am an ao ap | No description available 
    4158 ak | No description available 
    4159  
    4160 
    4161 > select clear
    4162 
    4163 > hide #7&protein
    4164 
    4165 > hide #!5 models
    4166 
    4167 > select #7/CG
    4168 
    4169 78 atoms, 81 bonds, 4 residues, 1 model selected 
    4170 
    4171 > hide #!7 models
    4172 
    4173 > delete sel
    4174 
    4175 > select clear
    4176 
    4177 > select clear
    4178 
    4179 > view #2/M:330
    4180 
    4181 > show #!7 models
    4182 
    4183 > select #7/MG
    4184 
    4185 78 atoms, 81 bonds, 4 residues, 1 model selected 
    4186 
    4187 > hide #!7 models
    4188 
    4189 > delete sel
    4190 
    4191 > select clear
    4192 
    4193 > select clear
    4194 
    4195 > save M331_glycan.jpg
    4196 
    4197 > save working.cxs
    4198 
    4199 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4200 
    4201 > select #2/ak
    4202 
    4203 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    4204 
    4205 > ui tool show "Build Structure"
    4206 
    4207 > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4208 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4209 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4210 
    4211 Chain information for custom built #8 
    4212 --- 
    4213 Chain | Description 
    4214 A | No description available 
    4215  
    4216 
    4217 > addh #8
    4218 
    4219 Summary of feedback from adding hydrogens to custom built #8 
    4220 --- 
    4221 notes | No usable SEQRES records for custom built (#8) chain A; guessing
    4222 termini instead 
    4223 Chain-initial residues that are actual N termini: custom built #8/A ALA 1 
    4224 Chain-initial residues that are not actual N termini: 
    4225 Chain-final residues that are actual C termini: custom built #8/A ARG 11 
    4226 Chain-final residues that are not actual C termini: 
    4227 0 hydrogen bonds 
    4228 80 hydrogens added 
    4229  
    4230 
    4231 > select #8
    4232 
    4233 158 atoms, 160 bonds, 11 residues, 1 model selected 
    4234 
    4235 > show sel
    4236 
    4237 > ui mousemode right "translate selected atoms"
    4238 
    4239 > ui mousemode right "rotate selected models"
    4240 
    4241 > ui mousemode right "translate selected models"
    4242 
    4243 > ui mousemode right "rotate selected models"
    4244 
    4245 > ui mousemode right "translate selected models"
    4246 
    4247 > ui mousemode right "rotate selected models"
    4248 
    4249 > ui mousemode right "translate selected models"
    4250 
    4251 > save working_2.cxs
    4252 
    4253 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4254 Restoring stepper: working_noh_real_space_refined.pdb 
    4255 opened ChimeraX session 
    4256 
    4257 > save
    4258 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4259 > models #2
    4260 
    4261 > close #2
    4262 
    4263 > open
    4264 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb
    4265 
    4266 Summary of feedback from opening
    4267 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_2.pdb 
    4268 --- 
    4269 warnings | End residue of secondary structure not found: HELIX 55 55 THR C 19
    4270 GLY C 21 1 3 
    4271 Start residue of secondary structure not found: HELIX 56 56 VAL C 28 HIS C 34
    4272 1 7 
    4273 Start residue of secondary structure not found: HELIX 57 57 ILE C 53 ASN C 55
    4274 1 3 
    4275 Start residue of secondary structure not found: HELIX 58 58 ILE C 64 TRP C 69
    4276 1 6 
    4277 Start residue of secondary structure not found: HELIX 59 59 ARG C 75 ARG C 81
    4278 1 7 
    4279 Start residue of secondary structure not found: HELIX 60 60 ALA C 89 GLN C 91
    4280 1 3 
    4281 5 messages similar to the above omitted 
    4282 Cannot find LINK/SSBOND residue GCU (2 ) 
    4283 Cannot find LINK/SSBOND residue XYS (3 ) 
    4284 Cannot find LINK/SSBOND residue RAM (4 ) 
    4285 Cannot find LINK/SSBOND residue MAN (1 ) 
    4286 Cannot find LINK/SSBOND residue GCU (2 ) 
    4287 3 messages similar to the above omitted 
    4288  
    4289 Chain information for working_2.pdb #8 
    4290 --- 
    4291 Chain | Description 
    4292 AA | No description available 
    4293 AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
    4294 description available 
    4295 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 bh
    4296 bi bj bk bl bm bo bp | No description available 
    4297 BB BD BE BI BV BW bn | No description available 
    4298 C | No description available 
    4299 C1 | No description available 
    4300 C2 | No description available 
    4301 H1 | No description available 
    4302 H2 | No description available 
    4303 L | No description available 
    4304 M | No description available 
    4305 aa | No description available 
    4306 ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available 
    4307  
    4308 
    4309 > open
    4310 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1b_26A.mrc
    4311 
    4312 Opened class1b_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    4313 0.0224, step 2, values float32 
    4314 
    4315 > clipper associate #9 toModel #8
    4316 
    4317 Chain information for working_2.pdb 
    4318 --- 
    4319 Chain | Description 
    4320 8.2/AA | No description available 
    4321 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 8.2/AL
    4322 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 8.2/AW
    4323 8.2/AX | No description available 
    4324 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 8.2/BO
    4325 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 8.2/bd
    4326 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 8.2/bp |
    4327 No description available 
    4328 8.2/BB 8.2/BD 8.2/BE 8.2/BI 8.2/BV 8.2/BW 8.2/bn | No description available 
    4329 8.2/C | No description available 
    4330 8.2/C1 | No description available 
    4331 8.2/C2 | No description available 
    4332 8.2/H1 | No description available 
    4333 8.2/H2 | No description available 
    4334 8.2/L | No description available 
    4335 8.2/M | No description available 
    4336 8.2/aa | No description available 
    4337 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 8.2/al
    4338 8.2/am 8.2/an 8.2/ao 8.2/ap | No description available 
    4339  
    4340 
    4341 > close #1
    4342 
    4343 > close #2
    4344 
    4345 > select #3
    4346 
    4347 508 atoms, 513 bonds, 36 residues, 8 models selected 
    4348 
    4349 > hide #!4 models
    4350 
    4351 > select #8/ak
    4352 
    4353 1079 atoms, 1095 bonds, 4 pseudobonds, 61 residues, 2 models selected 
    4354 
    4355 > hide #!3 models
    4356 
    4357 > show #!3 models
    4358 
    4359 > close #4
    4360 
    4361 > view #3
    4362 
    4363 > show #3
    4364 
    4365 > hide #!3 models
    4366 
    4367 > show #!3 models
    4368 
    4369 > view #3
    4370 
    4371 > close #3
    4372 
    4373 > close #5
    4374 
    4375 > close #6
    4376 
    4377 > close #7
    4378 
    4379 > volume gaussian #8 bfactor 50
    4380 
    4381 > clipper associate #1 toModel #8
    4382 
    4383 > select clear
    4384 
    4385 > save reopened.cxs
    4386 
    4387 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4388 Traceback (most recent call last): 
    4389 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4390 packages/chimerax/core/session.py", line 280, in process 
    4391 data = sm.take_snapshot(obj, session, self.state_flags) 
    4392 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4393 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4394 data = {'structure': self.structure, 
    4395 File "cymol.pyx", line 1437, in
    4396 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4397 RuntimeError: Residue already deleted 
    4398  
    4399 The above exception was the direct cause of the following exception: 
    4400  
    4401 Traceback (most recent call last): 
    4402 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4403 packages/chimerax/core/session.py", line 259, in discovery 
    4404 self.processed[key] = self.process(obj, parents) 
    4405 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4406 packages/chimerax/core/session.py", line 283, in process 
    4407 raise RuntimeError(msg) from e 
    4408 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4409 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4410 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4411  
    4412 During handling of the above exception, another exception occurred: 
    4413  
    4414 Traceback (most recent call last): 
    4415 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4416 packages/chimerax/core/session.py", line 826, in save 
    4417 session.save(output, version=version, include_maps=include_maps) 
    4418 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4419 packages/chimerax/core/session.py", line 583, in save 
    4420 mgr.discovery(self._state_containers) 
    4421 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4422 packages/chimerax/core/session.py", line 261, in discovery 
    4423 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4424 ValueError: error processing: 'isolde residue stepper 1' ->
    4425 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4426 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4427 saving session data for 'isolde residue stepper 1' ->
    4428 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4429 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4430  
    4431 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4432 saving session data for 'isolde residue stepper 1' -> -> 
    4433  
    4434 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4435 packages/chimerax/core/session.py", line 261, in discovery 
    4436 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4437  
    4438 See log for complete Python traceback. 
    4439  
    4440 Traceback (most recent call last): 
    4441 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4442 packages/chimerax/core/session.py", line 280, in process 
    4443 data = sm.take_snapshot(obj, session, self.state_flags) 
    4444 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4445 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4446 data = {'structure': self.structure, 
    4447 File "cymol.pyx", line 1437, in
    4448 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4449 RuntimeError: Residue already deleted 
    4450  
    4451 The above exception was the direct cause of the following exception: 
    4452  
    4453 Traceback (most recent call last): 
    4454 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4455 packages/chimerax/core/session.py", line 259, in discovery 
    4456 self.processed[key] = self.process(obj, parents) 
    4457 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4458 packages/chimerax/core/session.py", line 283, in process 
    4459 raise RuntimeError(msg) from e 
    4460 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4461 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4462 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4463  
    4464 During handling of the above exception, another exception occurred: 
    4465  
    4466 Traceback (most recent call last): 
    4467 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4468 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    4469 cmd.run(cmd_text) 
    4470 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4471 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4472 result = ci.function(session, **kw_args) 
    4473 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4474 packages/chimerax/save_command/cmd.py", line 66, in cmd_save 
    4475 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    4476 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4477 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4478 result = ci.function(session, **kw_args) 
    4479 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4480 packages/chimerax/save_command/cmd.py", line 79, in provider_save 
    4481 mgr).save(session, path, **provider_kw) 
    4482 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4483 packages/chimerax/core_formats/__init__.py", line 79, in save 
    4484 return cxs_save(session, path, **kw) 
    4485 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4486 packages/chimerax/core/session.py", line 826, in save 
    4487 session.save(output, version=version, include_maps=include_maps) 
    4488 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4489 packages/chimerax/core/session.py", line 583, in save 
    4490 mgr.discovery(self._state_containers) 
    4491 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4492 packages/chimerax/core/session.py", line 261, in discovery 
    4493 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4494 ValueError: error processing: 'isolde residue stepper 1' ->
    4495 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4496 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4497 saving session data for 'isolde residue stepper 1' ->
    4498 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4499 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4500  
    4501 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4502 saving session data for 'isolde residue stepper 1' -> -> 
    4503  
    4504 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4505 packages/chimerax/core/session.py", line 261, in discovery 
    4506 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4507  
    4508 See log for complete Python traceback. 
    4509  
    4510 
    4511 > isolde stepto sel
    4512 
    4513 > select up
    4514 
    4515 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4516 
    4517 > save reopened.cxs
    4518 
    4519 Taking snapshot of stepper: working_2.pdb 
    4520 Taking snapshot of stepper: working_noh_real_space_refined.pdb 
    4521 Traceback (most recent call last): 
    4522 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4523 packages/chimerax/core/session.py", line 280, in process 
    4524 data = sm.take_snapshot(obj, session, self.state_flags) 
    4525 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4526 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4527 data = {'structure': self.structure, 
    4528 File "cymol.pyx", line 1437, in
    4529 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4530 RuntimeError: Residue already deleted 
    4531  
    4532 The above exception was the direct cause of the following exception: 
    4533  
    4534 Traceback (most recent call last): 
    4535 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4536 packages/chimerax/core/session.py", line 259, in discovery 
    4537 self.processed[key] = self.process(obj, parents) 
    4538 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4539 packages/chimerax/core/session.py", line 283, in process 
    4540 raise RuntimeError(msg) from e 
    4541 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4542 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4543 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4544  
    4545 During handling of the above exception, another exception occurred: 
    4546  
    4547 Traceback (most recent call last): 
    4548 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4549 packages/chimerax/core/session.py", line 826, in save 
    4550 session.save(output, version=version, include_maps=include_maps) 
    4551 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4552 packages/chimerax/core/session.py", line 583, in save 
    4553 mgr.discovery(self._state_containers) 
    4554 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4555 packages/chimerax/core/session.py", line 261, in discovery 
    4556 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4557 ValueError: error processing: 'isolde residue stepper 1' ->
    4558 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4559 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4560 saving session data for 'isolde residue stepper 1' ->
    4561 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4562 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4563  
    4564 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4565 saving session data for 'isolde residue stepper 1' -> -> 
    4566  
    4567 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4568 packages/chimerax/core/session.py", line 261, in discovery 
    4569 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4570  
    4571 See log for complete Python traceback. 
    4572  
    4573 Traceback (most recent call last): 
    4574 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4575 packages/chimerax/core/session.py", line 280, in process 
    4576 data = sm.take_snapshot(obj, session, self.state_flags) 
    4577 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4578 packages/chimerax/atomic/molobject.py", line 633, in take_snapshot 
    4579 data = {'structure': self.structure, 
    4580 File "cymol.pyx", line 1437, in
    4581 chimerax.atomic.cymol.CyResidue.structure.__get__ 
    4582 RuntimeError: Residue already deleted 
    4583  
    4584 The above exception was the direct cause of the following exception: 
    4585  
    4586 Traceback (most recent call last): 
    4587 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4588 packages/chimerax/core/session.py", line 259, in discovery 
    4589 self.processed[key] = self.process(obj, parents) 
    4590 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4591 packages/chimerax/core/session.py", line 283, in process 
    4592 raise RuntimeError(msg) from e 
    4593 RuntimeError: Error while saving session data for 'isolde residue stepper 1'
    4594 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4595 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4596  
    4597 During handling of the above exception, another exception occurred: 
    4598  
    4599 Traceback (most recent call last): 
    4600 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4601 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    4602 cmd.run(cmd_text) 
    4603 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4604 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4605 result = ci.function(session, **kw_args) 
    4606 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4607 packages/chimerax/save_command/cmd.py", line 66, in cmd_save 
    4608 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    4609 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4610 packages/chimerax/core/commands/cli.py", line 2805, in run 
    4611 result = ci.function(session, **kw_args) 
    4612 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4613 packages/chimerax/save_command/cmd.py", line 79, in provider_save 
    4614 mgr).save(session, path, **provider_kw) 
    4615 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4616 packages/chimerax/core_formats/__init__.py", line 79, in save 
    4617 return cxs_save(session, path, **kw) 
    4618 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4619 packages/chimerax/core/session.py", line 826, in save 
    4620 session.save(output, version=version, include_maps=include_maps) 
    4621 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4622 packages/chimerax/core/session.py", line 583, in save 
    4623 mgr.discovery(self._state_containers) 
    4624 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4625 packages/chimerax/core/session.py", line 261, in discovery 
    4626 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4627 ValueError: error processing: 'isolde residue stepper 1' ->
    4628 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4629 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0>: Error while
    4630 saving session data for 'isolde residue stepper 1' ->
    4631 <chimerax.isolde.navigate.ResidueStepper object at 0x7f42c411fd50> ->
    4632 <chimerax.atomic.molobject.Residue object at 0x7f4301f68aa0> 
    4633  
    4634 ValueError: error processing: 'isolde residue stepper 1' -> -> : Error while
    4635 saving session data for 'isolde residue stepper 1' -> -> 
    4636  
    4637 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    4638 packages/chimerax/core/session.py", line 261, in discovery 
    4639 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    4640  
    4641 See log for complete Python traceback. 
    4642  
    4643 
    4644 > save reopened.cxs
    4645 
    4646 Taking snapshot of stepper: working_2.pdb 
    4647 
    4648 > ui tool show "Build Structure"
    4649 
    4650 > build start peptide "custom built" AAEMSPLPPGR -139.0,135.0 -139.0,135.0
    4651 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    4652 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    4653 
    4654 Chain information for custom built #1 
    4655 --- 
    4656 Chain | Description 
    4657 A | No description available 
    4658  
    4659 
    4660 > addh #1
    4661 
    4662 Summary of feedback from adding hydrogens to custom built #1 
    4663 --- 
    4664 notes | No usable SEQRES records for custom built (#1) chain A; guessing
    4665 termini instead 
    4666 Chain-initial residues that are actual N termini: custom built #1/A ALA 1 
    4667 Chain-initial residues that are not actual N termini: 
    4668 Chain-final residues that are actual C termini: custom built #1/A ARG 11 
    4669 Chain-final residues that are not actual C termini: 
    4670 0 hydrogen bonds 
    4671 80 hydrogens added 
    4672  
    4673 
    4674 > select #1
    4675 
    4676 158 atoms, 160 bonds, 11 residues, 1 model selected 
    4677 
    4678 > show sel
    4679 
    4680 > ui mousemode right "translate selected models"
    4681 
    4682 > ui mousemode right "rotate selected models"
    4683 
    4684 > ui mousemode right "translate selected models"
    4685 
    4686 > save reopened.cxs
    4687 
    4688 Taking snapshot of stepper: working_2.pdb 
    4689 Restoring stepper: working_2.pdb 
    4690 opened ChimeraX session 
    4691 
    4692 > ui tool show Shell
    4693 
    4694 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    4695 UserWarning: IPython History requires SQLite, your history will not be saved 
    4696 warn("IPython History requires SQLite, your history will not be saved") 
    4697 
    4698 > isolde start
    4699 
    4700 > set selectionWidth 4
    4701 
    4702 Done loading forcefield 
    4703 
    4704 > select clear
    4705 
    4706 > select clear
    4707 
    4708 > select ~protein
    4709 
    4710 16729 atoms, 17062 bonds, 366 pseudobonds, 140 residues, 23 models selected 
    4711 
    4712 > select /ak
    4713 
    4714 1238 atoms, 1261 bonds, 72 residues, 1 model selected 
    4715 
    4716 > hide #!1 models
    4717 
    4718 > select up
    4719 
    4720 45 atoms, 44 bonds, 2 residues, 1 model selected 
    4721 
    4722 > select up
    4723 
    4724 71 atoms, 71 bonds, 4 residues, 1 model selected 
    4725 
    4726 > isolde ignore sel
    4727 
    4728 ISOLDE: currently ignoring 4 residues in model 8.2 
    4729 
    4730 > select up
    4731 
    4732 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4733 
    4734 > select up
    4735 
    4736 939 atoms, 951 bonds, 60 residues, 1 model selected 
    4737 
    4738 > select up
    4739 
    4740 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    4741 
    4742 > select up
    4743 
    4744 1179 atoms, 1198 bonds, 62 residues, 1 model selected 
    4745 
    4746 > isolde ignore sel
    4747 
    4748 ISOLDE: currently ignoring 66 residues in model 8.2 
    4749 
    4750 > select up
    4751 
    4752 20 atoms, 19 bonds, 1 residue, 1 model selected 
    4753 
    4754 > select up
    4755 
    4756 159 atoms, 161 bonds, 11 residues, 1 model selected 
    4757 
    4758 Chain CG, residue 1 specifies more than one residue! The simulation can still
    4759 run, but this will probably cause problems later if not rectified by
    4760 renumbering. 
    4761 
    4762 Chain CG, residue 2 specifies more than one residue! The simulation can still
    4763 run, but this will probably cause problems later if not rectified by
    4764 renumbering. 
    4765 
    4766 Chain CG, residue 3 specifies more than one residue! The simulation can still
    4767 run, but this will probably cause problems later if not rectified by
    4768 renumbering. 
    4769 
    4770 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4771 run, but this will probably cause problems later if not rectified by
    4772 renumbering. 
    4773 
    4774 Chain CG, residue 1 specifies more than one residue! The simulation can still
    4775 run, but this will probably cause problems later if not rectified by
    4776 renumbering. 
    4777 
    4778 Chain CG, residue 2 specifies more than one residue! The simulation can still
    4779 run, but this will probably cause problems later if not rectified by
    4780 renumbering. 
    4781 
    4782 Chain CG, residue 3 specifies more than one residue! The simulation can still
    4783 run, but this will probably cause problems later if not rectified by
    4784 renumbering. 
    4785 
    4786 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4787 run, but this will probably cause problems later if not rectified by
    4788 renumbering. 
    4789 
    4790 > delete sel
    4791 
    4792 > delete sel
    4793 
    4794 > delete sel
    4795 
    4796 > delete sel
    4797 
    4798 > select up
    4799 
    4800 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4801 
    4802 > select clear
    4803 
    4804 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4805 run, but this will probably cause problems later if not rectified by
    4806 renumbering. 
    4807 
    4808 > select /ak
    4809 
    4810 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4811 
    4812 > select up
    4813 
    4814 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4815 
    4816 > select up
    4817 
    4818 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4819 
    4820 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4821 run, but this will probably cause problems later if not rectified by
    4822 renumbering. 
    4823 
    4824 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4825 run, but this will probably cause problems later if not rectified by
    4826 renumbering. 
    4827 
    4828 > select /MG
    4829 
    4830 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4831 
    4832 > select up
    4833 
    4834 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4835 
    4836 > select clear
    4837 
    4838 > select sel&:MG
    4839 
    4840 Nothing selected 
    4841 
    4842 > select sel&/MG
    4843 
    4844 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4845 
    4846 > select up
    4847 
    4848 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4849 
    4850 > select clear
    4851 
    4852 > select up
    4853 
    4854 99 atoms, 102 bonds, 4 residues, 1 model selected 
    4855 
    4856 > select clear
    4857 
    4858 > select up
    4859 
    4860 42 atoms, 42 bonds, 1 residue, 1 model selected 
    4861 
    4862 > delete sel
    4863 
    4864 > isolde add ligand RAM
    4865 
    4866 Deleted the following atoms from residue RAM CG4: O1, HO1 
    4867 
    4868 > ui mousemode right "translate selected atoms"
    4869 
    4870 > clipper set contourSensitivity 0.25
    4871 
    4872 > select clear
    4873 
    4874 > isolde add ligand RAM
    4875 
    4876 Deleted the following atoms from residue RAM MG4: HO1, O1 
    4877 
    4878 > delete sel
    4879 
    4880 > isolde add ligand RAM
    4881 
    4882 Deleted the following atoms from residue RAM MG4: HO1, O1 
    4883 
    4884 > ui mousemode right "translate selected atoms"
    4885 
    4886 > select clear
    4887 
    4888 > select /ak
    4889 
    4890 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4891 
    4892 > select up
    4893 
    4894 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4895 
    4896 > select up
    4897 
    4898 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4899 
    4900 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4901 run, but this will probably cause problems later if not rectified by
    4902 renumbering. 
    4903 
    4904 > select clear
    4905 
    4906 > select up
    4907 
    4908 15 atoms, 14 bonds, 1 residue, 1 model selected 
    4909 
    4910 > select up
    4911 
    4912 155 atoms, 157 bonds, 11 residues, 1 model selected 
    4913 
    4914 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4915 run, but this will probably cause problems later if not rectified by
    4916 renumbering. 
    4917 
    4918 > select clear
    4919 
    4920 Chain ak, residue 67 specifies more than one residue! The simulation can still
    4921 run, but this will probably cause problems later if not rectified by
    4922 renumbering. 
    4923 
    4924 > select clear
    4925 
    4926 > isolde ~ignore
    4927 
    4928 > save working_3.cxs
    4929 
    4930 Taking snapshot of stepper: working_2.pdb 
    4931 Restoring stepper: working_2.pdb 
    4932 opened ChimeraX session 
    4933 
    4934 > select /ak
    4935 
    4936 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    4937 
    4938 > select clear
    4939 
    4940 > dssp
    4941 
    4942 > select /AA
    4943 
    4944 981 atoms, 1002 bonds, 48 residues, 1 model selected 
    4945 
    4946 > isolde stepto /AB
    4947 
    4948 Multiple residues selected! Going to the first... 
    4949 
    4950 > clipper set contourSensitivity 0.25
    4951 
    4952 > select /AB
    4953 
    4954 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    4955 
    4956 > select clear
    4957 
    4958 > isolde stepto
    4959 
    4960 > isolde stepto
    4961 
    4962 > isolde stepto
    4963 
    4964 > isolde stepto
    4965 
    4966 > isolde stepto
    4967 
    4968 > isolde stepto
    4969 
    4970 > isolde stepto
    4971 
    4972 > isolde stepto
    4973 
    4974 > isolde stepto
    4975 
    4976 > isolde stepto
    4977 
    4978 > isolde stepto
    4979 
    4980 > isolde stepto
    4981 
    4982 > isolde stepto
    4983 
    4984 > isolde stepto
    4985 
    4986 > isolde stepto
    4987 
    4988 > isolde stepto
    4989 
    4990 > isolde stepto
    4991 
    4992 > isolde stepto
    4993 
    4994 > isolde stepto
    4995 
    4996 > isolde stepto
    4997 
    4998 > isolde stepto
    4999 
    5000 > isolde stepto
    5001 
    5002 > isolde stepto
    5003 
    5004 > isolde stepto
    5005 
    5006 > isolde stepto
    5007 
    5008 > isolde stepto
    5009 
    5010 > isolde stepto
    5011 
    5012 > isolde stepto
    5013 
    5014 > isolde stepto
    5015 
    5016 > isolde stepto
    5017 
    5018 > isolde stepto
    5019 
    5020 > isolde stepto
    5021 
    5022 > isolde stepto
    5023 
    5024 > isolde stepto
    5025 
    5026 > isolde stepto
    5027 
    5028 > isolde stepto
    5029 
    5030 > isolde stepto
    5031 
    5032 > isolde stepto
    5033 
    5034 > isolde stepto
    5035 
    5036 > isolde stepto
    5037 
    5038 > isolde stepto
    5039 
    5040 > isolde stepto
    5041 
    5042 > isolde stepto
    5043 
    5044 > isolde stepto
    5045 
    5046 > select clear
    5047 
    5048 > select clear
    5049 
    5050 > isolde stepto
    5051 
    5052 > isolde stepto
    5053 
    5054 > isolde stepto
    5055 
    5056 > isolde stepto
    5057 
    5058 > select /AC
    5059 
    5060 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5061 
    5062 > select clear
    5063 
    5064 > isolde stepto
    5065 
    5066 > isolde stepto
    5067 
    5068 > isolde stepto
    5069 
    5070 > isolde stepto
    5071 
    5072 > isolde stepto
    5073 
    5074 > isolde stepto
    5075 
    5076 > isolde stepto
    5077 
    5078 > isolde stepto
    5079 
    5080 > isolde stepto
    5081 
    5082 > isolde stepto
    5083 
    5084 > isolde stepto
    5085 
    5086 > isolde stepto
    5087 
    5088 > isolde stepto
    5089 
    5090 > isolde stepto
    5091 
    5092 > isolde stepto
    5093 
    5094 > isolde stepto
    5095 
    5096 > isolde stepto
    5097 
    5098 > isolde stepto
    5099 
    5100 > isolde stepto
    5101 
    5102 > isolde stepto
    5103 
    5104 > isolde stepto
    5105 
    5106 > isolde stepto
    5107 
    5108 > isolde stepto
    5109 
    5110 > isolde stepto
    5111 
    5112 > isolde stepto
    5113 
    5114 > isolde stepto
    5115 
    5116 > isolde stepto
    5117 
    5118 > isolde stepto
    5119 
    5120 > isolde stepto
    5121 
    5122 > isolde stepto
    5123 
    5124 > isolde stepto
    5125 
    5126 > isolde stepto
    5127 
    5128 > isolde stepto
    5129 
    5130 > isolde stepto
    5131 
    5132 > isolde stepto
    5133 
    5134 > isolde stepto
    5135 
    5136 > isolde stepto
    5137 
    5138 > isolde stepto
    5139 
    5140 > isolde stepto
    5141 
    5142 > isolde stepto
    5143 
    5144 > select clear
    5145 
    5146 > isolde stepto
    5147 
    5148 > isolde stepto
    5149 
    5150 > isolde stepto
    5151 
    5152 > isolde stepto
    5153 
    5154 > isolde stepto
    5155 
    5156 > isolde stepto prev
    5157 
    5158 > isolde ignore sel
    5159 
    5160 ISOLDE: currently ignoring 1 residues in model 8.2 
    5161 
    5162 > select clear
    5163 
    5164 > isolde stepto
    5165 
    5166 > isolde stepto
    5167 
    5168 > isolde stepto
    5169 
    5170 > select /AD
    5171 
    5172 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5173 
    5174 > select clear
    5175 
    5176 > isolde stepto
    5177 
    5178 > isolde stepto
    5179 
    5180 > isolde stepto
    5181 
    5182 > isolde stepto
    5183 
    5184 > isolde stepto
    5185 
    5186 > isolde stepto
    5187 
    5188 > isolde stepto
    5189 
    5190 > isolde stepto
    5191 
    5192 > isolde stepto
    5193 
    5194 > isolde stepto
    5195 
    5196 > isolde stepto
    5197 
    5198 > isolde stepto
    5199 
    5200 > isolde stepto
    5201 
    5202 > isolde stepto
    5203 
    5204 > isolde stepto
    5205 
    5206 > isolde stepto
    5207 
    5208 > isolde stepto
    5209 
    5210 > isolde stepto
    5211 
    5212 > isolde stepto
    5213 
    5214 > isolde stepto
    5215 
    5216 > isolde stepto
    5217 
    5218 > isolde stepto
    5219 
    5220 > isolde stepto
    5221 
    5222 > isolde stepto
    5223 
    5224 > isolde stepto
    5225 
    5226 > isolde stepto
    5227 
    5228 > isolde stepto
    5229 
    5230 > isolde stepto
    5231 
    5232 > isolde stepto
    5233 
    5234 > isolde stepto
    5235 
    5236 > isolde stepto
    5237 
    5238 > isolde stepto
    5239 
    5240 > isolde stepto
    5241 
    5242 > isolde stepto
    5243 
    5244 > isolde stepto
    5245 
    5246 > isolde stepto
    5247 
    5248 > isolde stepto
    5249 
    5250 > isolde stepto
    5251 
    5252 > isolde stepto
    5253 
    5254 > isolde stepto
    5255 
    5256 > isolde stepto
    5257 
    5258 > isolde stepto
    5259 
    5260 > isolde stepto
    5261 
    5262 > isolde stepto
    5263 
    5264 > select clear
    5265 
    5266 > isolde stepto
    5267 
    5268 > isolde stepto
    5269 
    5270 > isolde stepto
    5271 
    5272 > select /AE
    5273 
    5274 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5275 
    5276 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5277 bonded heavy atom. 
    5278 
    5279 > select clear
    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 > isolde stepto
    5338 
    5339 > isolde stepto
    5340 
    5341 > isolde stepto
    5342 
    5343 > isolde stepto
    5344 
    5345 > isolde stepto
    5346 
    5347 > isolde stepto
    5348 
    5349 > isolde stepto
    5350 
    5351 > isolde stepto
    5352 
    5353 > isolde stepto
    5354 
    5355 > isolde stepto
    5356 
    5357 > isolde stepto
    5358 
    5359 > select clear
    5360 
    5361 > isolde stepto
    5362 
    5363 > isolde stepto
    5364 
    5365 > isolde stepto
    5366 
    5367 > isolde stepto
    5368 
    5369 > isolde stepto
    5370 
    5371 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5372 bonded heavy atom. 
    5373 
    5374 > select clear
    5375 
    5376 > select clear
    5377 
    5378 > isolde stepto
    5379 
    5380 > isolde stepto
    5381 
    5382 > isolde stepto
    5383 
    5384 > isolde stepto
    5385 
    5386 > select /AF
    5387 
    5388 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5389 
    5390 > select clear
    5391 
    5392 > isolde stepto
    5393 
    5394 > isolde stepto
    5395 
    5396 > isolde stepto
    5397 
    5398 > isolde stepto
    5399 
    5400 > isolde stepto
    5401 
    5402 > isolde stepto
    5403 
    5404 > isolde stepto
    5405 
    5406 > isolde stepto
    5407 
    5408 > isolde stepto
    5409 
    5410 > isolde stepto
    5411 
    5412 > isolde stepto
    5413 
    5414 > isolde stepto
    5415 
    5416 > isolde stepto
    5417 
    5418 > isolde stepto
    5419 
    5420 > isolde stepto
    5421 
    5422 > isolde stepto
    5423 
    5424 > isolde stepto
    5425 
    5426 > isolde stepto
    5427 
    5428 > isolde stepto
    5429 
    5430 > isolde stepto
    5431 
    5432 > isolde stepto
    5433 
    5434 > isolde stepto
    5435 
    5436 > isolde stepto
    5437 
    5438 > isolde stepto
    5439 
    5440 > isolde stepto
    5441 
    5442 > isolde stepto
    5443 
    5444 > isolde stepto
    5445 
    5446 > isolde stepto
    5447 
    5448 > isolde stepto
    5449 
    5450 > isolde stepto
    5451 
    5452 > isolde stepto
    5453 
    5454 > isolde stepto
    5455 
    5456 > isolde stepto
    5457 
    5458 > isolde stepto
    5459 
    5460 > isolde stepto
    5461 
    5462 > isolde stepto
    5463 
    5464 > isolde stepto
    5465 
    5466 > isolde stepto
    5467 
    5468 > isolde stepto
    5469 
    5470 > isolde stepto
    5471 
    5472 > isolde stepto
    5473 
    5474 > isolde stepto
    5475 
    5476 > isolde stepto
    5477 
    5478 > isolde stepto
    5479 
    5480 > swapaa mousemode sel PRO
    5481 
    5482 Traceback (most recent call last): 
    5483 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5484 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    5485 self.start_sim() 
    5486 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5487 packages/chimerax/isolde/isolde.py", line 2724, in start_sim 
    5488 main_sel = self._last_main_sel = self._get_main_sim_selection() 
    5489 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5490 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    5491 raise TypeError('You must select at least one atom from the current ' 
    5492 TypeError: You must select at least one atom from the current working model
    5493 prior to starting a simulation! 
    5494  
    5495 TypeError: You must select at least one atom from the current working model
    5496 prior to starting a simulation! 
    5497  
    5498 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    5499 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    5500 raise TypeError('You must select at least one atom from the current ' 
    5501  
    5502 See log for complete Python traceback. 
    5503  
    5504 
    5505 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5506 bonded heavy atom. 
    5507 
    5508 > select clear
    5509 
    5510 > isolde stepto
    5511 
    5512 > isolde stepto
    5513 
    5514 > isolde stepto
    5515 
    5516 > isolde stepto
    5517 
    5518 > select /AG
    5519 
    5520 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5521 
    5522 > select clear
    5523 
    5524 > isolde stepto
    5525 
    5526 > isolde stepto
    5527 
    5528 > isolde stepto
    5529 
    5530 > isolde stepto
    5531 
    5532 > isolde stepto
    5533 
    5534 > isolde stepto
    5535 
    5536 > isolde stepto
    5537 
    5538 > isolde stepto
    5539 
    5540 > isolde stepto
    5541 
    5542 > isolde stepto
    5543 
    5544 > isolde stepto
    5545 
    5546 > isolde stepto
    5547 
    5548 > isolde stepto
    5549 
    5550 > select /AG
    5551 
    5552 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5553 
    5554 > select /AG, ak
    5555 
    5556 2214 atoms, 2258 bonds, 120 residues, 1 model selected 
    5557 
    5558 > select /AG
    5559 
    5560 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5561 
    5562 > select clear
    5563 
    5564 > isolde stepto
    5565 
    5566 > isolde stepto
    5567 
    5568 > isolde stepto
    5569 
    5570 > isolde stepto
    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 > select clear
    5619 
    5620 > isolde stepto
    5621 
    5622 > isolde stepto
    5623 
    5624 > isolde stepto
    5625 
    5626 > isolde stepto
    5627 
    5628 > select clear
    5629 
    5630 > select clear
    5631 
    5632 > isolde stepto
    5633 
    5634 > isolde stepto
    5635 
    5636 > isolde stepto
    5637 
    5638 > isolde stepto
    5639 
    5640 > select /AH
    5641 
    5642 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5643 
    5644 > select clear
    5645 
    5646 > isolde stepto
    5647 
    5648 > isolde stepto
    5649 
    5650 > isolde stepto
    5651 
    5652 > isolde stepto
    5653 
    5654 > isolde stepto
    5655 
    5656 > isolde stepto
    5657 
    5658 > isolde stepto
    5659 
    5660 > isolde stepto
    5661 
    5662 > isolde stepto
    5663 
    5664 > isolde stepto
    5665 
    5666 > isolde stepto
    5667 
    5668 > isolde stepto
    5669 
    5670 > isolde stepto
    5671 
    5672 > isolde stepto
    5673 
    5674 > isolde stepto
    5675 
    5676 > isolde stepto
    5677 
    5678 > isolde stepto
    5679 
    5680 > isolde stepto
    5681 
    5682 > isolde stepto
    5683 
    5684 > isolde stepto
    5685 
    5686 > isolde stepto
    5687 
    5688 > isolde stepto
    5689 
    5690 > isolde stepto
    5691 
    5692 > isolde stepto
    5693 
    5694 > isolde stepto
    5695 
    5696 > isolde stepto
    5697 
    5698 > isolde stepto
    5699 
    5700 > isolde stepto
    5701 
    5702 > isolde stepto
    5703 
    5704 > isolde stepto
    5705 
    5706 > isolde stepto
    5707 
    5708 > isolde stepto
    5709 
    5710 > isolde stepto
    5711 
    5712 > isolde stepto
    5713 
    5714 > isolde stepto
    5715 
    5716 > isolde stepto
    5717 
    5718 > isolde stepto
    5719 
    5720 > isolde stepto
    5721 
    5722 > isolde stepto
    5723 
    5724 > isolde stepto
    5725 
    5726 > isolde stepto
    5727 
    5728 > isolde stepto
    5729 
    5730 > isolde stepto
    5731 
    5732 > isolde stepto
    5733 
    5734 > select clear
    5735 
    5736 > isolde stepto
    5737 
    5738 > isolde stepto
    5739 
    5740 > isolde stepto
    5741 
    5742 > isolde stepto
    5743 
    5744 > select /AI
    5745 
    5746 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5747 
    5748 > select clear
    5749 
    5750 > isolde stepto
    5751 
    5752 > isolde stepto
    5753 
    5754 > isolde stepto
    5755 
    5756 > isolde stepto
    5757 
    5758 > isolde stepto
    5759 
    5760 > isolde stepto
    5761 
    5762 > isolde stepto
    5763 
    5764 > isolde stepto
    5765 
    5766 > isolde stepto
    5767 
    5768 > isolde stepto
    5769 
    5770 > isolde stepto
    5771 
    5772 > isolde stepto
    5773 
    5774 > isolde stepto
    5775 
    5776 > isolde stepto
    5777 
    5778 > isolde stepto
    5779 
    5780 > isolde stepto
    5781 
    5782 > isolde stepto
    5783 
    5784 > isolde stepto
    5785 
    5786 > isolde stepto
    5787 
    5788 > isolde stepto
    5789 
    5790 > isolde stepto
    5791 
    5792 > isolde stepto
    5793 
    5794 > isolde stepto
    5795 
    5796 > isolde stepto
    5797 
    5798 > isolde stepto
    5799 
    5800 > isolde stepto
    5801 
    5802 > isolde stepto
    5803 
    5804 > isolde stepto
    5805 
    5806 > isolde stepto
    5807 
    5808 > isolde stepto
    5809 
    5810 > isolde stepto
    5811 
    5812 > isolde stepto
    5813 
    5814 > isolde stepto
    5815 
    5816 > isolde stepto
    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 > select clear
    5839 
    5840 > isolde stepto
    5841 
    5842 > isolde stepto
    5843 
    5844 > isolde stepto
    5845 
    5846 > isolde stepto
    5847 
    5848 > save working_4.cxs
    5849 
    5850 Taking snapshot of stepper: working_2.pdb 
    5851 
    5852 > select /AJ
    5853 
    5854 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5855 
    5856 > select clear
    5857 
    5858 > select clear
    5859 
    5860 > select clear
    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 > select clear
    5901 
    5902 > isolde stepto
    5903 
    5904 > isolde stepto
    5905 
    5906 > isolde stepto
    5907 
    5908 > isolde stepto
    5909 
    5910 > isolde stepto
    5911 
    5912 > isolde stepto
    5913 
    5914 > isolde stepto
    5915 
    5916 > isolde stepto
    5917 
    5918 > isolde stepto
    5919 
    5920 > isolde stepto
    5921 
    5922 > isolde stepto
    5923 
    5924 > isolde stepto
    5925 
    5926 > isolde stepto
    5927 
    5928 > isolde stepto
    5929 
    5930 > isolde stepto
    5931 
    5932 > isolde stepto
    5933 
    5934 > isolde stepto
    5935 
    5936 > isolde stepto
    5937 
    5938 > isolde stepto
    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 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    5953 bonded heavy atom. 
    5954 
    5955 > select clear
    5956 
    5957 > isolde stepto
    5958 
    5959 > isolde stepto
    5960 
    5961 > isolde stepto
    5962 
    5963 > isolde stepto
    5964 
    5965 > select /AK
    5966 
    5967 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5968 
    5969 > select clear
    5970 
    5971 > select /AK
    5972 
    5973 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    5974 
    5975 > select clear
    5976 
    5977 > isolde stepto
    5978 
    5979 > isolde stepto
    5980 
    5981 > isolde stepto
    5982 
    5983 > isolde stepto
    5984 
    5985 > isolde stepto
    5986 
    5987 > isolde stepto
    5988 
    5989 > isolde stepto
    5990 
    5991 > isolde stepto
    5992 
    5993 > isolde stepto
    5994 
    5995 > isolde stepto
    5996 
    5997 > isolde stepto
    5998 
    5999 > isolde stepto
    6000 
    6001 > isolde stepto
    6002 
    6003 > isolde stepto
    6004 
    6005 > isolde stepto
    6006 
    6007 > isolde stepto
    6008 
    6009 > isolde stepto
    6010 
    6011 > isolde stepto
    6012 
    6013 > isolde stepto
    6014 
    6015 > isolde stepto
    6016 
    6017 > isolde stepto
    6018 
    6019 > isolde stepto
    6020 
    6021 > isolde stepto
    6022 
    6023 > isolde stepto
    6024 
    6025 > isolde stepto
    6026 
    6027 > isolde stepto
    6028 
    6029 > isolde stepto
    6030 
    6031 > isolde stepto
    6032 
    6033 > isolde stepto
    6034 
    6035 > isolde stepto
    6036 
    6037 > isolde stepto
    6038 
    6039 > isolde stepto
    6040 
    6041 > isolde stepto
    6042 
    6043 > isolde stepto
    6044 
    6045 > isolde stepto
    6046 
    6047 > isolde stepto
    6048 
    6049 > isolde stepto
    6050 
    6051 > isolde stepto
    6052 
    6053 > isolde stepto
    6054 
    6055 > isolde stepto
    6056 
    6057 > isolde stepto
    6058 
    6059 > isolde stepto
    6060 
    6061 > isolde stepto
    6062 
    6063 > isolde stepto
    6064 
    6065 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6066 bonded heavy atom. 
    6067 
    6068 > select clear
    6069 
    6070 > isolde stepto
    6071 
    6072 > isolde stepto
    6073 
    6074 > isolde stepto
    6075 
    6076 > isolde stepto
    6077 
    6078 > select /AL
    6079 
    6080 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6081 
    6082 > select clear
    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 > isolde stepto
    6143 
    6144 > isolde stepto
    6145 
    6146 > isolde stepto
    6147 
    6148 > isolde stepto
    6149 
    6150 > isolde stepto
    6151 
    6152 > isolde stepto
    6153 
    6154 > isolde stepto
    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 > select clear
    6175 
    6176 > isolde stepto
    6177 
    6178 > isolde stepto
    6179 
    6180 > isolde stepto
    6181 
    6182 > isolde stepto
    6183 
    6184 > select /AM
    6185 
    6186 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6187 
    6188 > select clear
    6189 
    6190 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6191 bonded heavy atom. 
    6192 
    6193 > select clear
    6194 
    6195 > select /AM
    6196 
    6197 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6198 
    6199 > select clear
    6200 
    6201 > isolde stepto
    6202 
    6203 > isolde stepto
    6204 
    6205 > isolde stepto
    6206 
    6207 > isolde stepto
    6208 
    6209 > isolde stepto
    6210 
    6211 > isolde stepto
    6212 
    6213 > isolde stepto
    6214 
    6215 > isolde stepto
    6216 
    6217 > isolde stepto
    6218 
    6219 > isolde stepto
    6220 
    6221 > isolde stepto
    6222 
    6223 > isolde stepto
    6224 
    6225 > isolde stepto
    6226 
    6227 > isolde stepto
    6228 
    6229 > isolde stepto
    6230 
    6231 > isolde stepto
    6232 
    6233 > isolde stepto
    6234 
    6235 > isolde stepto
    6236 
    6237 > isolde stepto
    6238 
    6239 > isolde stepto
    6240 
    6241 > isolde stepto
    6242 
    6243 > isolde stepto
    6244 
    6245 > isolde stepto
    6246 
    6247 > isolde stepto
    6248 
    6249 > isolde stepto
    6250 
    6251 > isolde stepto
    6252 
    6253 > isolde stepto
    6254 
    6255 > isolde stepto
    6256 
    6257 > isolde stepto
    6258 
    6259 > isolde stepto
    6260 
    6261 > isolde stepto
    6262 
    6263 > isolde stepto
    6264 
    6265 > isolde stepto
    6266 
    6267 > isolde stepto
    6268 
    6269 > isolde stepto
    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 > select /AN
    6298 
    6299 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6300 
    6301 > select clear
    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 > isolde stepto
    6360 
    6361 > isolde stepto
    6362 
    6363 > isolde stepto
    6364 
    6365 > isolde stepto
    6366 
    6367 > isolde stepto
    6368 
    6369 > isolde stepto
    6370 
    6371 > isolde stepto
    6372 
    6373 > isolde stepto
    6374 
    6375 > isolde stepto
    6376 
    6377 > isolde stepto
    6378 
    6379 > isolde stepto
    6380 
    6381 > isolde stepto
    6382 
    6383 > isolde stepto
    6384 
    6385 > isolde stepto
    6386 
    6387 > isolde stepto
    6388 
    6389 > isolde stepto
    6390 
    6391 > isolde ignore sel
    6392 
    6393 ISOLDE: currently ignoring 2 residues in model 8.2 
    6394 
    6395 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6396 bonded heavy atom. 
    6397 
    6398 > select clear
    6399 
    6400 > isolde ~ignore
    6401 
    6402 > isolde stepto
    6403 
    6404 > isolde stepto
    6405 
    6406 > isolde stepto
    6407 
    6408 > isolde stepto
    6409 
    6410 > select /AO
    6411 
    6412 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6413 
    6414 > select clear
    6415 
    6416 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6417 bonded heavy atom. 
    6418 
    6419 > isolde stepto
    6420 
    6421 > isolde stepto
    6422 
    6423 > isolde stepto
    6424 
    6425 > isolde stepto
    6426 
    6427 > isolde stepto
    6428 
    6429 > isolde stepto
    6430 
    6431 > isolde stepto
    6432 
    6433 > isolde stepto
    6434 
    6435 > isolde stepto
    6436 
    6437 > isolde stepto
    6438 
    6439 > isolde stepto
    6440 
    6441 > isolde stepto
    6442 
    6443 > isolde stepto
    6444 
    6445 > isolde stepto
    6446 
    6447 > isolde stepto
    6448 
    6449 > isolde stepto
    6450 
    6451 > isolde stepto
    6452 
    6453 > isolde stepto
    6454 
    6455 > isolde stepto
    6456 
    6457 > isolde stepto
    6458 
    6459 > isolde stepto
    6460 
    6461 > isolde stepto
    6462 
    6463 > isolde stepto
    6464 
    6465 > isolde stepto
    6466 
    6467 > isolde stepto
    6468 
    6469 > isolde stepto
    6470 
    6471 > isolde stepto
    6472 
    6473 > isolde stepto
    6474 
    6475 > isolde stepto
    6476 
    6477 > isolde stepto
    6478 
    6479 > isolde stepto
    6480 
    6481 > isolde stepto
    6482 
    6483 > isolde stepto
    6484 
    6485 > isolde stepto
    6486 
    6487 > isolde stepto
    6488 
    6489 > isolde stepto
    6490 
    6491 > isolde stepto
    6492 
    6493 > isolde stepto
    6494 
    6495 > isolde stepto
    6496 
    6497 > isolde stepto
    6498 
    6499 > isolde stepto
    6500 
    6501 > isolde stepto
    6502 
    6503 > isolde stepto
    6504 
    6505 > select clear
    6506 
    6507 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6508 bonded heavy atom. 
    6509 
    6510 > select clear
    6511 
    6512 > isolde stepto
    6513 
    6514 > isolde stepto
    6515 
    6516 > isolde stepto
    6517 
    6518 > isolde stepto
    6519 
    6520 > isolde stepto
    6521 
    6522 > select /AP
    6523 
    6524 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6525 
    6526 > select clear
    6527 
    6528 > select clear
    6529 
    6530 > isolde stepto
    6531 
    6532 > isolde stepto
    6533 
    6534 > isolde stepto
    6535 
    6536 > isolde stepto
    6537 
    6538 > isolde stepto
    6539 
    6540 > isolde stepto
    6541 
    6542 > isolde stepto
    6543 
    6544 > isolde stepto
    6545 
    6546 > isolde stepto
    6547 
    6548 > isolde stepto
    6549 
    6550 > isolde stepto
    6551 
    6552 > isolde stepto
    6553 
    6554 > isolde stepto
    6555 
    6556 > isolde stepto
    6557 
    6558 > isolde stepto
    6559 
    6560 > isolde stepto
    6561 
    6562 > isolde stepto
    6563 
    6564 > isolde stepto
    6565 
    6566 > isolde stepto
    6567 
    6568 > isolde stepto
    6569 
    6570 > isolde stepto
    6571 
    6572 > isolde stepto
    6573 
    6574 > isolde stepto
    6575 
    6576 > isolde stepto
    6577 
    6578 > isolde stepto
    6579 
    6580 > isolde stepto
    6581 
    6582 > isolde stepto
    6583 
    6584 > isolde stepto
    6585 
    6586 > isolde stepto
    6587 
    6588 > isolde stepto
    6589 
    6590 > isolde stepto
    6591 
    6592 > isolde stepto
    6593 
    6594 > isolde stepto
    6595 
    6596 > isolde stepto
    6597 
    6598 > isolde stepto
    6599 
    6600 > isolde stepto
    6601 
    6602 > isolde stepto
    6603 
    6604 > isolde stepto
    6605 
    6606 > isolde stepto
    6607 
    6608 > isolde stepto
    6609 
    6610 > isolde stepto
    6611 
    6612 > isolde stepto
    6613 
    6614 > isolde stepto
    6615 
    6616 > isolde stepto
    6617 
    6618 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6619 bonded heavy atom. 
    6620 
    6621 > select clear
    6622 
    6623 > isolde stepto
    6624 
    6625 > isolde stepto
    6626 
    6627 > isolde stepto
    6628 
    6629 > isolde stepto
    6630 
    6631 > select /AQ
    6632 
    6633 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6634 
    6635 > select clear
    6636 
    6637 > select clear
    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 stepto
    6686 
    6687 > isolde stepto
    6688 
    6689 > isolde stepto
    6690 
    6691 > isolde stepto
    6692 
    6693 > isolde stepto
    6694 
    6695 > isolde stepto
    6696 
    6697 > isolde stepto
    6698 
    6699 > isolde stepto
    6700 
    6701 > isolde stepto
    6702 
    6703 > isolde stepto
    6704 
    6705 > isolde stepto
    6706 
    6707 > isolde stepto
    6708 
    6709 > isolde stepto
    6710 
    6711 > isolde stepto
    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 > select clear
    6728 
    6729 > isolde stepto
    6730 
    6731 > isolde stepto
    6732 
    6733 > isolde stepto
    6734 
    6735 > isolde stepto
    6736 
    6737 > select /AR
    6738 
    6739 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6740 
    6741 > select clear
    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 > isolde stepto
    6800 
    6801 > isolde stepto
    6802 
    6803 > isolde stepto
    6804 
    6805 > isolde stepto
    6806 
    6807 > isolde stepto
    6808 
    6809 > isolde stepto
    6810 
    6811 > isolde stepto
    6812 
    6813 > isolde stepto
    6814 
    6815 > isolde stepto
    6816 
    6817 > isolde stepto
    6818 
    6819 > isolde stepto
    6820 
    6821 > isolde stepto
    6822 
    6823 > isolde stepto
    6824 
    6825 > isolde stepto
    6826 
    6827 > isolde stepto
    6828 
    6829 > isolde stepto
    6830 
    6831 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6832 bonded heavy atom. 
    6833 
    6834 > select clear
    6835 
    6836 > isolde stepto
    6837 
    6838 > isolde stepto
    6839 
    6840 > isolde stepto
    6841 
    6842 > isolde stepto
    6843 
    6844 > select /AS
    6845 
    6846 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6847 
    6848 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6849 bonded heavy atom. 
    6850 
    6851 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    6852 bonded heavy atom. 
    6853 
    6854 > isolde stepto
    6855 
    6856 > isolde stepto
    6857 
    6858 > select clear
    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 > select clear
    6913 
    6914 > isolde stepto
    6915 
    6916 > isolde stepto
    6917 
    6918 > isolde stepto
    6919 
    6920 > isolde stepto
    6921 
    6922 > isolde stepto
    6923 
    6924 > isolde stepto
    6925 
    6926 > isolde stepto
    6927 
    6928 > isolde stepto
    6929 
    6930 > isolde stepto
    6931 
    6932 > isolde stepto
    6933 
    6934 > isolde stepto
    6935 
    6936 > isolde stepto
    6937 
    6938 > isolde stepto
    6939 
    6940 > isolde stepto
    6941 
    6942 > isolde stepto
    6943 
    6944 > isolde stepto
    6945 
    6946 > select clear
    6947 
    6948 > isolde stepto
    6949 
    6950 > isolde stepto
    6951 
    6952 > isolde stepto
    6953 
    6954 > isolde stepto
    6955 
    6956 > select /AT
    6957 
    6958 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    6959 
    6960 > select clear
    6961 
    6962 > select clear
    6963 
    6964 > isolde stepto
    6965 
    6966 > isolde stepto
    6967 
    6968 > isolde stepto
    6969 
    6970 > isolde stepto
    6971 
    6972 > isolde stepto
    6973 
    6974 > isolde stepto
    6975 
    6976 > isolde stepto
    6977 
    6978 > isolde stepto
    6979 
    6980 > isolde stepto
    6981 
    6982 > isolde stepto
    6983 
    6984 > isolde stepto
    6985 
    6986 > isolde stepto
    6987 
    6988 > isolde stepto
    6989 
    6990 > isolde stepto
    6991 
    6992 > isolde stepto
    6993 
    6994 > isolde stepto
    6995 
    6996 > isolde stepto
    6997 
    6998 > isolde stepto
    6999 
    7000 > isolde stepto
    7001 
    7002 > isolde stepto
    7003 
    7004 > isolde stepto
    7005 
    7006 > isolde stepto
    7007 
    7008 > isolde stepto
    7009 
    7010 > isolde stepto
    7011 
    7012 > isolde stepto
    7013 
    7014 > isolde stepto
    7015 
    7016 > isolde stepto
    7017 
    7018 > isolde stepto
    7019 
    7020 > isolde stepto
    7021 
    7022 > isolde stepto
    7023 
    7024 > isolde stepto
    7025 
    7026 > isolde stepto
    7027 
    7028 > isolde stepto
    7029 
    7030 > isolde stepto
    7031 
    7032 > isolde stepto
    7033 
    7034 > isolde stepto
    7035 
    7036 > isolde stepto
    7037 
    7038 > isolde stepto
    7039 
    7040 > isolde stepto
    7041 
    7042 > isolde stepto
    7043 
    7044 > isolde stepto
    7045 
    7046 > isolde stepto
    7047 
    7048 > isolde stepto
    7049 
    7050 > isolde stepto
    7051 
    7052 > select clear
    7053 
    7054 > select clear
    7055 
    7056 > isolde stepto
    7057 
    7058 > isolde stepto
    7059 
    7060 > isolde stepto
    7061 
    7062 > isolde stepto
    7063 
    7064 > select /AU
    7065 
    7066 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7067 
    7068 > select clear
    7069 
    7070 > isolde stepto
    7071 
    7072 > isolde stepto
    7073 
    7074 > isolde stepto
    7075 
    7076 > isolde stepto
    7077 
    7078 > isolde stepto
    7079 
    7080 > isolde stepto
    7081 
    7082 > isolde stepto
    7083 
    7084 > isolde stepto
    7085 
    7086 > isolde stepto
    7087 
    7088 > isolde stepto
    7089 
    7090 > isolde stepto
    7091 
    7092 > select clear
    7093 
    7094 > isolde stepto
    7095 
    7096 > isolde stepto
    7097 
    7098 > isolde stepto
    7099 
    7100 > isolde stepto
    7101 
    7102 > isolde stepto
    7103 
    7104 > isolde stepto
    7105 
    7106 > isolde stepto
    7107 
    7108 > isolde stepto
    7109 
    7110 > isolde stepto
    7111 
    7112 > isolde stepto
    7113 
    7114 > isolde stepto
    7115 
    7116 > isolde stepto
    7117 
    7118 > isolde stepto
    7119 
    7120 > isolde stepto
    7121 
    7122 > isolde stepto
    7123 
    7124 > isolde stepto
    7125 
    7126 > isolde stepto
    7127 
    7128 > isolde stepto
    7129 
    7130 > isolde stepto
    7131 
    7132 > isolde stepto
    7133 
    7134 > isolde stepto
    7135 
    7136 > isolde stepto
    7137 
    7138 > isolde stepto
    7139 
    7140 > isolde stepto
    7141 
    7142 > isolde stepto
    7143 
    7144 > isolde stepto
    7145 
    7146 > isolde stepto
    7147 
    7148 > isolde stepto
    7149 
    7150 > isolde stepto
    7151 
    7152 > isolde stepto
    7153 
    7154 > isolde stepto
    7155 
    7156 > isolde stepto
    7157 
    7158 > isolde stepto
    7159 
    7160 > isolde stepto
    7161 
    7162 > isolde stepto prev
    7163 
    7164 > select clear
    7165 
    7166 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7167 bonded heavy atom. 
    7168 
    7169 > isolde stepto
    7170 
    7171 > isolde stepto
    7172 
    7173 > isolde stepto
    7174 
    7175 > isolde stepto
    7176 
    7177 > select /AV
    7178 
    7179 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7180 
    7181 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7182 bonded heavy atom. 
    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 > isolde stepto
    7207 
    7208 > select clear
    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 > isolde stepto
    7241 
    7242 > isolde stepto
    7243 
    7244 > isolde stepto
    7245 
    7246 > isolde stepto
    7247 
    7248 > isolde stepto
    7249 
    7250 > isolde stepto
    7251 
    7252 > isolde stepto
    7253 
    7254 > isolde stepto
    7255 
    7256 > isolde stepto
    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 > select clear
    7275 
    7276 > select clear
    7277 
    7278 > isolde stepto
    7279 
    7280 > isolde stepto
    7281 
    7282 > isolde stepto
    7283 
    7284 > isolde stepto
    7285 
    7286 > select /AW
    7287 
    7288 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7289 
    7290 > select clear
    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 > select clear
    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 > isolde stepto
    7347 
    7348 > isolde stepto
    7349 
    7350 > isolde stepto
    7351 
    7352 > isolde stepto
    7353 
    7354 > isolde stepto
    7355 
    7356 > isolde stepto
    7357 
    7358 > isolde stepto
    7359 
    7360 > isolde stepto
    7361 
    7362 > isolde stepto
    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 > isolde stepto
    7387 
    7388 > isolde stepto
    7389 
    7390 > select /AX
    7391 
    7392 980 atoms, 1001 bonds, 48 residues, 1 model selected 
    7393 
    7394 > select clear
    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
    7457 
    7458 > isolde stepto
    7459 
    7460 > isolde stepto
    7461 
    7462 > isolde stepto
    7463 
    7464 > isolde stepto
    7465 
    7466 > isolde stepto
    7467 
    7468 > isolde stepto
    7469 
    7470 > isolde stepto
    7471 
    7472 > isolde stepto
    7473 
    7474 > isolde stepto
    7475 
    7476 > isolde stepto
    7477 
    7478 > isolde stepto
    7479 
    7480 > isolde stepto
    7481 
    7482 > isolde stepto
    7483 
    7484 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7485 bonded heavy atom. 
    7486 
    7487 > select clear
    7488 
    7489 > select /AA
    7490 
    7491 981 atoms, 1002 bonds, 48 residues, 1 model selected 
    7492 
    7493 > select clear
    7494 
    7495 > save working.cxs
    7496 
    7497 Taking snapshot of stepper: working_2.pdb 
    7498 
    7499 > isolde stepto
    7500 
    7501 > isolde stepto
    7502 
    7503 > isolde stepto
    7504 
    7505 > isolde stepto
    7506 
    7507 > isolde stepto
    7508 
    7509 > select /BA
    7510 
    7511 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7512 
    7513 > select clear
    7514 
    7515 > isolde stepto
    7516 
    7517 > isolde stepto
    7518 
    7519 > isolde stepto
    7520 
    7521 > isolde stepto
    7522 
    7523 > isolde stepto
    7524 
    7525 > isolde stepto
    7526 
    7527 > isolde stepto
    7528 
    7529 > isolde stepto
    7530 
    7531 > isolde stepto
    7532 
    7533 > isolde stepto
    7534 
    7535 > isolde stepto
    7536 
    7537 > isolde stepto
    7538 
    7539 > isolde stepto
    7540 
    7541 > isolde stepto
    7542 
    7543 > isolde stepto
    7544 
    7545 > isolde stepto
    7546 
    7547 > isolde stepto
    7548 
    7549 > isolde stepto
    7550 
    7551 > isolde stepto
    7552 
    7553 > isolde stepto
    7554 
    7555 > isolde stepto
    7556 
    7557 > isolde stepto
    7558 
    7559 > isolde stepto
    7560 
    7561 > isolde stepto
    7562 
    7563 > isolde stepto
    7564 
    7565 > isolde stepto
    7566 
    7567 > isolde stepto
    7568 
    7569 > isolde stepto
    7570 
    7571 > isolde stepto
    7572 
    7573 > isolde stepto
    7574 
    7575 > isolde stepto
    7576 
    7577 > isolde stepto
    7578 
    7579 > isolde stepto
    7580 
    7581 > isolde stepto
    7582 
    7583 > isolde stepto
    7584 
    7585 > isolde stepto
    7586 
    7587 > isolde stepto
    7588 
    7589 > isolde stepto
    7590 
    7591 > select /BB
    7592 
    7593 773 atoms, 794 bonds, 41 residues, 1 model selected 
    7594 
    7595 > select clear
    7596 
    7597 > isolde stepto
    7598 
    7599 > isolde stepto
    7600 
    7601 > isolde stepto
    7602 
    7603 > isolde stepto
    7604 
    7605 > isolde stepto
    7606 
    7607 > isolde stepto
    7608 
    7609 > isolde stepto
    7610 
    7611 > isolde stepto
    7612 
    7613 > isolde stepto
    7614 
    7615 > isolde stepto
    7616 
    7617 > isolde stepto
    7618 
    7619 > isolde stepto
    7620 
    7621 > isolde stepto
    7622 
    7623 > isolde stepto
    7624 
    7625 > isolde stepto
    7626 
    7627 > isolde stepto
    7628 
    7629 > isolde stepto
    7630 
    7631 > isolde stepto
    7632 
    7633 > isolde stepto
    7634 
    7635 > isolde stepto
    7636 
    7637 > isolde stepto
    7638 
    7639 > isolde stepto
    7640 
    7641 > isolde stepto
    7642 
    7643 > isolde stepto
    7644 
    7645 > isolde stepto
    7646 
    7647 > isolde stepto
    7648 
    7649 > isolde stepto
    7650 
    7651 > isolde stepto
    7652 
    7653 > isolde stepto
    7654 
    7655 > isolde stepto
    7656 
    7657 > isolde stepto
    7658 
    7659 > isolde stepto
    7660 
    7661 > isolde stepto
    7662 
    7663 > isolde stepto
    7664 
    7665 > isolde stepto
    7666 
    7667 > isolde stepto
    7668 
    7669 > isolde stepto
    7670 
    7671 > isolde stepto
    7672 
    7673 > isolde stepto
    7674 
    7675 > isolde stepto
    7676 
    7677 > select up
    7678 
    7679 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7680 
    7681 > select up
    7682 
    7683 40 atoms, 39 bonds, 3 residues, 1 model selected 
    7684 
    7685 > select up
    7686 
    7687 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7688 
    7689 > select clear
    7690 
    7691 > select clear
    7692 
    7693 > isolde stepto
    7694 
    7695 > isolde stepto
    7696 
    7697 > isolde stepto
    7698 
    7699 > isolde stepto
    7700 
    7701 > isolde stepto
    7702 
    7703 > isolde stepto
    7704 
    7705 > isolde stepto
    7706 
    7707 > isolde stepto
    7708 
    7709 > isolde stepto
    7710 
    7711 > isolde stepto
    7712 
    7713 > isolde stepto
    7714 
    7715 > isolde stepto
    7716 
    7717 > isolde stepto
    7718 
    7719 > isolde stepto
    7720 
    7721 > isolde stepto
    7722 
    7723 > isolde stepto
    7724 
    7725 > isolde stepto
    7726 
    7727 > isolde stepto
    7728 
    7729 > isolde stepto
    7730 
    7731 > isolde stepto
    7732 
    7733 > isolde stepto
    7734 
    7735 > isolde stepto
    7736 
    7737 > isolde stepto
    7738 
    7739 > isolde stepto
    7740 
    7741 > isolde stepto
    7742 
    7743 > isolde stepto
    7744 
    7745 > isolde stepto
    7746 
    7747 > isolde stepto
    7748 
    7749 > isolde stepto
    7750 
    7751 > isolde stepto
    7752 
    7753 > isolde stepto
    7754 
    7755 > isolde stepto
    7756 
    7757 > isolde stepto
    7758 
    7759 > isolde stepto
    7760 
    7761 > isolde stepto
    7762 
    7763 > isolde stepto
    7764 
    7765 > isolde stepto
    7766 
    7767 > isolde stepto
    7768 
    7769 > isolde stepto
    7770 
    7771 > select clear
    7772 
    7773 > isolde stepto
    7774 
    7775 > isolde stepto
    7776 
    7777 > clipper spotlight radius 13.00
    7778 
    7779 > clipper spotlight radius 14.00
    7780 
    7781 > clipper spotlight radius 15.00
    7782 
    7783 > isolde stepto
    7784 
    7785 > isolde stepto
    7786 
    7787 > save working.cxs
    7788 
    7789 Taking snapshot of stepper: working_2.pdb 
    7790 
    7791 > isolde add ligand LMT
    7792 
    7793 place_ligand() was called with use_md_template=True, but no suitable template
    7794 was found. This command has been ignored. 
    7795 
    7796 Chain ak, residue 67 specifies more than one residue! The simulation can still
    7797 run, but this will probably cause problems later if not rectified by
    7798 renumbering. 
    7799 
    7800 Chain ak, residue 67 specifies more than one residue! The simulation can still
    7801 run, but this will probably cause problems later if not rectified by
    7802 renumbering. 
    7803 
    7804 > select up
    7805 
    7806 140 atoms, 148 bonds, 1 residue, 1 model selected 
    7807 
    7808 > isolde ignore sel
    7809 
    7810 ISOLDE: currently ignoring 1 residues in model 8.2 
    7811 
    7812 > isolde ~ignore
    7813 
    7814 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    7815 bonded heavy atom. 
    7816 
    7817 > select clear
    7818 
    7819 > select up
    7820 
    7821 81 atoms, 82 bonds, 1 residue, 1 model selected 
    7822 
    7823 > delete sel
    7824 
    7825 > save working.cxs
    7826 
    7827 Taking snapshot of stepper: working_2.pdb 
    7828 opened ChimeraX session 
    7829 
    7830 > isolde start
    7831 
    7832 > set selectionWidth 4
    7833 
    7834 Done loading forcefield 
    7835 
    7836 > isolde stepto
    7837 
    7838 > clipper set contourSensitivity 0.25
    7839 
    7840 > select /AA
    7841 
    7842 1019 atoms, 1041 bonds, 51 residues, 1 model selected 
    7843 
    7844 > show #!1 models
    7845 
    7846 > select #1
    7847 
    7848 158 atoms, 160 bonds, 11 residues, 8 models selected 
    7849 
    7850 > select #1
    7851 
    7852 158 atoms, 160 bonds, 11 residues, 8 models selected 
    7853 
    7854 > close #1
    7855 
    7856 > isolde stepto /BA
    7857 
    7858 Multiple residues selected! Going to the first... 
    7859 
    7860 > isolde stepto /BB
    7861 
    7862 Multiple residues selected! Going to the first... 
    7863 
    7864 > select clear
    7865 
    7866 > select /BB
    7867 
    7868 773 atoms, 794 bonds, 41 residues, 1 model selected 
    7869 
    7870 > select clear
    7871 
    7872 > select clear
    7873 
    7874 > isolde stepto
    7875 
    7876 > isolde stepto
    7877 
    7878 > isolde stepto
    7879 
    7880 > isolde stepto
    7881 
    7882 > isolde stepto
    7883 
    7884 > isolde stepto
    7885 
    7886 > isolde stepto
    7887 
    7888 > isolde stepto
    7889 
    7890 > isolde stepto
    7891 
    7892 > isolde stepto
    7893 
    7894 > isolde stepto
    7895 
    7896 > isolde stepto
    7897 
    7898 > isolde stepto
    7899 
    7900 > isolde stepto
    7901 
    7902 > isolde stepto
    7903 
    7904 > isolde stepto
    7905 
    7906 > isolde stepto
    7907 
    7908 > isolde stepto
    7909 
    7910 > isolde stepto
    7911 
    7912 > isolde stepto
    7913 
    7914 > isolde stepto
    7915 
    7916 > isolde stepto
    7917 
    7918 > isolde stepto
    7919 
    7920 > isolde stepto
    7921 
    7922 > isolde stepto
    7923 
    7924 > isolde stepto
    7925 
    7926 > isolde stepto
    7927 
    7928 > isolde stepto
    7929 
    7930 > isolde stepto
    7931 
    7932 > isolde stepto
    7933 
    7934 > isolde stepto
    7935 
    7936 > isolde stepto
    7937 
    7938 > isolde stepto
    7939 
    7940 > isolde stepto
    7941 
    7942 > isolde stepto
    7943 
    7944 > isolde stepto
    7945 
    7946 > isolde stepto
    7947 
    7948 > isolde stepto
    7949 
    7950 > isolde stepto
    7951 
    7952 > isolde stepto
    7953 
    7954 > select up
    7955 
    7956 17 atoms, 16 bonds, 1 residue, 1 model selected 
    7957 
    7958 > select up
    7959 
    7960 40 atoms, 39 bonds, 3 residues, 1 model selected 
    7961 
    7962 > select up
    7963 
    7964 766 atoms, 787 bonds, 40 residues, 1 model selected 
    7965 
    7966 > select clear
    7967 
    7968 > isolde stepto
    7969 
    7970 > isolde stepto
    7971 
    7972 > isolde stepto
    7973 
    7974 > isolde stepto
    7975 
    7976 > isolde stepto
    7977 
    7978 > isolde stepto
    7979 
    7980 > isolde stepto
    7981 
    7982 > isolde stepto
    7983 
    7984 > isolde stepto
    7985 
    7986 > isolde stepto
    7987 
    7988 > isolde stepto
    7989 
    7990 > isolde stepto
    7991 
    7992 > isolde stepto
    7993 
    7994 > isolde stepto
    7995 
    7996 > isolde stepto
    7997 
    7998 > isolde stepto
    7999 
    8000 > isolde stepto
    8001 
    8002 > isolde stepto
    8003 
    8004 > isolde stepto
    8005 
    8006 > isolde stepto
    8007 
    8008 > isolde stepto
    8009 
    8010 > isolde stepto
    8011 
    8012 > isolde stepto
    8013 
    8014 > isolde stepto
    8015 
    8016 > isolde stepto
    8017 
    8018 > isolde stepto
    8019 
    8020 > isolde stepto
    8021 
    8022 > isolde stepto
    8023 
    8024 > isolde stepto
    8025 
    8026 > isolde stepto
    8027 
    8028 > isolde stepto
    8029 
    8030 > isolde stepto
    8031 
    8032 > isolde stepto
    8033 
    8034 > isolde stepto
    8035 
    8036 > isolde stepto
    8037 
    8038 > isolde stepto
    8039 
    8040 > isolde stepto
    8041 
    8042 > isolde stepto
    8043 
    8044 > isolde stepto
    8045 
    8046 > select clear
    8047 
    8048 > select up
    8049 
    8050 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8051 
    8052 > select up
    8053 
    8054 47 atoms, 46 bonds, 4 residues, 1 model selected 
    8055 
    8056 > select up
    8057 
    8058 773 atoms, 794 bonds, 41 residues, 1 model selected 
    8059 
    8060 > select clear
    8061 
    8062 > isolde stepto
    8063 
    8064 > isolde stepto
    8065 
    8066 > isolde stepto
    8067 
    8068 > isolde stepto
    8069 
    8070 > isolde stepto
    8071 
    8072 > isolde stepto
    8073 
    8074 > isolde stepto
    8075 
    8076 > isolde stepto
    8077 
    8078 > isolde stepto
    8079 
    8080 > isolde stepto
    8081 
    8082 > isolde stepto
    8083 
    8084 > isolde stepto
    8085 
    8086 > isolde stepto
    8087 
    8088 > isolde stepto
    8089 
    8090 > isolde stepto
    8091 
    8092 > isolde stepto
    8093 
    8094 > isolde stepto
    8095 
    8096 > isolde stepto
    8097 
    8098 > isolde stepto
    8099 
    8100 > isolde stepto
    8101 
    8102 > isolde stepto
    8103 
    8104 > isolde stepto
    8105 
    8106 > isolde stepto
    8107 
    8108 > isolde stepto
    8109 
    8110 > isolde stepto
    8111 
    8112 > isolde stepto
    8113 
    8114 > isolde stepto
    8115 
    8116 > isolde stepto
    8117 
    8118 > isolde stepto
    8119 
    8120 > isolde stepto
    8121 
    8122 > isolde stepto
    8123 
    8124 > isolde stepto
    8125 
    8126 > isolde stepto
    8127 
    8128 > isolde stepto
    8129 
    8130 > isolde stepto
    8131 
    8132 > isolde stepto
    8133 
    8134 > isolde stepto
    8135 
    8136 > isolde stepto
    8137 
    8138 > isolde stepto
    8139 
    8140 > isolde stepto
    8141 
    8142 > select up
    8143 
    8144 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8145 
    8146 > select up
    8147 
    8148 47 atoms, 46 bonds, 4 residues, 1 model selected 
    8149 
    8150 > select up
    8151 
    8152 773 atoms, 794 bonds, 41 residues, 1 model selected 
    8153 
    8154 > select clear
    8155 
    8156 > isolde stepto
    8157 
    8158 > isolde stepto
    8159 
    8160 > isolde stepto
    8161 
    8162 > isolde stepto
    8163 
    8164 > isolde stepto
    8165 
    8166 > isolde stepto
    8167 
    8168 > isolde stepto
    8169 
    8170 > isolde stepto
    8171 
    8172 > isolde stepto
    8173 
    8174 > isolde stepto
    8175 
    8176 > isolde stepto
    8177 
    8178 > isolde stepto
    8179 
    8180 > isolde stepto
    8181 
    8182 > isolde stepto
    8183 
    8184 > isolde stepto
    8185 
    8186 > isolde stepto
    8187 
    8188 > isolde stepto
    8189 
    8190 > isolde stepto
    8191 
    8192 > isolde stepto
    8193 
    8194 > isolde stepto
    8195 
    8196 > isolde stepto
    8197 
    8198 > isolde stepto
    8199 
    8200 > isolde stepto
    8201 
    8202 > isolde stepto
    8203 
    8204 > isolde stepto
    8205 
    8206 > isolde stepto
    8207 
    8208 > isolde stepto
    8209 
    8210 > isolde stepto
    8211 
    8212 > isolde stepto
    8213 
    8214 > isolde stepto
    8215 
    8216 > isolde stepto
    8217 
    8218 > isolde stepto
    8219 
    8220 > isolde stepto
    8221 
    8222 > isolde stepto
    8223 
    8224 > isolde stepto
    8225 
    8226 > isolde stepto
    8227 
    8228 > isolde stepto
    8229 
    8230 > isolde stepto
    8231 
    8232 > isolde stepto
    8233 
    8234 > isolde stepto
    8235 
    8236 > select up
    8237 
    8238 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8239 
    8240 > select up
    8241 
    8242 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8243 
    8244 > select up
    8245 
    8246 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8247 
    8248 > select clear
    8249 
    8250 > isolde stepto
    8251 
    8252 > isolde stepto
    8253 
    8254 > isolde stepto
    8255 
    8256 > isolde stepto
    8257 
    8258 > isolde stepto
    8259 
    8260 > select clear
    8261 
    8262 > isolde stepto
    8263 
    8264 > isolde stepto
    8265 
    8266 > isolde stepto
    8267 
    8268 > isolde stepto
    8269 
    8270 > isolde stepto
    8271 
    8272 > isolde stepto
    8273 
    8274 > isolde stepto
    8275 
    8276 > isolde stepto
    8277 
    8278 > isolde stepto
    8279 
    8280 > isolde stepto
    8281 
    8282 > isolde stepto
    8283 
    8284 > isolde stepto
    8285 
    8286 > isolde stepto
    8287 
    8288 > isolde stepto
    8289 
    8290 > isolde stepto
    8291 
    8292 > isolde stepto
    8293 
    8294 > isolde stepto
    8295 
    8296 > isolde stepto
    8297 
    8298 > isolde stepto
    8299 
    8300 > isolde stepto
    8301 
    8302 > isolde stepto
    8303 
    8304 > isolde stepto
    8305 
    8306 > isolde stepto
    8307 
    8308 > isolde stepto
    8309 
    8310 > isolde stepto
    8311 
    8312 > isolde stepto
    8313 
    8314 > isolde stepto
    8315 
    8316 > isolde stepto
    8317 
    8318 > isolde stepto
    8319 
    8320 > isolde stepto
    8321 
    8322 > select clear
    8323 
    8324 > isolde stepto
    8325 
    8326 > isolde stepto
    8327 
    8328 > isolde stepto
    8329 
    8330 > isolde stepto
    8331 
    8332 > select up
    8333 
    8334 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8335 
    8336 > select up
    8337 
    8338 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8339 
    8340 > select up
    8341 
    8342 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8343 
    8344 > select up
    8345 
    8346 96639 atoms, 98747 bonds, 5194 residues, 1 model selected 
    8347 
    8348 Chain ak, residue 67 specifies more than one residue! The simulation can still
    8349 run, but this will probably cause problems later if not rectified by
    8350 renumbering. 
    8351 
    8352 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    8353 more memory-efficient implementation. 
    8354 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    8355 more memory-efficient implementation. 
    8356 
    8357 > select clear
    8358 
    8359 > select clear
    8360 
    8361 > select up
    8362 
    8363 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8364 
    8365 > select up
    8366 
    8367 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8368 
    8369 > select up
    8370 
    8371 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8372 
    8373 > select up
    8374 
    8375 96639 atoms, 98747 bonds, 5194 residues, 1 model selected 
    8376 
    8377 > select down
    8378 
    8379 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8380 
    8381 > select clear
    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 > isolde stepto
    8440 
    8441 > isolde stepto
    8442 
    8443 > isolde stepto
    8444 
    8445 > isolde stepto
    8446 
    8447 > isolde stepto
    8448 
    8449 > isolde stepto
    8450 
    8451 > isolde stepto
    8452 
    8453 > isolde stepto
    8454 
    8455 > isolde stepto
    8456 
    8457 > isolde stepto
    8458 
    8459 > isolde stepto
    8460 
    8461 > select up
    8462 
    8463 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8464 
    8465 > select up
    8466 
    8467 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8468 
    8469 > select up
    8470 
    8471 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8472 
    8473 > select clear
    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 > isolde stepto
    8534 
    8535 > isolde stepto
    8536 
    8537 > isolde stepto
    8538 
    8539 > isolde stepto
    8540 
    8541 > isolde stepto
    8542 
    8543 > isolde stepto
    8544 
    8545 > isolde stepto
    8546 
    8547 > isolde stepto
    8548 
    8549 > isolde stepto
    8550 
    8551 > isolde stepto
    8552 
    8553 > select up
    8554 
    8555 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8556 
    8557 > select up
    8558 
    8559 47 atoms, 46 bonds, 4 residues, 1 model selected 
    8560 
    8561 > select up
    8562 
    8563 773 atoms, 794 bonds, 41 residues, 1 model selected 
    8564 
    8565 > select clear
    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 > isolde stepto
    8620 
    8621 > isolde stepto
    8622 
    8623 > isolde stepto
    8624 
    8625 > isolde stepto
    8626 
    8627 > isolde stepto
    8628 
    8629 > isolde stepto
    8630 
    8631 > isolde stepto
    8632 
    8633 > isolde stepto
    8634 
    8635 > isolde stepto
    8636 
    8637 > isolde stepto
    8638 
    8639 > isolde stepto
    8640 
    8641 > isolde stepto
    8642 
    8643 > isolde stepto
    8644 
    8645 > isolde stepto
    8646 
    8647 > select up
    8648 
    8649 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8650 
    8651 > select up
    8652 
    8653 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8654 
    8655 > select up
    8656 
    8657 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8658 
    8659 > select clear
    8660 
    8661 > isolde stepto
    8662 
    8663 > isolde stepto
    8664 
    8665 > isolde stepto
    8666 
    8667 > isolde stepto
    8668 
    8669 > isolde stepto
    8670 
    8671 > isolde stepto
    8672 
    8673 > isolde stepto
    8674 
    8675 > isolde stepto
    8676 
    8677 > isolde stepto
    8678 
    8679 > isolde stepto
    8680 
    8681 > isolde stepto
    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 > select up
    8740 
    8741 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8742 
    8743 > select up
    8744 
    8745 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8746 
    8747 > select up
    8748 
    8749 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8750 
    8751 > select clear
    8752 
    8753 > isolde stepto
    8754 
    8755 > isolde stepto
    8756 
    8757 > isolde stepto
    8758 
    8759 > isolde stepto
    8760 
    8761 > isolde stepto
    8762 
    8763 > isolde stepto
    8764 
    8765 > isolde stepto
    8766 
    8767 > isolde stepto
    8768 
    8769 > isolde stepto
    8770 
    8771 > isolde stepto
    8772 
    8773 > isolde stepto
    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 > select up
    8832 
    8833 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8834 
    8835 > select up
    8836 
    8837 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8838 
    8839 > select up
    8840 
    8841 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8842 
    8843 > select clear
    8844 
    8845 > isolde stepto
    8846 
    8847 > isolde stepto
    8848 
    8849 > isolde stepto
    8850 
    8851 > isolde stepto
    8852 
    8853 > isolde stepto
    8854 
    8855 > isolde stepto
    8856 
    8857 > isolde stepto
    8858 
    8859 > isolde stepto
    8860 
    8861 > isolde stepto
    8862 
    8863 > isolde stepto
    8864 
    8865 > isolde stepto
    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 > select clear
    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 > select up
    8926 
    8927 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8928 
    8929 > select up
    8930 
    8931 40 atoms, 39 bonds, 3 residues, 1 model selected 
    8932 
    8933 > select up
    8934 
    8935 766 atoms, 787 bonds, 40 residues, 1 model selected 
    8936 
    8937 > select clear
    8938 
    8939 > isolde stepto
    8940 
    8941 > isolde stepto
    8942 
    8943 > isolde stepto
    8944 
    8945 > isolde stepto
    8946 
    8947 > isolde stepto
    8948 
    8949 > isolde stepto
    8950 
    8951 > isolde stepto
    8952 
    8953 > isolde stepto
    8954 
    8955 > isolde stepto
    8956 
    8957 > isolde stepto
    8958 
    8959 > isolde stepto
    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 > select up
    9018 
    9019 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9020 
    9021 > select up
    9022 
    9023 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9024 
    9025 > select up
    9026 
    9027 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9028 
    9029 > select clear
    9030 
    9031 > isolde stepto
    9032 
    9033 > isolde stepto
    9034 
    9035 > isolde stepto
    9036 
    9037 > isolde stepto
    9038 
    9039 > isolde stepto
    9040 
    9041 > isolde stepto
    9042 
    9043 > isolde stepto
    9044 
    9045 > isolde stepto
    9046 
    9047 > select up
    9048 
    9049 100 atoms, 99 bonds, 1 residue, 1 model selected 
    9050 
    9051 > show sel
    9052 
    9053 > select clear
    9054 
    9055 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9056 bonded heavy atom. 
    9057 
    9058 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9059 bonded heavy atom. 
    9060 
    9061 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    9062 bonded heavy atom. 
    9063 
    9064 > select clear
    9065 
    9066 > isolde stepto
    9067 
    9068 > isolde stepto
    9069 
    9070 > isolde stepto
    9071 
    9072 > isolde stepto
    9073 
    9074 > isolde stepto
    9075 
    9076 > isolde stepto
    9077 
    9078 > isolde stepto
    9079 
    9080 > isolde stepto
    9081 
    9082 > isolde stepto
    9083 
    9084 > isolde stepto
    9085 
    9086 > isolde stepto
    9087 
    9088 > isolde stepto
    9089 
    9090 > isolde stepto
    9091 
    9092 > isolde stepto
    9093 
    9094 > isolde stepto
    9095 
    9096 > isolde stepto
    9097 
    9098 > isolde stepto
    9099 
    9100 > isolde stepto
    9101 
    9102 > isolde stepto
    9103 
    9104 > isolde stepto
    9105 
    9106 > isolde stepto
    9107 
    9108 > isolde stepto
    9109 
    9110 > isolde stepto
    9111 
    9112 > isolde stepto
    9113 
    9114 > isolde stepto
    9115 
    9116 > isolde stepto
    9117 
    9118 > isolde stepto
    9119 
    9120 > isolde stepto
    9121 
    9122 > isolde stepto
    9123 
    9124 > isolde stepto
    9125 
    9126 > isolde stepto
    9127 
    9128 > select up
    9129 
    9130 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9131 
    9132 > select up
    9133 
    9134 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9135 
    9136 > select up
    9137 
    9138 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9139 
    9140 > select clear
    9141 
    9142 > isolde stepto
    9143 
    9144 > isolde stepto
    9145 
    9146 > isolde stepto
    9147 
    9148 > isolde stepto
    9149 
    9150 > isolde stepto
    9151 
    9152 > isolde stepto
    9153 
    9154 > isolde stepto
    9155 
    9156 > isolde stepto
    9157 
    9158 > isolde stepto
    9159 
    9160 > isolde stepto
    9161 
    9162 > isolde stepto
    9163 
    9164 > isolde stepto
    9165 
    9166 > isolde stepto
    9167 
    9168 > isolde stepto
    9169 
    9170 > isolde stepto
    9171 
    9172 > isolde stepto
    9173 
    9174 > isolde stepto
    9175 
    9176 > isolde stepto
    9177 
    9178 > isolde stepto
    9179 
    9180 > isolde stepto
    9181 
    9182 > isolde stepto
    9183 
    9184 > isolde stepto
    9185 
    9186 > isolde stepto
    9187 
    9188 > isolde stepto
    9189 
    9190 > isolde stepto
    9191 
    9192 > isolde stepto
    9193 
    9194 > isolde stepto
    9195 
    9196 > isolde stepto
    9197 
    9198 > isolde stepto
    9199 
    9200 > isolde stepto
    9201 
    9202 > isolde stepto
    9203 
    9204 > isolde stepto
    9205 
    9206 > isolde stepto
    9207 
    9208 > isolde stepto
    9209 
    9210 > isolde stepto
    9211 
    9212 > isolde stepto
    9213 
    9214 > isolde stepto
    9215 
    9216 > isolde stepto
    9217 
    9218 > isolde stepto
    9219 
    9220 > select up
    9221 
    9222 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9223 
    9224 > select up
    9225 
    9226 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9227 
    9228 > select clear
    9229 
    9230 > isolde stepto
    9231 
    9232 > isolde stepto
    9233 
    9234 > isolde stepto
    9235 
    9236 > isolde stepto
    9237 
    9238 > isolde stepto
    9239 
    9240 > isolde stepto
    9241 
    9242 > isolde stepto
    9243 
    9244 > isolde stepto
    9245 
    9246 > isolde stepto
    9247 
    9248 > isolde stepto
    9249 
    9250 > isolde stepto
    9251 
    9252 > isolde stepto
    9253 
    9254 > isolde stepto
    9255 
    9256 > isolde stepto
    9257 
    9258 > select up
    9259 
    9260 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9261 
    9262 > select up
    9263 
    9264 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9265 
    9266 > select up
    9267 
    9268 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9269 
    9270 > select clear
    9271 
    9272 > isolde stepto
    9273 
    9274 > isolde stepto
    9275 
    9276 > isolde stepto
    9277 
    9278 > isolde stepto
    9279 
    9280 > isolde stepto
    9281 
    9282 > isolde stepto
    9283 
    9284 > isolde stepto
    9285 
    9286 > isolde stepto
    9287 
    9288 > isolde stepto
    9289 
    9290 > isolde stepto
    9291 
    9292 > isolde stepto
    9293 
    9294 > isolde stepto
    9295 
    9296 > isolde stepto
    9297 
    9298 > isolde stepto
    9299 
    9300 > isolde stepto
    9301 
    9302 > isolde stepto
    9303 
    9304 > isolde stepto
    9305 
    9306 > isolde stepto
    9307 
    9308 > isolde stepto
    9309 
    9310 > isolde stepto
    9311 
    9312 > isolde stepto
    9313 
    9314 > isolde stepto
    9315 
    9316 > isolde stepto
    9317 
    9318 > isolde stepto
    9319 
    9320 > isolde stepto
    9321 
    9322 > select up
    9323 
    9324 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9325 
    9326 > select up
    9327 
    9328 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9329 
    9330 > select up
    9331 
    9332 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9333 
    9334 > ui tool show Shell
    9335 
    9336 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    9337 UserWarning: IPython History requires SQLite, your history will not be saved 
    9338 warn("IPython History requires SQLite, your history will not be saved") 
    9339 
    9340 > select up
    9341 
    9342 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9343 
    9344 > select up
    9345 
    9346 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9347 
    9348 > select up
    9349 
    9350 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9351 
    9352 > select clear
    9353 
    9354 > select clear
    9355 
    9356 > isolde stepto
    9357 
    9358 > isolde stepto
    9359 
    9360 > isolde stepto
    9361 
    9362 > isolde stepto
    9363 
    9364 > isolde stepto
    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 > isolde stepto
    9429 
    9430 > isolde stepto
    9431 
    9432 > isolde stepto
    9433 
    9434 > select up
    9435 
    9436 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9437 
    9438 > select up
    9439 
    9440 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9441 
    9442 > select clear
    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 > select up
    9467 
    9468 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9469 
    9470 > select up
    9471 
    9472 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9473 
    9474 > select down
    9475 
    9476 503 atoms, 512 bonds, 32 residues, 1 model selected 
    9477 
    9478 > select up
    9479 
    9480 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9481 
    9482 > select clear
    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 > isolde stepto
    9521 
    9522 > isolde stepto
    9523 
    9524 > isolde stepto
    9525 
    9526 > isolde stepto
    9527 
    9528 > isolde stepto
    9529 
    9530 > isolde stepto
    9531 
    9532 > isolde stepto
    9533 
    9534 > isolde stepto
    9535 
    9536 > isolde stepto
    9537 
    9538 > isolde stepto
    9539 
    9540 > select up
    9541 
    9542 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9543 
    9544 > select up
    9545 
    9546 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9547 
    9548 > select up
    9549 
    9550 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9551 
    9552 > select clear
    9553 
    9554 > isolde stepto
    9555 
    9556 > isolde stepto
    9557 
    9558 > isolde stepto
    9559 
    9560 > isolde stepto
    9561 
    9562 > isolde stepto
    9563 
    9564 > isolde stepto
    9565 
    9566 > isolde stepto
    9567 
    9568 > isolde stepto
    9569 
    9570 > isolde stepto
    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 > isolde stepto
    9623 
    9624 > isolde stepto
    9625 
    9626 > isolde stepto
    9627 
    9628 > isolde stepto
    9629 
    9630 > isolde stepto
    9631 
    9632 > select up
    9633 
    9634 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9635 
    9636 > select up
    9637 
    9638 38 atoms, 37 bonds, 3 residues, 1 model selected 
    9639 
    9640 > select up
    9641 
    9642 771 atoms, 792 bonds, 41 residues, 1 model selected 
    9643 
    9644 > select clear
    9645 
    9646 > isolde stepto
    9647 
    9648 > isolde stepto
    9649 
    9650 > isolde stepto
    9651 
    9652 > isolde stepto
    9653 
    9654 > isolde stepto
    9655 
    9656 > select up
    9657 
    9658 63 atoms, 60 bonds, 3 residues, 1 model selected 
    9659 
    9660 > select up
    9661 
    9662 1073 atoms, 1092 bonds, 67 residues, 1 model selected 
    9663 
    9664 > select clear
    9665 
    9666 > select clear
    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 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9739 
    9740 > select up
    9741 
    9742 40 atoms, 39 bonds, 3 residues, 1 model selected 
    9743 
    9744 > select up
    9745 
    9746 766 atoms, 787 bonds, 40 residues, 1 model selected 
    9747 
    9748 > select clear
    9749 
    9750 > select clear
    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 > isolde stepto
    9769 
    9770 > isolde stepto
    9771 
    9772 > isolde stepto
    9773 
    9774 > isolde stepto
    9775 
    9776 > isolde stepto
    9777 
    9778 > isolde stepto
    9779 
    9780 > isolde stepto
    9781 
    9782 > isolde stepto
    9783 
    9784 > isolde stepto
    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 > select up
    9831 
    9832 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9833 
    9834 > select up
    9835 
    9836 47 atoms, 46 bonds, 4 residues, 1 model selected 
    9837 
    9838 > select up
    9839 
    9840 773 atoms, 794 bonds, 41 residues, 1 model selected 
    9841 
    9842 > select clear
    9843 
    9844 > isolde stepto
    9845 
    9846 > isolde stepto
    9847 
    9848 > isolde stepto
    9849 
    9850 > isolde stepto
    9851 
    9852 > isolde stepto
    9853 
    9854 > isolde stepto
    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 > select up
    9925 
    9926 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9927 
    9928 > select up
    9929 
    9930 47 atoms, 46 bonds, 4 residues, 1 model selected 
    9931 
    9932 > select up
    9933 
    9934 773 atoms, 794 bonds, 41 residues, 1 model selected 
    9935 
    9936 > select clear
    9937 
    9938 > select clear
    9939 
    9940 > select clear
    9941 
    9942 > isolde stepto
    9943 
    9944 > isolde stepto
    9945 
    9946 > isolde stepto
    9947 
    9948 > isolde stepto
    9949 
    9950 > isolde stepto
    9951 
    9952 > isolde stepto
    9953 
    9954 > isolde stepto
    9955 
    9956 > isolde stepto
    9957 
    9958 > isolde stepto
    9959 
    9960 > isolde stepto
    9961 
    9962 > isolde stepto
    9963 
    9964 > isolde stepto
    9965 
    9966 > isolde stepto
    9967 
    9968 > isolde stepto
    9969 
    9970 > isolde stepto
    9971 
    9972 > isolde stepto
    9973 
    9974 > isolde stepto
    9975 
    9976 > isolde stepto
    9977 
    9978 > isolde stepto
    9979 
    9980 > select clear
    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 > select clear
    10023 
    10024 > save working.cxs
    10025 
    10026 Taking snapshot of stepper: working_2.pdb 
    10027 
    10028 > isolde stepto
    10029 
    10030 > select up
    10031 
    10032 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10033 
    10034 > select up
    10035 
    10036 40 atoms, 39 bonds, 3 residues, 1 model selected 
    10037 
    10038 > select up
    10039 
    10040 766 atoms, 787 bonds, 40 residues, 1 model selected 
    10041 
    10042 > select clear
    10043 
    10044 > isolde stepto
    10045 
    10046 > isolde stepto
    10047 
    10048 > isolde stepto
    10049 
    10050 > isolde stepto
    10051 
    10052 > isolde stepto
    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 > select clear
    10123 
    10124 > select clear
    10125 
    10126 > isolde stepto /aa
    10127 
    10128 Multiple residues selected! Going to the first... 
    10129 
    10130 > select up
    10131 
    10132 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10133 
    10134 > select up
    10135 
    10136 86 atoms, 87 bonds, 4 residues, 1 model selected 
    10137 
    10138 > select up
    10139 
    10140 1062 atoms, 1082 bonds, 60 residues, 1 model selected 
    10141 
    10142 > select clear
    10143 
    10144 > isolde stepto
    10145 
    10146 > select clear
    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 > select clear
    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 > isolde stepto
    10227 
    10228 > isolde stepto
    10229 
    10230 > isolde stepto
    10231 
    10232 > isolde stepto
    10233 
    10234 > isolde stepto
    10235 
    10236 > isolde stepto
    10237 
    10238 > isolde stepto
    10239 
    10240 > isolde stepto
    10241 
    10242 > isolde stepto
    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 > select up
    10267 
    10268 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10269 
    10270 > select up
    10271 
    10272 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10273 
    10274 > select up
    10275 
    10276 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10277 
    10278 > select up
    10279 
    10280 96659 atoms, 98767 bonds, 5198 residues, 1 model selected 
    10281 
    10282 > select down
    10283 
    10284 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10285 
    10286 > select clear
    10287 
    10288 > select clear
    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 > isolde stepto
    10325 
    10326 > isolde stepto
    10327 
    10328 > isolde stepto
    10329 
    10330 > isolde stepto
    10331 
    10332 > isolde stepto
    10333 
    10334 > isolde stepto
    10335 
    10336 > isolde stepto
    10337 
    10338 > isolde stepto
    10339 
    10340 > select clear
    10341 
    10342 > isolde stepto
    10343 
    10344 > isolde stepto
    10345 
    10346 > isolde stepto
    10347 
    10348 > isolde stepto
    10349 
    10350 > isolde stepto
    10351 
    10352 > isolde stepto
    10353 
    10354 > select clear
    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 > select clear
    10405 
    10406 > isolde stepto
    10407 
    10408 > isolde stepto
    10409 
    10410 > isolde stepto
    10411 
    10412 > isolde stepto
    10413 
    10414 > isolde stepto
    10415 
    10416 > view /ab:2
    10417 
    10418 > select clear
    10419 
    10420 > isolde stepto
    10421 
    10422 > view /ab:2
    10423 
    10424 > select clear
    10425 
    10426 > select clear
    10427 
    10428 > isolde stepto
    10429 
    10430 > select up
    10431 
    10432 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10433 
    10434 > select up
    10435 
    10436 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10437 
    10438 > select up
    10439 
    10440 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10441 
    10442 > select clear
    10443 
    10444 > isolde stepto
    10445 
    10446 > isolde stepto
    10447 
    10448 > isolde stepto
    10449 
    10450 > isolde stepto
    10451 
    10452 > select clear
    10453 
    10454 > isolde stepto
    10455 
    10456 > isolde stepto
    10457 
    10458 > isolde stepto
    10459 
    10460 > isolde stepto
    10461 
    10462 > select clear
    10463 
    10464 > isolde stepto
    10465 
    10466 > isolde stepto
    10467 
    10468 > isolde stepto
    10469 
    10470 > isolde stepto
    10471 
    10472 > isolde stepto
    10473 
    10474 > isolde stepto
    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 > select clear
    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 > select clear
    10553 
    10554 > delete sel
    10555 
    10556 > select clear
    10557 
    10558 > isolde stepto
    10559 
    10560 > isolde stepto
    10561 
    10562 > isolde stepto
    10563 
    10564 > select up
    10565 
    10566 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10567 
    10568 > select up
    10569 
    10570 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10571 
    10572 > save working.cxs
    10573 
    10574 Taking snapshot of stepper: working_2.pdb 
    10575 
    10576 > select clear
    10577 
    10578 > select up
    10579 
    10580 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10581 
    10582 > select up
    10583 
    10584 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10585 
    10586 > select up
    10587 
    10588 96615 atoms, 98722 bonds, 5194 residues, 1 model selected 
    10589 
    10590 > select down
    10591 
    10592 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10593 
    10594 > select clear
    10595 
    10596 > select clear
    10597 
    10598 > save working.cxs
    10599 
    10600 Taking snapshot of stepper: working_2.pdb 
    10601 
    10602 > select up
    10603 
    10604 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10605 
    10606 > select up
    10607 
    10608 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10609 
    10610 > select clear
    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 add ligand CDL
    10635 
    10636 place_ligand() was called with use_md_template=True, but no suitable template
    10637 was found. This command has been ignored. 
    10638 
    10639 > select up
    10640 
    10641 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10642 
    10643 > isolde ignore ~sel
    10644 
    10645 ISOLDE: currently ignoring 5194 residues in model 8.2 
    10646 
    10647 > select up
    10648 
    10649 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10650 
    10651 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10652 bonded heavy atom. 
    10653 
    10654 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10655 bonded heavy atom. 
    10656 
    10657 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10658 bonded heavy atom. 
    10659 
    10660 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10661 bonded heavy atom. 
    10662 
    10663 > isolde ~ignore
    10664 
    10665 > select up
    10666 
    10667 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10668 
    10669 > select up
    10670 
    10671 140 atoms, 148 bonds, 1 residue, 1 model selected 
    10672 
    10673 > isolde ignore sel
    10674 
    10675 ISOLDE: currently ignoring 1 residues in model 8.2 
    10676 
    10677 > select up
    10678 
    10679 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10680 
    10681 > select down
    10682 
    10683 2 atoms, 1 bond, 1 residue, 1 model selected 
    10684 
    10685 > isolde ~ignore
    10686 
    10687 > select up
    10688 
    10689 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10690 
    10691 > isolde ignore sel
    10692 
    10693 ISOLDE: currently ignoring 1 residues in model 8.2 
    10694 
    10695 > isolde ~ignore
    10696 
    10697 Chain ak, residue 67 specifies more than one residue! The simulation can still
    10698 run, but this will probably cause problems later if not rectified by
    10699 renumbering. 
    10700 
    10701 > select clear
    10702 
    10703 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10704 bonded heavy atom. 
    10705 
    10706 > select up
    10707 
    10708 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10709 
    10710 > clipper isolate sel contextDistance 0 maskRadius 3
    10711 
    10712 > select clear
    10713 
    10714 > ~cartoon
    10715 
    10716 > hide HC
    10717 
    10718 > hide #!8.1.1.2 models
    10719 
    10720 > show #!8.1.1.2 models
    10721 
    10722 > select clear
    10723 
    10724 > save resolved_cdl.jpg
    10725 
    10726 > cartoon
    10727 
    10728 > select /ae:CDL
    10729 
    10730 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10731 
    10732 > select /ae:11-30@CA
    10733 
    10734 20 atoms, 20 residues, 1 model selected 
    10735 
    10736 > select /af:11-30@CA
    10737 
    10738 20 atoms, 20 residues, 1 model selected 
    10739 
    10740 > save working_cdl.cxs
    10741 
    10742 Taking snapshot of stepper: working_2.pdb 
    10743 
    10744 > select up
    10745 
    10746 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10747 
    10748 > isolde ignore ~sel
    10749 
    10750 ISOLDE: currently ignoring 5195 residues in model 8.2 
    10751 
    10752 > select up
    10753 
    10754 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10755 
    10756 > isolde ignore sel
    10757 
    10758 ISOLDE: currently ignoring 5196 residues in model 8.2 
    10759 Traceback (most recent call last): 
    10760 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10761 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    10762 self.start_sim() 
    10763 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10764 packages/chimerax/isolde/isolde.py", line 2727, in start_sim 
    10765 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    10766 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10767 packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__ 
    10768 self._prepare_mdff_managers() 
    10769 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10770 packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    10771 _prepare_mdff_managers 
    10772 focus = False) 
    10773 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10774 packages/chimerax/clipper/symmetry.py", line 982, in
    10775 isolate_and_cover_selection 
    10776 extra_padding=extra_padding) 
    10777 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10778 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    10779 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    10780 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10781 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    10782 self.structure = self._unique_structure(atoms) 
    10783 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10784 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    10785 _unique_structure 
    10786 raise TypeError('All atoms for zone mask must be from a single model!') 
    10787 TypeError: All atoms for zone mask must be from a single model! 
    10788  
    10789 TypeError: All atoms for zone mask must be from a single model! 
    10790  
    10791 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    10792 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    10793 _unique_structure 
    10794 raise TypeError('All atoms for zone mask must be from a single model!') 
    10795  
    10796 See log for complete Python traceback. 
    10797  
    10798 
    10799 > isolde ~ignore
    10800 
    10801 > color bychain
    10802 
    10803 > color byhetero
    10804 
    10805 > select up
    10806 
    10807 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10808 
    10809 > isolde ignore sel
    10810 
    10811 ISOLDE: currently ignoring 1 residues in model 8.2 
    10812 
    10813 > select up
    10814 
    10815 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10816 
    10817 > isolde ~ignore
    10818 
    10819 > isolde ignore ~sel
    10820 
    10821 ISOLDE: currently ignoring 5195 residues in model 8.2 
    10822 
    10823 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10824 bonded heavy atom. 
    10825 
    10826 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10827 bonded heavy atom. 
    10828 
    10829 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10830 bonded heavy atom. 
    10831 
    10832 > select up
    10833 
    10834 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10835 
    10836 > isolde ~ignore
    10837 
    10838 > select clear
    10839 
    10840 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10841 bonded heavy atom. 
    10842 
    10843 > select /ag:11-30@CA
    10844 
    10845 20 atoms, 20 residues, 1 model selected 
    10846 
    10847 > select up
    10848 
    10849 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10850 
    10851 > isolde ignore ~sel
    10852 
    10853 ISOLDE: currently ignoring 5196 residues in model 8.2 
    10854 
    10855 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10856 bonded heavy atom. 
    10857 
    10858 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10859 bonded heavy atom. 
    10860 
    10861 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    10862 bonded heavy atom. 
    10863 
    10864 > select up
    10865 
    10866 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10867 
    10868 > isolde ~ignore
    10869 
    10870 > select up
    10871 
    10872 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10873 
    10874 > isolde ignore sel
    10875 
    10876 ISOLDE: currently ignoring 1 residues in model 8.2 
    10877 
    10878 > select clear
    10879 
    10880 > isolde ~ignore
    10881 
    10882 > select clear
    10883 
    10884 > save working_cdl.cxs
    10885 
    10886 Taking snapshot of stepper: working_2.pdb 
    10887 
    10888 > select /ah:11-30@CA
    10889 
    10890 20 atoms, 20 residues, 1 model selected 
    10891 
    10892 > select /AH
    10893 
    10894 1018 atoms, 1040 bonds, 51 residues, 1 model selected 
    10895 
    10896 > cartoon
    10897 
    10898 > select :CDL
    10899 
    10900 768 atoms, 765 bonds, 3 residues, 1 model selected 
    10901 
    10902 > select /ae, af, ag
    10903 
    10904 4005 atoms, 4062 bonds, 186 residues, 1 model selected 
    10905 
    10906 > select /ae, af, ag,ah
    10907 
    10908 5084 atoms, 5161 bonds, 247 residues, 1 model selected 
    10909 
    10910 > select clear
    10911 
    10912 > select /ah:11-30@CA
    10913 
    10914 20 atoms, 20 residues, 1 model selected 
    10915 
    10916 > select up
    10917 
    10918 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10919 
    10920 > delete sel
    10921 
    10922 > select /ad
    10923 
    10924 1079 atoms, 1099 bonds, 61 residues, 1 model selected 
    10925 
    10926 > select /ad,ae
    10927 
    10928 2414 atoms, 2453 bonds, 123 residues, 1 model selected 
    10929 
    10930 > select /ad:11-30@CA
    10931 
    10932 20 atoms, 20 residues, 1 model selected 
    10933 
    10934 > select up
    10935 
    10936 256 atoms, 255 bonds, 1 residue, 1 model selected 
    10937 
    10938 > delete sel
    10939 
    10940 > select clear
    10941 
    10942 > isolde stepto
    10943 
    10944 > select clear
    10945 
    10946 > select up
    10947 
    10948 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10949 
    10950 > select up
    10951 
    10952 84 atoms, 86 bonds, 4 residues, 1 model selected 
    10953 
    10954 > select up
    10955 
    10956 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10957 
    10958 > select up
    10959 
    10960 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10961 
    10962 > select down
    10963 
    10964 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10965 
    10966 > select up
    10967 
    10968 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10969 
    10970 > select down
    10971 
    10972 184 atoms, 185 bonds, 5 residues, 1 model selected 
    10973 
    10974 > select up
    10975 
    10976 2037 atoms, 2081 bonds, 102 residues, 1 model selected 
    10977 
    10978 > select clear
    10979 
    10980 > isolde stepto
    10981 
    10982 > isolde stepto
    10983 
    10984 > isolde stepto
    10985 
    10986 > isolde stepto
    10987 
    10988 > isolde stepto
    10989 
    10990 > isolde stepto
    10991 
    10992 > isolde stepto
    10993 
    10994 > isolde stepto
    10995 
    10996 > isolde stepto
    10997 
    10998 > isolde stepto
    10999 
    11000 > isolde stepto
    11001 
    11002 > isolde stepto
    11003 
    11004 > select clear
    11005 
    11006 > isolde stepto
    11007 
    11008 > isolde stepto
    11009 
    11010 > isolde stepto
    11011 
    11012 > isolde stepto
    11013 
    11014 > isolde stepto
    11015 
    11016 > isolde stepto
    11017 
    11018 > isolde stepto
    11019 
    11020 > isolde stepto
    11021 
    11022 > isolde stepto
    11023 
    11024 > isolde stepto
    11025 
    11026 > isolde stepto
    11027 
    11028 > isolde stepto
    11029 
    11030 > isolde stepto
    11031 
    11032 > isolde stepto
    11033 
    11034 > isolde stepto
    11035 
    11036 > isolde stepto
    11037 
    11038 > isolde stepto
    11039 
    11040 > isolde stepto
    11041 
    11042 > isolde stepto
    11043 
    11044 > isolde stepto
    11045 
    11046 > isolde stepto
    11047 
    11048 > isolde stepto
    11049 
    11050 > isolde stepto
    11051 
    11052 > isolde stepto
    11053 
    11054 > isolde stepto
    11055 
    11056 > isolde stepto
    11057 
    11058 > isolde stepto
    11059 
    11060 > isolde stepto
    11061 
    11062 > isolde stepto
    11063 
    11064 > isolde stepto
    11065 
    11066 > select clear
    11067 
    11068 > isolde stepto
    11069 
    11070 > isolde stepto
    11071 
    11072 > isolde stepto
    11073 
    11074 > isolde stepto
    11075 
    11076 > isolde stepto
    11077 
    11078 > isolde stepto
    11079 
    11080 > isolde stepto
    11081 
    11082 > select up
    11083 
    11084 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11085 
    11086 > select up
    11087 
    11088 1018 atoms, 1040 bonds, 51 residues, 1 model selected 
    11089 
    11090 > select clear
    11091 
    11092 > select clear
    11093 
    11094 > select clear
    11095 
    11096 > isolde stepto
    11097 
    11098 > isolde stepto
    11099 
    11100 > isolde stepto
    11101 
    11102 > isolde stepto
    11103 
    11104 > isolde stepto
    11105 
    11106 > isolde stepto
    11107 
    11108 > isolde stepto
    11109 
    11110 > isolde stepto
    11111 
    11112 > isolde stepto
    11113 
    11114 > isolde stepto
    11115 
    11116 > isolde stepto
    11117 
    11118 > isolde stepto
    11119 
    11120 > isolde stepto
    11121 
    11122 > isolde stepto
    11123 
    11124 > isolde stepto
    11125 
    11126 > isolde stepto
    11127 
    11128 > isolde stepto
    11129 
    11130 > isolde stepto
    11131 
    11132 > isolde stepto
    11133 
    11134 > isolde stepto
    11135 
    11136 > isolde stepto
    11137 
    11138 > isolde stepto
    11139 
    11140 > isolde stepto
    11141 
    11142 > isolde stepto
    11143 
    11144 > isolde stepto
    11145 
    11146 > isolde stepto
    11147 
    11148 > isolde stepto
    11149 
    11150 > isolde stepto
    11151 
    11152 > isolde stepto
    11153 
    11154 > isolde stepto
    11155 
    11156 > isolde stepto
    11157 
    11158 > isolde stepto
    11159 
    11160 > isolde stepto
    11161 
    11162 > isolde stepto
    11163 
    11164 > isolde stepto
    11165 
    11166 > isolde stepto
    11167 
    11168 > isolde stepto
    11169 
    11170 > isolde stepto
    11171 
    11172 > isolde stepto
    11173 
    11174 > isolde stepto
    11175 
    11176 > isolde stepto
    11177 
    11178 > isolde stepto
    11179 
    11180 > isolde stepto
    11181 
    11182 > isolde stepto
    11183 
    11184 > isolde stepto
    11185 
    11186 > isolde stepto
    11187 
    11188 > isolde stepto
    11189 
    11190 > isolde stepto
    11191 
    11192 > isolde stepto
    11193 
    11194 > select up
    11195 
    11196 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11197 
    11198 > select up
    11199 
    11200 1004 atoms, 1025 bonds, 50 residues, 1 model selected 
    11201 
    11202 > select clear
    11203 
    11204 > isolde stepto
    11205 
    11206 > isolde stepto
    11207 
    11208 > isolde stepto
    11209 
    11210 > isolde stepto
    11211 
    11212 > isolde stepto
    11213 
    11214 > isolde stepto
    11215 
    11216 > isolde stepto
    11217 
    11218 > isolde stepto
    11219 
    11220 > isolde stepto
    11221 
    11222 > isolde stepto
    11223 
    11224 > isolde stepto
    11225 
    11226 > isolde stepto
    11227 
    11228 > isolde stepto
    11229 
    11230 > isolde stepto
    11231 
    11232 > isolde stepto
    11233 
    11234 > isolde stepto
    11235 
    11236 > isolde stepto
    11237 
    11238 > isolde stepto
    11239 
    11240 > isolde stepto
    11241 
    11242 > isolde stepto
    11243 
    11244 > isolde stepto
    11245 
    11246 > isolde stepto
    11247 
    11248 > isolde stepto
    11249 
    11250 > isolde stepto
    11251 
    11252 > isolde stepto
    11253 
    11254 > isolde stepto
    11255 
    11256 > isolde stepto
    11257 
    11258 > isolde stepto
    11259 
    11260 > isolde stepto
    11261 
    11262 > isolde stepto
    11263 
    11264 > isolde stepto
    11265 
    11266 > isolde stepto
    11267 
    11268 > isolde stepto
    11269 
    11270 > isolde stepto
    11271 
    11272 > isolde stepto
    11273 
    11274 > isolde stepto
    11275 
    11276 > isolde stepto
    11277 
    11278 > isolde stepto
    11279 
    11280 > isolde stepto
    11281 
    11282 > isolde stepto
    11283 
    11284 > isolde stepto
    11285 
    11286 > isolde stepto
    11287 
    11288 > select clear
    11289 
    11290 > isolde stepto
    11291 
    11292 > isolde stepto
    11293 
    11294 > isolde stepto
    11295 
    11296 > isolde stepto
    11297 
    11298 > isolde stepto
    11299 
    11300 > select clear
    11301 
    11302 > isolde stepto
    11303 
    11304 > select up
    11305 
    11306 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11307 
    11308 > select up
    11309 
    11310 1004 atoms, 1025 bonds, 50 residues, 1 model selected 
    11311 
    11312 > select clear
    11313 
    11314 > usage isolde jupm
    11315 
    11316 Subcommands are:
    11317 
    11318   * isolde add ligand
    11319   * isolde add water
    11320   * isolde adjust distances
    11321   * isolde adjust torsions
    11322   * isolde cisflip
    11323   * isolde demo
    11324   * isolde ignore
    11325   * isolde ~ignore
    11326   * isolde jumpto
    11327   * isolde pepflip
    11328   * isolde release distances
    11329   * isolde release torsions
    11330   * isolde remote rest info
    11331   * isolde remote rest start
    11332   * isolde remote rest stop
    11333   * isolde remote xmlrpc
    11334   * isolde replace ligand
    11335   * isolde report
    11336   * isolde reset forcefield
    11337   * isolde restrain distances
    11338   * isolde restrain ligands
    11339   * isolde restrain single distance
    11340   * isolde restrain torsions
    11341   * isolde set
    11342   * isolde sim
    11343   * isolde start
    11344   * isolde stepto
    11345   * isolde tutorial
    11346 
    11347  
    11348 
    11349 > usage isolde jump
    11350 
    11351 isolde jumpto [direction] 
    11352 — Jump the view to the first residue of the next chain or the last residue of
    11353 the previous chain. 
    11354 direction: one of next or prev 
    11355 
    11356 > isolde jumpto prev
    11357 
    11358 > isolde jumpto prev
    11359 
    11360 > isolde jumpto prev
    11361 
    11362 > isolde jumpto prev
    11363 
    11364 > save working.cxs
    11365 
    11366 Taking snapshot of stepper: working_2.pdb 
    11367 Restoring stepper: working_2.pdb 
    11368 opened ChimeraX session 
    11369 
    11370 > usage volume mask
    11371 
    11372 volume mask volumes surfaces a surfaces specifier [pad a number] [extend an
    11373 integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis
    11374 an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId
    11375 modelId] 
    11376 — Mask a map to a surface 
    11377 slab: a number or some numbers 
    11378 modelId: a model id 
    11379 
    11380 > usage volume zone
    11381 
    11382 volume zone volumes nearAtoms an atoms specifier [range a number]
    11383 [bondPointSpacing a number] [minimalBounds true or false] [newMap true or
    11384 false] [invert true or false] [subregion map region] [step map step] [modelId
    11385 modelId] 
    11386 — Zero map values beyond a distance range from atoms 
    11387 modelId: a model id 
    11388 
    11389 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11390 
    11391 > close #1
    11392 
    11393 > select #1
    11394 
    11395 Nothing selected 
    11396 
    11397 > select #8
    11398 
    11399 97383 atoms, 99487 bonds, 14 pseudobonds, 5197 residues, 21 models selected 
    11400 
    11401 > select clear
    11402 
    11403 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    11404 
    11405 > usage volume subtr
    11406 
    11407 volume subtract volumes [onGrid a density maps specifier] [boundingGrid true
    11408 or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
    11409 floats] [valueType numeric value type] [hideMaps true or false] [subregion map
    11410 region] [step map step] [modelId modelId] [inPlace true or false]
    11411 [scaleFactors scaleFactors] [minRms true or false] 
    11412 — Subtract maps pointwise 
    11413 modelId: a model id 
    11414 scaleFactors: some numbers 
    11415 
    11416 > volume subtract #8.1.1.1 #1 inPlace false
    11417 
    11418 > close #1
    11419 
    11420 > volume #2 level 0.03352
    11421 
    11422 > volume #2 level 0.03748
    11423 
    11424 > select :CDL
    11425 
    11426 768 atoms, 765 bonds, 3 residues, 1 model selected 
    11427 
    11428 > select /C1
    11429 
    11430 1472 atoms, 1487 bonds, 92 residues, 1 model selected 
    11431 
    11432 > select clear
    11433 
    11434 > delete sel
    11435 
    11436 > select up
    11437 
    11438 12 atoms, 11 bonds, 1 residue, 1 model selected 
    11439 
    11440 > select up
    11441 
    11442 125 atoms, 128 bonds, 9 residues, 1 model selected 
    11443 
    11444 > hide #!2 models
    11445 
    11446 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11447 bonded heavy atom. 
    11448 
    11449 > show #!2 models
    11450 
    11451 > select clear
    11452 
    11453 > hide #!2 models
    11454 
    11455 > show #!2 models
    11456 
    11457 > hide #!2 models
    11458 
    11459 > ui tool show "Build Structure"
    11460 
    11461 > build start peptide "custom built" AAAAAAAAAAAAAA -139.0,135.0 -139.0,135.0
    11462 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11463 > -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
    11464 > -139.0,135.0 -139.0,135.0 rotLib Dunbrack
    11465 
    11466 Chain information for custom built #1 
    11467 --- 
    11468 Chain | Description 
    11469 A | No description available 
    11470  
    11471 
    11472 > select #1
    11473 
    11474 71 atoms, 70 bonds, 14 residues, 1 model selected 
    11475 
    11476 > ui mousemode right "translate selected models"
    11477 
    11478 > ui mousemode right "rotate selected models"
    11479 
    11480 > ui mousemode right "translate selected models"
    11481 
    11482 > delete /C1:1-14
    11483 
    11484 > addh #1
    11485 
    11486 Summary of feedback from adding hydrogens to custom built #1 
    11487 --- 
    11488 notes | No usable SEQRES records for custom built (#1) chain A; guessing
    11489 termini instead 
    11490 Chain-initial residues that are actual N termini: custom built #1/A ALA 1 
    11491 Chain-initial residues that are not actual N termini: 
    11492 Chain-final residues that are actual C termini: custom built #1/A ALA 14 
    11493 Chain-final residues that are not actual C termini: 
    11494 0 hydrogen bonds 
    11495 72 hydrogens added 
    11496  
    11497 
    11498 > hide #1 models
    11499 
    11500 > select /C1:1-14
    11501 
    11502 143 atoms, 142 bonds, 14 residues, 1 model selected 
    11503 
    11504 > select /C1:1-14
    11505 
    11506 143 atoms, 142 bonds, 14 residues, 1 model selected 
    11507 
    11508 > swapaa mousemode sel PRO
    11509 
    11510 > select clear
    11511 
    11512 > swapaa mousemode sel PRO
    11513 
    11514 > swapaa mousemode sel GLN
    11515 
    11516 > swapaa mousemode sel THR
    11517 
    11518 > swapaa mousemode sel GLY
    11519 
    11520 > open
    11521 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class1a_24A.mrc
    11522 
    11523 Opened class1a_24A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11524 0.0212, step 2, values float32 
    11525 
    11526 > ui tool show "Volume Viewer"
    11527 
    11528 > volume #3 step 1
    11529 
    11530 > volume #3 level 0.04119
    11531 
    11532 > volume #3 level 0.03163
    11533 
    11534 > open
    11535 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/class2a_26A.mrc
    11536 
    11537 Opened class2a_26A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    11538 0.0249, step 2, values float32 
    11539 
    11540 > volume #4 step 1
    11541 
    11542 > volume #4 level 0.05455
    11543 
    11544 > fitmap #4 inMap #8.1.1.1
    11545 
    11546 Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points 
    11547 correlation = 0.0582, correlation about mean = 0.003368, overlap = 2.152 
    11548 steps = 964, shift = 6.3, angle = 5.34 degrees 
    11549  
    11550 Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11551 coordinates: 
    11552 Matrix rotation and translation 
    11553 0.99577666 -0.02365016 -0.08871027 25.10161578 
    11554 0.02499610 0.99958822 0.01409207 -14.07791580 
    11555 0.08834046 -0.01624996 0.99595778 -13.06451755 
    11556 Axis -0.16303956 -0.95136249 0.26139533 
    11557 Axis point 178.35759174 0.00000000 285.28764281 
    11558 Rotation angle (degrees) 5.33916146 
    11559 Shift along axis 5.88564083 
    11560  
    11561 
    11562 > fitmap #4 inMap #8.1.1.1
    11563 
    11564 Fit map class2a_26A.mrc in map class1b_26A.mrc using 135602 points 
    11565 correlation = 0.1152, correlation about mean = 0.06419, overlap = 9.627 
    11566 steps = 672, shift = 6.89, angle = 21.3 degrees 
    11567  
    11568 Position of class2a_26A.mrc (#4) relative to class1b_26A.mrc (#8.1.1.1)
    11569 coordinates: 
    11570 Matrix rotation and translation 
    11571 0.92701975 -0.37501178 0.00074524 89.89128138 
    11572 0.37500543 0.92701261 0.00430577 -61.35976247 
    11573 -0.00230557 -0.00371206 0.99999045 1.56396515 
    11574 Axis -0.01068950 0.00406739 0.99993459 
    11575 Axis point 202.60869093 200.28337525 0.00000000 
    11576 Rotation angle (degrees) 22.02636092 
    11577 Shift along axis 0.35339585 
    11578  
    11579 
    11580 > select /C1:1-14
    11581 
    11582 159 atoms, 160 bonds, 14 residues, 1 model selected 
    11583 
    11584 > select /C1
    11585 
    11586 1784 atoms, 1805 bonds, 117 residues, 1 model selected 
    11587 
    11588 > volume #4 level 0.04206
    11589 
    11590 > swapaa mousemode sel GLN
    11591 
    11592 > select up
    11593 
    11594 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11595 
    11596 > select up
    11597 
    11598 166 atoms, 167 bonds, 14 residues, 1 model selected 
    11599 
    11600 > swapaa mousemode sel ASSP
    11601 
    11602 Missing or invalid "restype" argument: Should be one of 'ALA', 'ARG', 'ASN',
    11603 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE',
    11604 'PRO', 'SER', 'THR', 'TRP', 'TYR', or 'VAL' 
    11605 
    11606 > swapaa mousemode sel ASP
    11607 
    11608 > swapaa mousemode sel ARG
    11609 
    11610 > swapaa mousemode sel GLY
    11611 
    11612 > swapaa mousemode sel VAL
    11613 
    11614 > swapaa mousemode sel PRO
    11615 
    11616 > select up
    11617 
    11618 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11619 
    11620 > select up
    11621 
    11622 190 atoms, 193 bonds, 14 residues, 1 model selected 
    11623 
    11624 > select clear
    11625 
    11626 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11627 bonded heavy atom. 
    11628 
    11629 Unable to flip peptide bond after 50 rounds. Giving up. 
    11630 
    11631 > select /C1:1-14
    11632 
    11633 190 atoms, 193 bonds, 14 residues, 1 model selected 
    11634 
    11635 > select clear
    11636 
    11637 > save working.cxs
    11638 
    11639 Taking snapshot of stepper: working_2.pdb 
    11640 
    11641 > select /C1
    11642 
    11643 1815 atoms, 1838 bonds, 117 residues, 1 model selected 
    11644 
    11645 > select clear
    11646 
    11647 > select /ak
    11648 
    11649 1234 atoms, 1257 bonds, 72 residues, 1 model selected 
    11650 
    11651 > isolde stepto /c
    11652 
    11653 Selection contains no residues! 
    11654 
    11655 > isolde stepto /ac
    11656 
    11657 Multiple residues selected! Going to the first... 
    11658 
    11659 > select up
    11660 
    11661 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11662 
    11663 > select up
    11664 
    11665 84 atoms, 86 bonds, 4 residues, 1 model selected 
    11666 
    11667 > select up
    11668 
    11669 1035 atoms, 1054 bonds, 57 residues, 1 model selected 
    11670 
    11671 > select clear
    11672 
    11673 > isolde stepto
    11674 
    11675 > isolde stepto
    11676 
    11677 > isolde stepto
    11678 
    11679 > isolde stepto
    11680 
    11681 > isolde stepto
    11682 
    11683 > isolde stepto
    11684 
    11685 > isolde stepto
    11686 
    11687 > isolde stepto
    11688 
    11689 > isolde stepto
    11690 
    11691 > isolde stepto
    11692 
    11693 > isolde stepto
    11694 
    11695 > isolde stepto
    11696 
    11697 > isolde stepto
    11698 
    11699 > isolde stepto
    11700 
    11701 > isolde stepto
    11702 
    11703 > isolde stepto
    11704 
    11705 > isolde stepto
    11706 
    11707 > isolde stepto
    11708 
    11709 > isolde stepto
    11710 
    11711 > isolde stepto
    11712 
    11713 > isolde stepto
    11714 
    11715 > isolde stepto
    11716 
    11717 > isolde stepto
    11718 
    11719 > isolde stepto
    11720 
    11721 > isolde stepto
    11722 
    11723 > isolde stepto
    11724 
    11725 > isolde stepto
    11726 
    11727 > isolde stepto
    11728 
    11729 > isolde stepto
    11730 
    11731 > isolde stepto
    11732 
    11733 > isolde stepto
    11734 
    11735 > isolde stepto
    11736 
    11737 > isolde stepto
    11738 
    11739 > isolde stepto
    11740 
    11741 > isolde stepto
    11742 
    11743 > isolde stepto
    11744 
    11745 > isolde stepto
    11746 
    11747 > isolde stepto
    11748 
    11749 > isolde stepto
    11750 
    11751 > isolde stepto
    11752 
    11753 > isolde stepto
    11754 
    11755 > isolde stepto
    11756 
    11757 > isolde stepto
    11758 
    11759 > isolde stepto
    11760 
    11761 > isolde stepto
    11762 
    11763 > isolde stepto
    11764 
    11765 > isolde stepto
    11766 
    11767 > isolde stepto
    11768 
    11769 > isolde stepto
    11770 
    11771 > isolde stepto
    11772 
    11773 > close #1
    11774 
    11775 > show #!2 models
    11776 
    11777 > select :CDL
    11778 
    11779 768 atoms, 765 bonds, 3 residues, 1 model selected 
    11780 
    11781 > hide #!2 models
    11782 
    11783 > clipper set contourSensitivity o.25
    11784 
    11785 Missing or invalid "sensitivity" argument: Expected a number 
    11786 
    11787 > clipper set contourSensitivity 0.25
    11788 
    11789 > show #!2 models
    11790 
    11791 > select :BCL
    11792 
    11793 11760 atoms, 12432 bonds, 84 residues, 1 model selected 
    11794 
    11795 > hide #!2 models
    11796 
    11797 > show #!2 models
    11798 
    11799 > select clear
    11800 
    11801 > hide #!2 models
    11802 
    11803 > select /af
    11804 
    11805 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11806 
    11807 > select /ag
    11808 
    11809 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11810 
    11811 > select /ae
    11812 
    11813 1335 atoms, 1354 bonds, 62 residues, 1 model selected 
    11814 
    11815 > select down
    11816 
    11817 2 atoms, 1 bond, 1 residue, 1 model selected 
    11818 
    11819 > select up
    11820 
    11821 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11822 
    11823 > save working.cxs
    11824 
    11825 Taking snapshot of stepper: working_2.pdb 
    11826 
    11827 > isolde add ligand CDL
    11828 
    11829 place_ligand() was called with use_md_template=True, but no suitable template
    11830 was found. This command has been ignored. 
    11831 
    11832 > show #!2 models
    11833 
    11834 > hide #!2 models
    11835 
    11836 > select up
    11837 
    11838 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11839 
    11840 > hide ~sel
    11841 
    11842 > isolde ignore ~sel
    11843 
    11844 ISOLDE: currently ignoring 5222 residues in model 8.2 
    11845 
    11846 > show #!2 models
    11847 
    11848 > show ~HC
    11849 
    11850 > hide protein&~@CA
    11851 
    11852 > select up
    11853 
    11854 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11855 
    11856 > select up
    11857 
    11858 1282 atoms, 1300 bonds, 63 residues, 1 model selected 
    11859 
    11860 > select down
    11861 
    11862 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11863 
    11864 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11865 bonded heavy atom. 
    11866 
    11867 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11868 bonded heavy atom. 
    11869 
    11870 > select clear
    11871 
    11872 > select clear
    11873 
    11874 > isolde ~ignore
    11875 
    11876 > select up
    11877 
    11878 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11879 
    11880 > show ~HC
    11881 
    11882 > isolde ignore sel
    11883 
    11884 ISOLDE: currently ignoring 1 residues in model 8.2 
    11885 
    11886 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11887 bonded heavy atom. 
    11888 
    11889 > select up
    11890 
    11891 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11892 
    11893 > isolde ~ignore
    11894 
    11895 > select clear
    11896 
    11897 > save working.cxs
    11898 
    11899 Taking snapshot of stepper: working_2.pdb 
    11900 
    11901 > hide
    11902 
    11903 > hide #!8 models
    11904 
    11905 > volume #2 level 0.03016
    11906 
    11907 > volume #2 level 0.03131
    11908 
    11909 > show #!8 models
    11910 
    11911 > show ~HC
    11912 
    11913 > hide #!8 models
    11914 
    11915 > show #!8 models
    11916 
    11917 > select :CDL
    11918 
    11919 1024 atoms, 1020 bonds, 4 residues, 1 model selected 
    11920 
    11921 > hide #!2 models
    11922 
    11923 > show #!2 models
    11924 
    11925 > hide #!2 models
    11926 
    11927 > select clear
    11928 
    11929 > select :CDL
    11930 
    11931 1024 atoms, 1020 bonds, 4 residues, 1 model selected 
    11932 
    11933 > select up
    11934 
    11935 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11936 
    11937 > save cdl_ref.pdb #8 selectedOnly true
    11938 
    11939 > open cdl_ref.pdb
    11940 
    11941 Summary of feedback from opening cdl_ref.pdb 
    11942 --- 
    11943 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    11944 TRP A 5 1 4 
    11945 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    11946 26 
    11947 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    11948 6 
    11949 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    11950 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    11951 27 
    11952 267 messages similar to the above omitted 
    11953 Cannot find LINK/SSBOND residue CYS (95 ) 
    11954 Cannot find LINK/SSBOND residue CYS (98 ) 
    11955 Cannot find LINK/SSBOND residue THR (108 ) 
    11956 Cannot find LINK/SSBOND residue CYS (146 ) 
    11957 Cannot find LINK/SSBOND residue CYS (149 ) 
    11958 25 messages similar to the above omitted 
    11959  
    11960 
    11961 > select #1
    11962 
    11963 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11964 
    11965 > ui mousemode right "translate selected models"
    11966 
    11967 > hide #1 models
    11968 
    11969 > select up
    11970 
    11971 256 atoms, 255 bonds, 1 residue, 1 model selected 
    11972 
    11973 > isolde ~ignore
    11974 
    11975 > isolde ignore ~sel
    11976 
    11977 ISOLDE: currently ignoring 5223 residues in model 8.2 
    11978 ISOLDE: currently ignoring 1 residues in model 1 
    11979 
    11980 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    11981 bonded heavy atom. 
    11982 
    11983 > isolde ~ignore
    11984 
    11985 > save working.cxs
    11986 
    11987 Taking snapshot of stepper: working_2.pdb 
    11988 
    11989 > show #!2 models
    11990 
    11991 > close #2
    11992 
    11993 > select #8
    11994 
    11995 98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected 
    11996 
    11997 > select clear
    11998 
    11999 > volume zone #8.1.1.1 nearAtoms #8 dist 1.5 newMap true
    12000 
    12001 Expected a keyword 
    12002 
    12003 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12004 
    12005 > volume subtract #8.1.1.1 #2 inPlace false
    12006 
    12007 > close #2
    12008 
    12009 > volume #5 level 0.03153
    12010 
    12011 > volume #5 color #73d216
    12012 
    12013 > select clear
    12014 
    12015 > hide #!5 models
    12016 
    12017 > show #!5 models
    12018 
    12019 > volume #5 level 0.03261
    12020 
    12021 > select :CDL
    12022 
    12023 1536 atoms, 1530 bonds, 6 residues, 2 models selected 
    12024 
    12025 > volume #3 level 0.03461
    12026 
    12027 > volume #5 level 0.03526
    12028 
    12029 > volume #5 level 0.0345
    12030 
    12031 > hide #!5 models
    12032 
    12033 > select :MAN
    12034 
    12035 40 atoms, 40 bonds, 2 residues, 1 model selected 
    12036 
    12037 > show #!5 models
    12038 
    12039 > select ~CDL
    12040 
    12041 Expected an objects specifier or a keyword 
    12042 
    12043 > select :CDL
    12044 
    12045 1536 atoms, 1530 bonds, 6 residues, 2 models selected 
    12046 
    12047 > hide #!5 models
    12048 
    12049 > select :GPC
    12050 
    12051 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    12052 
    12053 > select clear
    12054 
    12055 > select ~protein
    12056 
    12057 18265 atoms, 18944 bonds, 14 pseudobonds, 147 residues, 35 models selected 
    12058 
    12059 > select clear
    12060 
    12061 > select clear
    12062 
    12063 > select up
    12064 
    12065 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12066 
    12067 > show sel
    12068 
    12069 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12070 bonded heavy atom. 
    12071 
    12072 > select clear
    12073 
    12074 > select clear
    12075 
    12076 > select clear
    12077 
    12078 > show sel
    12079 
    12080 > show sel
    12081 
    12082 > select clear
    12083 
    12084 > select clear
    12085 
    12086 > select clear
    12087 
    12088 > select clear
    12089 
    12090 > select clear
    12091 
    12092 > select clear
    12093 
    12094 > select clear
    12095 
    12096 > select clear
    12097 
    12098 > select clear
    12099 
    12100 > select clear
    12101 
    12102 > select clear
    12103 
    12104 > select clear
    12105 
    12106 > select clear
    12107 
    12108 > select clear
    12109 
    12110 > select clear
    12111 
    12112 > select clear
    12113 
    12114 > show sel
    12115 
    12116 > select clear
    12117 
    12118 > select up
    12119 
    12120 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12121 
    12122 > select clear
    12123 
    12124 > select clear
    12125 
    12126 > select clear
    12127 
    12128 > select clear
    12129 
    12130 > show sel
    12131 
    12132 > select clear
    12133 
    12134 > select clear
    12135 
    12136 > select clear
    12137 
    12138 > select clear
    12139 
    12140 > select clear
    12141 
    12142 > select clear
    12143 
    12144 > select clear
    12145 
    12146 > select clear
    12147 
    12148 > select clear
    12149 
    12150 > select clear
    12151 
    12152 > select clear
    12153 
    12154 > select clear
    12155 
    12156 > select clear
    12157 
    12158 > select clear
    12159 
    12160 > select clear
    12161 
    12162 > select clear
    12163 
    12164 > select clear
    12165 
    12166 > select clear
    12167 
    12168 > select clear
    12169 
    12170 > select clear
    12171 
    12172 > select clear
    12173 
    12174 > select clear
    12175 
    12176 > select clear
    12177 
    12178 > select clear
    12179 
    12180 > select clear
    12181 
    12182 > select clear
    12183 
    12184 > select clear
    12185 
    12186 > select clear
    12187 
    12188 > select clear
    12189 
    12190 > select clear
    12191 
    12192 > select clear
    12193 
    12194 > select up
    12195 
    12196 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12197 
    12198 > select clear
    12199 
    12200 > select clear
    12201 
    12202 > select clear
    12203 
    12204 > save working.cxs
    12205 
    12206 Taking snapshot of stepper: working_2.pdb 
    12207 
    12208 > select clear
    12209 
    12210 > select clear
    12211 
    12212 > select clear
    12213 
    12214 > select clear
    12215 
    12216 > select clear
    12217 
    12218 > select clear
    12219 
    12220 > select clear
    12221 
    12222 > select clear
    12223 
    12224 > select clear
    12225 
    12226 > select clear
    12227 
    12228 > select clear
    12229 
    12230 > select clear
    12231 
    12232 Chain L, residue 68 specifies more than one residue! The simulation can still
    12233 run, but this will probably cause problems later if not rectified by
    12234 renumbering. 
    12235 
    12236 > select clear
    12237 
    12238 > select clear
    12239 
    12240 > select clear
    12241 
    12242 > select clear
    12243 
    12244 > select clear
    12245 
    12246 > select up
    12247 
    12248 138 atoms, 139 bonds, 1 residue, 1 model selected 
    12249 
    12250 > show sel
    12251 
    12252 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12253 bonded heavy atom. 
    12254 
    12255 Chain ak, residue 67 specifies more than one residue! The simulation can still
    12256 run, but this will probably cause problems later if not rectified by
    12257 renumbering. 
    12258 
    12259 > select clear
    12260 
    12261 > isolde ignore ~sel
    12262 
    12263 ISOLDE: currently ignoring 5223 residues in model 8.2 
    12264 ISOLDE: currently ignoring 1 residues in model 1 
    12265 
    12266 > isolde ~ignore
    12267 
    12268 > select clear
    12269 
    12270 > isolde ~ignore
    12271 
    12272 > select clear
    12273 
    12274 > select clear
    12275 
    12276 > select clear
    12277 
    12278 > select clear
    12279 
    12280 > select clear
    12281 
    12282 > select clear
    12283 
    12284 > select clear
    12285 
    12286 > select clear
    12287 
    12288 > view /C:234
    12289 
    12290 > swapaa mousemode sel GLN
    12291 
    12292 Traceback (most recent call last): 
    12293 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12294 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    12295 self.start_sim() 
    12296 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12297 packages/chimerax/isolde/isolde.py", line 2724, in start_sim 
    12298 main_sel = self._last_main_sel = self._get_main_sim_selection() 
    12299 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12300 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    12301 raise TypeError('You must select at least one atom from the current ' 
    12302 TypeError: You must select at least one atom from the current working model
    12303 prior to starting a simulation! 
    12304  
    12305 TypeError: You must select at least one atom from the current working model
    12306 prior to starting a simulation! 
    12307  
    12308 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    12309 packages/chimerax/isolde/isolde.py", line 2907, in _get_main_sim_selection 
    12310 raise TypeError('You must select at least one atom from the current ' 
    12311  
    12312 See log for complete Python traceback. 
    12313  
    12314 
    12315 > swapaa mousemode sel ALA
    12316 
    12317 > select clear
    12318 
    12319 > select clear
    12320 
    12321 > select clear
    12322 
    12323 > select clear
    12324 
    12325 > select clear
    12326 
    12327 > select clear
    12328 
    12329 > select clear
    12330 
    12331 > select clear
    12332 
    12333 > select clear
    12334 
    12335 > select clear
    12336 
    12337 > select clear
    12338 
    12339 > select clear
    12340 
    12341 > select clear
    12342 
    12343 > select clear
    12344 
    12345 > select clear
    12346 
    12347 > select clear
    12348 
    12349 > select clear
    12350 
    12351 > select clear
    12352 
    12353 > select clear
    12354 
    12355 > select clear
    12356 
    12357 > select clear
    12358 
    12359 > select up
    12360 
    12361 100 atoms, 99 bonds, 1 residue, 1 model selected 
    12362 
    12363 > select clear
    12364 
    12365 > select clear
    12366 
    12367 > select clear
    12368 
    12369 > select clear
    12370 
    12371 > select clear
    12372 
    12373 > select clear
    12374 
    12375 > select clear
    12376 
    12377 > select clear
    12378 
    12379 > select clear
    12380 
    12381 > select up
    12382 
    12383 98238 atoms, 100348 bonds, 5224 residues, 1 model selected 
    12384 
    12385 > select clear
    12386 
    12387 > select clear
    12388 
    12389 > select clear
    12390 
    12391 > select clear
    12392 
    12393 > select clear
    12394 
    12395 > select clear
    12396 
    12397 > select clear
    12398 
    12399 > select clear
    12400 
    12401 > select clear
    12402 
    12403 > select clear
    12404 
    12405 > select clear
    12406 
    12407 > select clear
    12408 
    12409 > select clear
    12410 
    12411 > select clear
    12412 
    12413 > select clear
    12414 
    12415 > save working.cxs
    12416 
    12417 Taking snapshot of stepper: working_2.pdb 
    12418 
    12419 > close #5
    12420 
    12421 > select #8
    12422 
    12423 98238 atoms, 100348 bonds, 14 pseudobonds, 5224 residues, 22 models selected 
    12424 
    12425 > select clear
    12426 
    12427 > volume zone #8.1.1.1.1 nearAtoms #8 range 1.5 newMap true
    12428 
    12429 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12430 
    12431 > volume subtract #8.1.1.1 #2 inPlace false
    12432 
    12433 > close #2
    12434 
    12435 > volume #5 level 0.04033
    12436 
    12437 > volume #5 level 0.03573
    12438 
    12439 > isolde add ligand LMT
    12440 
    12441 place_ligand() was called with use_md_template=True, but no suitable template
    12442 was found. This command has been ignored. 
    12443 
    12444 > select up
    12445 
    12446 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12447 
    12448 > ui mousemode right "translate selected atoms"
    12449 
    12450 > isolde ignore ~sel
    12451 
    12452 ISOLDE: currently ignoring 5224 residues in model 8.2 
    12453 ISOLDE: currently ignoring 1 residues in model 1 
    12454 
    12455 Chain L, residue 68 specifies more than one residue! The simulation can still
    12456 run, but this will probably cause problems later if not rectified by
    12457 renumbering. 
    12458 
    12459 Chain ak, residue 67 specifies more than one residue! The simulation can still
    12460 run, but this will probably cause problems later if not rectified by
    12461 renumbering. 
    12462 
    12463 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12464 bonded heavy atom. 
    12465 
    12466 > isolde ~ignore
    12467 
    12468 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12469 bonded heavy atom. 
    12470 
    12471 > select /AG:10-30@CA
    12472 
    12473 21 atoms, 21 residues, 1 model selected 
    12474 
    12475 > select /AH:10-30@CA
    12476 
    12477 21 atoms, 21 residues, 1 model selected 
    12478 
    12479 > select up
    12480 
    12481 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12482 
    12483 > delete sel
    12484 
    12485 > show #!5 models
    12486 
    12487 > select /AG,AH,AI,AJ
    12488 
    12489 4153 atoms, 4242 bonds, 205 residues, 1 model selected 
    12490 
    12491 > select /AI:10-30@CA
    12492 
    12493 21 atoms, 21 residues, 1 model selected 
    12494 
    12495 > select clear
    12496 
    12497 > select up
    12498 
    12499 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12500 
    12501 > ui mousemode right "translate selected atoms"
    12502 
    12503 > hide #!5 models
    12504 
    12505 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12506 bonded heavy atom. 
    12507 
    12508 > select /AG,AI:LMT
    12509 
    12510 162 atoms, 164 bonds, 2 residues, 1 model selected 
    12511 
    12512 > show #!5 models
    12513 
    12514 > select /AG,AJ
    12515 
    12516 2117 atoms, 2162 bonds, 103 residues, 1 model selected 
    12517 
    12518 > select /AJ:10-30@CA
    12519 
    12520 21 atoms, 21 residues, 1 model selected 
    12521 
    12522 > select /AG:LMT
    12523 
    12524 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12525 
    12526 > select /AI:LMT
    12527 
    12528 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12529 
    12530 > select /AJ:10-30@CA
    12531 
    12532 21 atoms, 21 residues, 1 model selected 
    12533 
    12534 > hide #!5 models
    12535 
    12536 > select up
    12537 
    12538 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12539 
    12540 > select clear
    12541 
    12542 > view /AL:LMT
    12543 
    12544 > select clear
    12545 
    12546 > select /AM:10-30@CA
    12547 
    12548 21 atoms, 21 residues, 1 model selected 
    12549 
    12550 > select up
    12551 
    12552 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12553 
    12554 > select /AM:10-30@CA
    12555 
    12556 21 atoms, 21 residues, 1 model selected 
    12557 
    12558 > view /AM:LMT
    12559 
    12560 > select up
    12561 
    12562 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12563 
    12564 > view /AO:LMT
    12565 
    12566 > select /AP:10-30@CA
    12567 
    12568 21 atoms, 21 residues, 1 model selected 
    12569 
    12570 > select up
    12571 
    12572 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12573 
    12574 > view /AP:LMT
    12575 
    12576 > select up
    12577 
    12578 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12579 
    12580 > view /AR:LMT
    12581 
    12582 > select clear
    12583 
    12584 > select /AS:10-30@CA
    12585 
    12586 21 atoms, 21 residues, 1 model selected 
    12587 
    12588 > select up
    12589 
    12590 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12591 
    12592 > view /AS:LMT
    12593 
    12594 > select up
    12595 
    12596 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12597 
    12598 > view /AU:LMT
    12599 
    12600 > select /AV:10-30@CA
    12601 
    12602 21 atoms, 21 residues, 1 model selected 
    12603 
    12604 > select up
    12605 
    12606 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12607 
    12608 > view /AV:LMT
    12609 
    12610 > view /AV:LMT
    12611 
    12612 > select up
    12613 
    12614 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12615 
    12616 > select clear
    12617 
    12618 > view /AX:LMT
    12619 
    12620 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12621 bonded heavy atom. 
    12622 
    12623 > select up
    12624 
    12625 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12626 
    12627 > select /AA:10-30@CA
    12628 
    12629 21 atoms, 21 residues, 1 model selected 
    12630 
    12631 > view /AA:LMT
    12632 
    12633 > select clear
    12634 
    12635 > select up
    12636 
    12637 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12638 
    12639 > view /AC:LMT
    12640 
    12641 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12642 bonded heavy atom. 
    12643 
    12644 > select up
    12645 
    12646 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12647 
    12648 > select /AD:10-30@CA
    12649 
    12650 21 atoms, 21 residues, 1 model selected 
    12651 
    12652 > select up
    12653 
    12654 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12655 
    12656 > view /AD:LMT
    12657 
    12658 > select up
    12659 
    12660 81 atoms, 82 bonds, 1 residue, 1 model selected 
    12661 
    12662 > view /AF:LMT
    12663 
    12664 > save working.cxs
    12665 
    12666 Taking snapshot of stepper: working_2.pdb 
    12667 opened ChimeraX session 
    12668 
    12669 > open
    12670 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    12671 
    12672 Summary of feedback from opening
    12673 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb 
    12674 --- 
    12675 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    12676 TRP A 5 1 4 
    12677 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    12678 26 
    12679 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    12680 6 
    12681 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    12682 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    12683 27 
    12684 264 messages similar to the above omitted 
    12685 Cannot find LINK/SSBOND residue CYS (95 ) 
    12686 Cannot find LINK/SSBOND residue CYS (98 ) 
    12687 Cannot find LINK/SSBOND residue THR (108 ) 
    12688 Cannot find LINK/SSBOND residue CYS (146 ) 
    12689 Cannot find LINK/SSBOND residue CYS (149 ) 
    12690 25 messages similar to the above omitted 
    12691  
    12692 
    12693 > view #2
    12694 
    12695 > select #2/AJ:61@C5'
    12696 
    12697 1 atom, 1 residue, 1 model selected 
    12698 
    12699 > select #2:61
    12700 
    12701 162 atoms, 164 bonds, 2 residues, 1 model selected 
    12702 
    12703 > delete sel
    12704 
    12705 > close #2
    12706 
    12707 > open
    12708 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb
    12709 
    12710 Summary of feedback from opening
    12711 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/lipid_group.pdb 
    12712 --- 
    12713 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    12714 TRP A 5 1 4 
    12715 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
    12716 26 
    12717 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
    12718 6 
    12719 Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3 
    12720 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
    12721 27 
    12722 264 messages similar to the above omitted 
    12723 Cannot find LINK/SSBOND residue CYS (95 ) 
    12724 Cannot find LINK/SSBOND residue CYS (98 ) 
    12725 Cannot find LINK/SSBOND residue THR (108 ) 
    12726 Cannot find LINK/SSBOND residue CYS (146 ) 
    12727 Cannot find LINK/SSBOND residue CYS (149 ) 
    12728 25 messages similar to the above omitted 
    12729  
    12730 
    12731 > delete #2/AJ:61
    12732 
    12733 > isolde start
    12734 
    12735 > set selectionWidth 4
    12736 
    12737 Done loading forcefield 
    12738 
    12739 > ui tool show Shell
    12740 
    12741 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    12742 UserWarning: IPython History requires SQLite, your history will not be saved 
    12743 warn("IPython History requires SQLite, your history will not be saved") 
    12744 
    12745 > select #2
    12746 
    12747 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12748 
    12749 > hide #2 models
    12750 
    12751 > hide #!1 models
    12752 
    12753 > select clear
    12754 
    12755 > select clear
    12756 
    12757 > select /AK
    12758 
    12759 1406 atoms, 1428 bonds, 55 residues, 2 models selected 
    12760 
    12761 > select /AK:10-30@CA
    12762 
    12763 21 atoms, 21 residues, 1 model selected 
    12764 
    12765 > view /AA:PEX
    12766 
    12767 > select /AA:PEX
    12768 
    12769 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12770 
    12771 > select up
    12772 
    12773 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12774 
    12775 > delete sel
    12776 
    12777 > view /AC:PEX
    12778 
    12779 > select up
    12780 
    12781 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12782 
    12783 > select up
    12784 
    12785 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12786 
    12787 > delete sel
    12788 
    12789 > view /AE:PEX
    12790 
    12791 > select /AA, AC, AE,
    12792 
    12793 Expected an objects specifier or a keyword 
    12794 
    12795 > select /AA, AC, AE
    12796 
    12797 3397 atoms, 3464 bonds, 156 residues, 1 model selected 
    12798 
    12799 > select clear
    12800 
    12801 > view /AG:PEX
    12802 
    12803 > select /AG:PEX
    12804 
    12805 113 atoms, 112 bonds, 1 residue, 1 model selected 
    12806 
    12807 > delete /AA,AC,AE,AG,AI,AM,AO,AQ,AS,AU,AW:61,62
    12808 
    12809 > view /AB:PEX
    12810 
    12811 > view /AE:PEX
    12812 
    12813 > view /AH:PEX
    12814 
    12815 > view /AB:PEX
    12816 
    12817 > select /AB:PEX,LMT
    12818 
    12819 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12820 
    12821 > select clear
    12822 
    12823 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12824 bonded heavy atom. 
    12825 
    12826 > select /AE:PEX,LMT
    12827 
    12828 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12829 
    12830 > view sel
    12831 
    12832 > select clear
    12833 
    12834 > select /AH:PEX,LMT
    12835 
    12836 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12837 
    12838 > view sel
    12839 
    12840 > select clear
    12841 
    12842 > isolde add ligand LMT
    12843 
    12844 > ui mousemode right "translate selected atoms"
    12845 
    12846 > isolde add ligand BCL
    12847 
    12848 > ui mousemode right "translate selected atoms"
    12849 
    12850 > isolde ignore ~sel
    12851 
    12852 ISOLDE: currently ignoring 2 residues in model 2 
    12853 ISOLDE: currently ignoring 5249 residues in model 8.2 
    12854 ISOLDE: currently ignoring 1 residues in model 1.2 
    12855 
    12856 > select up
    12857 
    12858 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12859 
    12860 > delete sel
    12861 
    12862 > isolde add ligand BPH
    12863 
    12864 > ui mousemode right "translate selected atoms"
    12865 
    12866 > isolde add ligand BCL
    12867 
    12868 > ui mousemode right "translate selected atoms"
    12869 
    12870 > select up
    12871 
    12872 141 atoms, 146 bonds, 1 residue, 1 model selected 
    12873 
    12874 > delete sel
    12875 
    12876 > select up
    12877 
    12878 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12879 
    12880 > isolde ~ignore
    12881 
    12882 > select clear
    12883 
    12884 > select up
    12885 
    12886 140 atoms, 148 bonds, 1 residue, 1 model selected 
    12887 
    12888 > save extra_bcl.pdb #1 selectedOnly true
    12889 
    12890 > select /AN:PEX,LMT
    12891 
    12892 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12893 
    12894 > view sel
    12895 
    12896 > select clear
    12897 
    12898 > isolde add ligand LMT
    12899 
    12900 > ui mousemode right "translate selected atoms"
    12901 
    12902 > isolde ignore ~sel
    12903 
    12904 ISOLDE: currently ignoring 2 residues in model 2 
    12905 ISOLDE: currently ignoring 5250 residues in model 8.2 
    12906 ISOLDE: currently ignoring 1 residues in model 1.2 
    12907 
    12908 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12909 bonded heavy atom. 
    12910 
    12911 > isolde ~ignore
    12912 
    12913 > select up
    12914 
    12915 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12916 
    12917 > isolde ignore sel
    12918 
    12919 ISOLDE: currently ignoring 1 residues in model 8.2 
    12920 
    12921 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12922 bonded heavy atom. 
    12923 
    12924 > isolde ~ignore
    12925 
    12926 > select clear
    12927 
    12928 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12929 bonded heavy atom. 
    12930 
    12931 > select /AQ:PEX,LMT
    12932 
    12933 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12934 
    12935 > view sel
    12936 
    12937 > select clear
    12938 
    12939 > select /AT:PEX,LMT
    12940 
    12941 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12942 
    12943 > view sel
    12944 
    12945 > select clear
    12946 
    12947 > isolde add ligand LMT
    12948 
    12949 > ui mousemode right "translate selected atoms"
    12950 
    12951 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    12952 bonded heavy atom. 
    12953 
    12954 > select clear
    12955 
    12956 > select /AW:PEX,LMT
    12957 
    12958 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12959 
    12960 > view sel
    12961 
    12962 > select clear
    12963 
    12964 > select clear
    12965 
    12966 > save working.cxs
    12967 
    12968 Taking snapshot of stepper: working_2.pdb 
    12969 
    12970 > close #5
    12971 
    12972 > select #8
    12973 
    12974 100821 atoms, 102950 bonds, 14 pseudobonds, 5252 residues, 22 models selected 
    12975 
    12976 > select clear
    12977 
    12978 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    12979 
    12980 > volume diff #8.1.1.1 #5 inpl f
    12981 
    12982 Expected a density maps specifier or a keyword 
    12983 
    12984 > volume subtract #8.1.1.1 #5 inPlace false
    12985 
    12986 > close #5
    12987 
    12988 > show #2 models
    12989 
    12990 > select #2
    12991 
    12992 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12993 
    12994 > select clear
    12995 
    12996 > select #2
    12997 
    12998 194 atoms, 194 bonds, 2 residues, 1 model selected 
    12999 
    13000 > hide #!6 models
    13001 
    13002 > show #!6 models
    13003 
    13004 > ui mousemode right "translate selected models"
    13005 
    13006 > select #2:PEX
    13007 
    13008 113 atoms, 112 bonds, 1 residue, 1 model selected 
    13009 
    13010 > select clear
    13011 
    13012 > volume #6 level 0.0417
    13013 
    13014 > hide #2 models
    13015 
    13016 > hide #!6 models
    13017 
    13018 > select up
    13019 
    13020 113 atoms, 112 bonds, 1 residue, 1 model selected 
    13021 
    13022 > isolde ignore ~sel
    13023 
    13024 ISOLDE: currently ignoring 2 residues in model 2 
    13025 ISOLDE: currently ignoring 5252 residues in model 8.2 
    13026 ISOLDE: currently ignoring 1 residues in model 1.2 
    13027 
    13028 > select clear
    13029 
    13030 > select clear
    13031 
    13032 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13033 bonded heavy atom. 
    13034 
    13035 > isolde ~ignore
    13036 
    13037 > isolde add ligand LMT
    13038 
    13039 > ui mousemode right "translate selected atoms"
    13040 
    13041 > select up
    13042 
    13043 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13044 
    13045 > select /AX:10-30@CA
    13046 
    13047 21 atoms, 21 residues, 1 model selected 
    13048 
    13049 > select /AC:PEX,LMT
    13050 
    13051 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13052 
    13053 > view sel
    13054 
    13055 > select up
    13056 
    13057 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13058 
    13059 > ui mousemode right "translate selected atoms"
    13060 
    13061 > select /AF:PEX,LMT
    13062 
    13063 275 atoms, 276 bonds, 3 residues, 1 model selected 
    13064 
    13065 > view sel
    13066 
    13067 > select up
    13068 
    13069 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13070 
    13071 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13072 bonded heavy atom. 
    13073 
    13074 > select /AI:PEX,LMT
    13075 
    13076 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13077 
    13078 > view sel
    13079 
    13080 > isolde add ligand LMT
    13081 
    13082 > ui mousemode right "translate selected atoms"
    13083 
    13084 > select up
    13085 
    13086 140 atoms, 148 bonds, 1 residue, 1 model selected 
    13087 
    13088 > isolde ignore sel
    13089 
    13090 ISOLDE: currently ignoring 1 residues in model 8.2 
    13091 
    13092 > select up
    13093 
    13094 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13095 
    13096 > isolde ~ignore
    13097 
    13098 > select /AL:PEX,LMT
    13099 
    13100 275 atoms, 276 bonds, 3 residues, 1 model selected 
    13101 
    13102 > view sel
    13103 
    13104 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13105 bonded heavy atom. 
    13106 
    13107 > select /AO:PEX,LMT
    13108 
    13109 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13110 
    13111 > view sel
    13112 
    13113 > isolde add ligand LMT
    13114 
    13115 > ui mousemode right "translate selected atoms"
    13116 
    13117 > select up
    13118 
    13119 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13120 
    13121 > delete sel
    13122 
    13123 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13124 bonded heavy atom. 
    13125 
    13126 > select /AR:PEX,LMT
    13127 
    13128 275 atoms, 276 bonds, 3 residues, 1 model selected 
    13129 
    13130 > view sel
    13131 
    13132 > select up
    13133 
    13134 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13135 
    13136 > delete sel
    13137 
    13138 > select /AU:PEX,LMT
    13139 
    13140 194 atoms, 194 bonds, 2 residues, 1 model selected 
    13141 
    13142 > view sel
    13143 
    13144 > isolde add ligand LMT
    13145 
    13146 > ui mousemode right "translate selected atoms"
    13147 
    13148 > select clear
    13149 
    13150 > save working.cxs
    13151 
    13152 Taking snapshot of stepper: working_2.pdb 
    13153 
    13154 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13155 bonded heavy atom. 
    13156 
    13157 > select clear
    13158 
    13159 > close #6
    13160 
    13161 > select #8
    13162 
    13163 102454 atoms, 104584 bonds, 14 pseudobonds, 5269 residues, 22 models selected 
    13164 
    13165 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13166 
    13167 > volume subtract #8.1.1.1 #5 inPlace false
    13168 
    13169 > close #5
    13170 
    13171 > select clear
    13172 
    13173 > select :LMT
    13174 
    13175 2349 atoms, 2378 bonds, 29 residues, 2 models selected 
    13176 
    13177 > isolde add ligand LMT
    13178 
    13179 > ui mousemode right "translate selected atoms"
    13180 
    13181 > delete sel
    13182 
    13183 > isolde add ligand LMT
    13184 
    13185 > ui mousemode right "translate selected atoms"
    13186 
    13187 > isolde add ligand LMT
    13188 
    13189 > ui mousemode right "translate selected atoms"
    13190 
    13191 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13192 bonded heavy atom. 
    13193 
    13194 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13195 bonded heavy atom. 
    13196 
    13197 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13198 bonded heavy atom. 
    13199 
    13200 > isolde add ligand LMT
    13201 
    13202 > ui mousemode right "translate selected atoms"
    13203 
    13204 > save working.cxs
    13205 
    13206 Taking snapshot of stepper: working_2.pdb 
    13207 opened ChimeraX session 
    13208 
    13209 > isolde start
    13210 
    13211 > set selectionWidth 4
    13212 
    13213 Done loading forcefield 
    13214 
    13215 > select up
    13216 
    13217 162 atoms, 164 bonds, 2 residues, 1 model selected 
    13218 
    13219 > ui tool show Shell
    13220 
    13221 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    13222 UserWarning: IPython History requires SQLite, your history will not be saved 
    13223 warn("IPython History requires SQLite, your history will not be saved") 
    13224 
    13225 > select /BH:10-30@CA
    13226 
    13227 21 atoms, 21 residues, 1 model selected 
    13228 
    13229 > select /BH:10-40@CA
    13230 
    13231 31 atoms, 31 residues, 1 model selected 
    13232 
    13233 > select up
    13234 
    13235 81 atoms, 82 bonds, 1 residue, 1 model selected 
    13236 
    13237 > select /BG:10-40@CA
    13238 
    13239 31 atoms, 31 residues, 1 model selected 
    13240 Loading residue template for PEX from internal database 
    13241 
    13242 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13243 run, but this will probably cause problems later if not rectified by
    13244 renumbering. 
    13245 
    13246 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13247 run, but this will probably cause problems later if not rectified by
    13248 renumbering. 
    13249 
    13250 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13251 run, but this will probably cause problems later if not rectified by
    13252 renumbering. 
    13253 
    13254 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13255 run, but this will probably cause problems later if not rectified by
    13256 renumbering. 
    13257 
    13258 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13259 run, but this will probably cause problems later if not rectified by
    13260 renumbering. 
    13261 
    13262 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13263 run, but this will probably cause problems later if not rectified by
    13264 renumbering. 
    13265 
    13266 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13267 run, but this will probably cause problems later if not rectified by
    13268 renumbering. 
    13269 
    13270 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13271 run, but this will probably cause problems later if not rectified by
    13272 renumbering. 
    13273 
    13274 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13275 run, but this will probably cause problems later if not rectified by
    13276 renumbering. 
    13277 
    13278 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13279 run, but this will probably cause problems later if not rectified by
    13280 renumbering. 
    13281 
    13282 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13283 run, but this will probably cause problems later if not rectified by
    13284 renumbering. 
    13285 
    13286 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13287 run, but this will probably cause problems later if not rectified by
    13288 renumbering. 
    13289 
    13290 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13291 run, but this will probably cause problems later if not rectified by
    13292 renumbering. 
    13293 
    13294 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13295 run, but this will probably cause problems later if not rectified by
    13296 renumbering. 
    13297 
    13298 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13299 run, but this will probably cause problems later if not rectified by
    13300 renumbering. 
    13301 
    13302 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13303 run, but this will probably cause problems later if not rectified by
    13304 renumbering. 
    13305 
    13306 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13307 run, but this will probably cause problems later if not rectified by
    13308 renumbering. 
    13309 
    13310 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13311 run, but this will probably cause problems later if not rectified by
    13312 renumbering. 
    13313 
    13314 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13315 run, but this will probably cause problems later if not rectified by
    13316 renumbering. 
    13317 
    13318 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13319 run, but this will probably cause problems later if not rectified by
    13320 renumbering. 
    13321 
    13322 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13323 run, but this will probably cause problems later if not rectified by
    13324 renumbering. 
    13325 
    13326 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13327 run, but this will probably cause problems later if not rectified by
    13328 renumbering. 
    13329 
    13330 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13331 run, but this will probably cause problems later if not rectified by
    13332 renumbering. 
    13333 
    13334 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13335 run, but this will probably cause problems later if not rectified by
    13336 renumbering. 
    13337 
    13338 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13339 run, but this will probably cause problems later if not rectified by
    13340 renumbering. 
    13341 
    13342 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13343 run, but this will probably cause problems later if not rectified by
    13344 renumbering. 
    13345 
    13346 Chain L, residue 68 specifies more than one residue! The simulation can still
    13347 run, but this will probably cause problems later if not rectified by
    13348 renumbering. 
    13349 
    13350 Chain ak, residue 67 specifies more than one residue! The simulation can still
    13351 run, but this will probably cause problems later if not rectified by
    13352 renumbering. 
    13353 
    13354 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13355 run, but this will probably cause problems later if not rectified by
    13356 renumbering. 
    13357 
    13358 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13359 run, but this will probably cause problems later if not rectified by
    13360 renumbering. 
    13361 
    13362 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13363 run, but this will probably cause problems later if not rectified by
    13364 renumbering. 
    13365 
    13366 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13367 run, but this will probably cause problems later if not rectified by
    13368 renumbering. 
    13369 
    13370 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13371 run, but this will probably cause problems later if not rectified by
    13372 renumbering. 
    13373 
    13374 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13375 run, but this will probably cause problems later if not rectified by
    13376 renumbering. 
    13377 
    13378 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13379 run, but this will probably cause problems later if not rectified by
    13380 renumbering. 
    13381 
    13382 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13383 run, but this will probably cause problems later if not rectified by
    13384 renumbering. 
    13385 
    13386 > select ~protein
    13387 
    13388 28426 atoms, 29196 bonds, 14 pseudobonds, 265 residues, 39 models selected 
    13389 
    13390 > select clear
    13391 
    13392 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13393 run, but this will probably cause problems later if not rectified by
    13394 renumbering. 
    13395 
    13396 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13397 run, but this will probably cause problems later if not rectified by
    13398 renumbering. 
    13399 
    13400 > select clear
    13401 
    13402 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13403 run, but this will probably cause problems later if not rectified by
    13404 renumbering. 
    13405 
    13406 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13407 run, but this will probably cause problems later if not rectified by
    13408 renumbering. 
    13409 
    13410 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13411 bonded heavy atom. 
    13412 
    13413 Chain BN, residue 60 specifies more than one residue! The simulation can still
    13414 run, but this will probably cause problems later if not rectified by
    13415 renumbering. 
    13416 
    13417 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13418 run, but this will probably cause problems later if not rectified by
    13419 renumbering. 
    13420 
    13421 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13422 bonded heavy atom. 
    13423 
    13424 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13425 bonded heavy atom. 
    13426 
    13427 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13428 bonded heavy atom. 
    13429 
    13430 Chain BO, residue 60 specifies more than one residue! The simulation can still
    13431 run, but this will probably cause problems later if not rectified by
    13432 renumbering. 
    13433 
    13434 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13435 run, but this will probably cause problems later if not rectified by
    13436 renumbering. 
    13437 
    13438 > select clear
    13439 
    13440 Chain BP, residue 60 specifies more than one residue! The simulation can still
    13441 run, but this will probably cause problems later if not rectified by
    13442 renumbering. 
    13443 
    13444 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13445 run, but this will probably cause problems later if not rectified by
    13446 renumbering. 
    13447 
    13448 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13449 bonded heavy atom. 
    13450 
    13451 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    13452 run, but this will probably cause problems later if not rectified by
    13453 renumbering. 
    13454 
    13455 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13456 run, but this will probably cause problems later if not rectified by
    13457 renumbering. 
    13458 
    13459 > select clear
    13460 
    13461 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13462 bonded heavy atom. 
    13463 
    13464 > hide #!6 models
    13465 
    13466 Chain BR, residue 60 specifies more than one residue! The simulation can still
    13467 run, but this will probably cause problems later if not rectified by
    13468 renumbering. 
    13469 
    13470 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13471 run, but this will probably cause problems later if not rectified by
    13472 renumbering. 
    13473 
    13474 > select clear
    13475 
    13476 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13477 bonded heavy atom. 
    13478 
    13479 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13480 bonded heavy atom. 
    13481 
    13482 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13483 bonded heavy atom. 
    13484 
    13485 Chain BS, residue 60 specifies more than one residue! The simulation can still
    13486 run, but this will probably cause problems later if not rectified by
    13487 renumbering. 
    13488 
    13489 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13490 run, but this will probably cause problems later if not rectified by
    13491 renumbering. 
    13492 
    13493 Chain BT, residue 60 specifies more than one residue! The simulation can still
    13494 run, but this will probably cause problems later if not rectified by
    13495 renumbering. 
    13496 
    13497 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13498 run, but this will probably cause problems later if not rectified by
    13499 renumbering. 
    13500 
    13501 > select clear
    13502 
    13503 Chain BU, residue 60 specifies more than one residue! The simulation can still
    13504 run, but this will probably cause problems later if not rectified by
    13505 renumbering. 
    13506 
    13507 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13508 run, but this will probably cause problems later if not rectified by
    13509 renumbering. 
    13510 
    13511 Chain BV, residue 60 specifies more than one residue! The simulation can still
    13512 run, but this will probably cause problems later if not rectified by
    13513 renumbering. 
    13514 
    13515 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13516 run, but this will probably cause problems later if not rectified by
    13517 renumbering. 
    13518 
    13519 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13520 bonded heavy atom. 
    13521 
    13522 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13523 bonded heavy atom. 
    13524 
    13525 Chain BW, residue 60 specifies more than one residue! The simulation can still
    13526 run, but this will probably cause problems later if not rectified by
    13527 renumbering. 
    13528 
    13529 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13530 run, but this will probably cause problems later if not rectified by
    13531 renumbering. 
    13532 
    13533 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13534 run, but this will probably cause problems later if not rectified by
    13535 renumbering. 
    13536 
    13537 Chain BX, residue 60 specifies more than one residue! The simulation can still
    13538 run, but this will probably cause problems later if not rectified by
    13539 renumbering. 
    13540 
    13541 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13542 bonded heavy atom. 
    13543 
    13544 Chain BA, residue 60 specifies more than one residue! The simulation can still
    13545 run, but this will probably cause problems later if not rectified by
    13546 renumbering. 
    13547 
    13548 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13549 run, but this will probably cause problems later if not rectified by
    13550 renumbering. 
    13551 
    13552 Chain BB, residue 60 specifies more than one residue! The simulation can still
    13553 run, but this will probably cause problems later if not rectified by
    13554 renumbering. 
    13555 
    13556 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13557 run, but this will probably cause problems later if not rectified by
    13558 renumbering. 
    13559 
    13560 Chain BC, residue 60 specifies more than one residue! The simulation can still
    13561 run, but this will probably cause problems later if not rectified by
    13562 renumbering. 
    13563 
    13564 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13565 run, but this will probably cause problems later if not rectified by
    13566 renumbering. 
    13567 
    13568 Chain BD, residue 60 specifies more than one residue! The simulation can still
    13569 run, but this will probably cause problems later if not rectified by
    13570 renumbering. 
    13571 
    13572 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13573 run, but this will probably cause problems later if not rectified by
    13574 renumbering. 
    13575 
    13576 > select clear
    13577 
    13578 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13579 bonded heavy atom. 
    13580 
    13581 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13582 run, but this will probably cause problems later if not rectified by
    13583 renumbering. 
    13584 
    13585 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13586 run, but this will probably cause problems later if not rectified by
    13587 renumbering. 
    13588 
    13589 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13590 bonded heavy atom. 
    13591 
    13592 Chain BE, residue 60 specifies more than one residue! The simulation can still
    13593 run, but this will probably cause problems later if not rectified by
    13594 renumbering. 
    13595 
    13596 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13597 run, but this will probably cause problems later if not rectified by
    13598 renumbering. 
    13599 
    13600 Chain BF, residue 60 specifies more than one residue! The simulation can still
    13601 run, but this will probably cause problems later if not rectified by
    13602 renumbering. 
    13603 
    13604 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13605 run, but this will probably cause problems later if not rectified by
    13606 renumbering. 
    13607 
    13608 Chain BG, residue 60 specifies more than one residue! The simulation can still
    13609 run, but this will probably cause problems later if not rectified by
    13610 renumbering. 
    13611 
    13612 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13613 run, but this will probably cause problems later if not rectified by
    13614 renumbering. 
    13615 
    13616 Chain BH, residue 60 specifies more than one residue! The simulation can still
    13617 run, but this will probably cause problems later if not rectified by
    13618 renumbering. 
    13619 
    13620 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13621 run, but this will probably cause problems later if not rectified by
    13622 renumbering. 
    13623 
    13624 Chain BI, residue 60 specifies more than one residue! The simulation can still
    13625 run, but this will probably cause problems later if not rectified by
    13626 renumbering. 
    13627 
    13628 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13629 run, but this will probably cause problems later if not rectified by
    13630 renumbering. 
    13631 
    13632 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13633 bonded heavy atom. 
    13634 
    13635 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    13636 run, but this will probably cause problems later if not rectified by
    13637 renumbering. 
    13638 
    13639 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13640 run, but this will probably cause problems later if not rectified by
    13641 renumbering. 
    13642 
    13643 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13644 bonded heavy atom. 
    13645 
    13646 Chain BK, residue 60 specifies more than one residue! The simulation can still
    13647 run, but this will probably cause problems later if not rectified by
    13648 renumbering. 
    13649 
    13650 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13651 run, but this will probably cause problems later if not rectified by
    13652 renumbering. 
    13653 
    13654 > select clear
    13655 
    13656 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13657 bonded heavy atom. 
    13658 
    13659 Chain BL, residue 60 specifies more than one residue! The simulation can still
    13660 run, but this will probably cause problems later if not rectified by
    13661 renumbering. 
    13662 
    13663 Chain BM, residue 60 specifies more than one residue! The simulation can still
    13664 run, but this will probably cause problems later if not rectified by
    13665 renumbering. 
    13666 
    13667 Chain BM, residue 60 specifies more than one residue! The simulation can 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 still
    13672 run, but this will probably cause problems later if not rectified by
    13673 renumbering. 
    13674 
    13675 > save working.cxs
    13676 
    13677 Taking snapshot of stepper: working_2.pdb 
    13678 
    13679 > close #6
    13680 
    13681 > select #8
    13682 
    13683 108286 atoms, 110488 bonds, 14 pseudobonds, 5341 residues, 22 models selected 
    13684 
    13685 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    13686 
    13687 > volume subtract #8.1.1.1 #5 inPlace false
    13688 
    13689 > close #5
    13690 
    13691 > select clear
    13692 
    13693 > hide #!6 models
    13694 
    13695 > show #!6 models
    13696 
    13697 > isolde add ligand PC1
    13698 
    13699 > ui mousemode right "translate selected atoms"
    13700 
    13701 > isolde ignore ~sel
    13702 
    13703 ISOLDE: currently ignoring 5341 residues in model 8.2 
    13704 ISOLDE: currently ignoring 1 residues in model 2 
    13705 ISOLDE: currently ignoring 1 residues in model 1.2 
    13706 
    13707 > volume #6 level 0.04625
    13708 
    13709 > hide #!6 models
    13710 
    13711 > isolde ~ignore
    13712 
    13713 > select up
    13714 
    13715 142 atoms, 141 bonds, 1 residue, 1 model selected 
    13716 
    13717 > isolde ignore sel
    13718 
    13719 ISOLDE: currently ignoring 1 residues in model 8.2 
    13720 
    13721 > isolde ~ignore
    13722 
    13723 > select up
    13724 
    13725 256 atoms, 255 bonds, 1 residue, 1 model selected 
    13726 
    13727 > select clear
    13728 
    13729 Chain L, residue 68 specifies more than one residue! The simulation can still
    13730 run, but this will probably cause problems later if not rectified by
    13731 renumbering. 
    13732 
    13733 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13734 bonded heavy atom. 
    13735 
    13736 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13737 bonded heavy atom. 
    13738 
    13739 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13740 bonded heavy atom. 
    13741 
    13742 > select up
    13743 
    13744 142 atoms, 141 bonds, 1 residue, 1 model selected 
    13745 
    13746 > isolde replace ligand sel P5S
    13747 
    13748 Deleted the following atoms from residue PC1 H11001: H143, H151, H122, C14,
    13749 C15, H152, H131, H142, H141, H153, H132, C13, H133 
    13750 
    13751 126 atoms were automatically renamed to match the template: C12->CA, C11->CB,
    13752 O13->OG, P->P12, H111->HB, H112->HBA, H121->HA, O11->O16, C1->C3, C3->C1,
    13753 O21->O37, C21->C38, C22->C39, C23->C40, C24->C41, C25->C42, C26->C43,
    13754 C27->C44, C28->C45, C29->C46, C2A->C48, C2B->C49, C2C->C50, C2D->C51,
    13755 C2E->C52, C2F->C53, C2G->C54, C2H->C55, C2I->C56, O31->O19, C31->C17,
    13756 C32->C20, C33->C21, C34->C22, C35->C23, C36->C24, C37->C25, C38->C26,
    13757 C39->C27, C3A->C28, C3B->C29, C3C->C30, C3D->C31, C3E->C32, C3F->C33,
    13758 C3G->C34, C3H->C35, C3I->C36, O22->O47, O32->O18, H11->H3, H12->H3A,
    13759 H221->H39, H222->H39A, H231->H40, H232->H40A, H241->H41, H242->H41A,
    13760 H251->H42, H252->H42A, H261->H43, H262->H43A, H271->H44, H272->H44A,
    13761 H281->H45, H282->H45A, H291->H46, H292->H46A, H2A1->H48, H2A2->H48A,
    13762 H2B1->H49, H2B2->H49A, H2C1->H50, H2C2->H50A, H2D1->H51, H2D2->H51A,
    13763 H2E1->H52, H2E2->H52A, H2F1->H53, H2F2->H53A, H2G1->H54, H2G2->H54A,
    13764 H2H1->H55, H2H2->H55A, H31->H1, H32->H1A, H321->H20, H322->H20A, H331->H21,
    13765 H332->H21A, H341->H22, H342->H22A, H351->H23, H352->H23A, H361->H24,
    13766 H362->H24A, H371->H25, H372->H25A, H381->H26, H382->H26A, H391->H27,
    13767 H392->H27A, H3A1->H28, H3A2->H28A, H3B1->H29, H3B2->H29A, H3C1->H30,
    13768 H3C2->H30A, H3D1->H31, H3D2->H31A, H3E1->H32, H3E2->H32A, H3F1->H33,
    13769 H3F2->H33A, H3G1->H34, H3G2->H34A, H3H1->H35, H3H2->H35A, O12->O15, O14->O13,
    13770 H2I1->H56, H2I2->H56A, H2I3->H56B, H3I1->H36, H3I2->H36A, H3I3->H36B 
    13771 
    13772 Rebuilt ligand P5S has chiral centres at atoms CA,C2 (highlighted). Since the
    13773 current algorithm used to match topologies is not chirality aware, you should
    13774 check these sites carefully to ensure they are sensible. If in doubt, it is
    13775 best to delete with "del #8.2/H1:1001" and replace with "isolde add ligand
    13776 P5S". 
    13777 
    13778 > isolde replace ligand sel P5S
    13779 
    13780 Deleted the following atoms from residue P5S H11001: HXT, HO15 
    13781 Traceback (most recent call last): 
    13782 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13783 packages/chimerax/cmd_line/tool.py", line 275, in execute 
    13784 cmd.run(cmd_text) 
    13785 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13786 packages/chimerax/core/commands/cli.py", line 2805, in run 
    13787 result = ci.function(session, **kw_args) 
    13788 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    13789 packages/chimerax/isolde/atomic/building/cmd.py", line 44, in replace_residue 
    13790 chiral_centers = Atoms([a for a in residue.atoms if
    13791 residue.ideal_chirality(a.name) != 'N']) 
    13792 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    13793 packages/chimerax/isolde/atomic/building/cmd.py", line 44, in <listcomp> 
    13794 chiral_centers = Atoms([a for a in residue.atoms if
    13795 residue.ideal_chirality(a.name) != 'N']) 
    13796 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13797 packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality 
    13798 return f(self.name.encode('utf-8'), atom_name.encode('utf-8')) 
    13799 KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S' 
    13800  
    13801 KeyError: 'Atom H6 not in mmCIF Chemical Component Dictionary for P5S' 
    13802  
    13803 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    13804 packages/chimerax/atomic/molobject.py", line 652, in ideal_chirality 
    13805 return f(self.name.encode('utf-8'), atom_name.encode('utf-8')) 
    13806  
    13807 See log for complete Python traceback. 
    13808  
    13809 
    13810 Chain L, residue 68 specifies more than one residue! The simulation can still
    13811 run, but this will probably cause problems later if not rectified by
    13812 renumbering. 
    13813 
    13814 > select clear
    13815 
    13816 > isolde add ligand P5S
    13817 
    13818 Deleted the following atoms from residue P5S H11002: HO15, HXT 
    13819 
    13820 > ui mousemode right "translate selected atoms"
    13821 
    13822 > delete sel
    13823 
    13824 Chain L, residue 68 specifies more than one residue! The simulation can still
    13825 run, but this will probably cause problems later if not rectified by
    13826 renumbering. 
    13827 
    13828 > show #!6 models
    13829 
    13830 running convert_amber_files 
    13831 
    13832 > isolde add ligand 2Y5
    13833 
    13834 Fetching CCD 2Y5 from http://ligand-expo.rcsb.org/reports/2/2Y5/2Y5.cif 
    13835 Deleted the following atoms from residue 2Y5 L607: H81, H18, H78 
    13836 
    13837 > ui mousemode right "translate selected atoms"
    13838 
    13839 > isolde ignore ~sel
    13840 
    13841 ISOLDE: currently ignoring 5342 residues in model 8.2 
    13842 ISOLDE: currently ignoring 1 residues in model 2 
    13843 ISOLDE: currently ignoring 1 residues in model 1.2 
    13844 
    13845 > hide #!6 models
    13846 
    13847 > delete sel
    13848 
    13849 > isolde add ligand LMG
    13850 
    13851 Fetching CCD LMG from http://ligand-expo.rcsb.org/reports/L/LMG/LMG.cif 
    13852 
    13853 > ui mousemode right "translate selected atoms"
    13854 
    13855 > isolde ignore ~sel
    13856 
    13857 ISOLDE: currently ignoring 5342 residues in model 8.2 
    13858 ISOLDE: currently ignoring 1 residues in model 2 
    13859 ISOLDE: currently ignoring 1 residues in model 1.2 
    13860 
    13861 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13862 bonded heavy atom. 
    13863 
    13864 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13865 bonded heavy atom. 
    13866 
    13867 > select clear
    13868 
    13869 > delete sel
    13870 
    13871 > select up
    13872 
    13873 129 atoms, 129 bonds, 1 residue, 1 model selected 
    13874 
    13875 > save LMX.pdb #8 selectedOnly true
    13876 
    13877 running convert_amber_files 
    13878 
    13879 > isolde ~ignore
    13880 
    13881 > select clear
    13882 
    13883 Failed to add
    13884 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/PEE.xml:
    13885 Residue template USER_PEE with the same override level 0 already exists. 
    13886 
    13887 > isolde add ligand PEE
    13888 
    13889 Deleted the following atoms from residue PEE L608: H83 
    13890 
    13891 > ui mousemode right "translate selected atoms"
    13892 
    13893 > isolde ignore ~sel
    13894 
    13895 ISOLDE: currently ignoring 5343 residues in model 8.2 
    13896 ISOLDE: currently ignoring 1 residues in model 2 
    13897 ISOLDE: currently ignoring 1 residues in model 1.2 
    13898 
    13899 > isolde ~ignore
    13900 
    13901 > select up
    13902 
    13903 133 atoms, 132 bonds, 1 residue, 1 model selected 
    13904 
    13905 > isolde ignore sel
    13906 
    13907 ISOLDE: currently ignoring 1 residues in model 8.2 
    13908 
    13909 > select clear
    13910 
    13911 > select up
    13912 
    13913 256 atoms, 255 bonds, 1 residue, 1 model selected 
    13914 
    13915 > isolde ~ignore
    13916 
    13917 > select clear
    13918 
    13919 > select :PEE@H35
    13920 
    13921 1 atom, 1 residue, 1 model selected 
    13922 
    13923 > select up
    13924 
    13925 133 atoms, 132 bonds, 1 residue, 1 model selected 
    13926 
    13927 > isolde ignore sel
    13928 
    13929 ISOLDE: currently ignoring 1 residues in model 8.2 
    13930 
    13931 > isolde ~ignore
    13932 
    13933 > select clear
    13934 
    13935 > select clear
    13936 
    13937 > isolde add ligand LMT
    13938 
    13939 > ui mousemode right "translate selected atoms"
    13940 
    13941 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13942 bonded heavy atom. 
    13943 
    13944 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13945 bonded heavy atom. 
    13946 
    13947 > select clear
    13948 
    13949 > save working.cxs
    13950 
    13951 Taking snapshot of stepper: working_2.pdb 
    13952 
    13953 > isolde add ligand LMT
    13954 
    13955 > ui mousemode right "translate selected atoms"
    13956 
    13957 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13958 bonded heavy atom. 
    13959 
    13960 > isolde add ligand LMG
    13961 
    13962 > ui mousemode right "translate selected atoms"
    13963 
    13964 > isolde ignore sel
    13965 
    13966 ISOLDE: currently ignoring 1 residues in model 8.2 
    13967 
    13968 > isolde ~ignore
    13969 
    13970 > isolde ignore ~sel
    13971 
    13972 ISOLDE: currently ignoring 5346 residues in model 8.2 
    13973 ISOLDE: currently ignoring 1 residues in model 2 
    13974 ISOLDE: currently ignoring 1 residues in model 1.2 
    13975 
    13976 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13977 bonded heavy atom. 
    13978 
    13979 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    13980 bonded heavy atom. 
    13981 
    13982 > isolde ~ignore
    13983 
    13984 > select clear
    13985 
    13986 > isolde add ligand PEE
    13987 
    13988 Deleted the following atoms from residue PEE H11002: H83 
    13989 
    13990 > ui mousemode right "translate selected atoms"
    13991 
    13992 > isolde ignore ~sel
    13993 
    13994 ISOLDE: currently ignoring 5347 residues in model 8.2 
    13995 ISOLDE: currently ignoring 1 residues in model 2 
    13996 ISOLDE: currently ignoring 1 residues in model 1.2 
    13997 
    13998 > isolde ~ignore
    13999 
    14000 > select up
    14001 
    14002 133 atoms, 132 bonds, 1 residue, 1 model selected 
    14003 
    14004 > select clear
    14005 
    14006 > show #!6 models
    14007 
    14008 > hide #!6 models
    14009 
    14010 > isolde add ligand PEE
    14011 
    14012 Deleted the following atoms from residue PEE M704: H83 
    14013 
    14014 > ui mousemode right "translate selected atoms"
    14015 
    14016 > isolde ignore ~sel
    14017 
    14018 ISOLDE: currently ignoring 5348 residues in model 8.2 
    14019 ISOLDE: currently ignoring 1 residues in model 2 
    14020 ISOLDE: currently ignoring 1 residues in model 1.2 
    14021 
    14022 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14023 bonded heavy atom. 
    14024 
    14025 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14026 bonded heavy atom. 
    14027 
    14028 > isolde ~ignore
    14029 
    14030 Chain ak, residue 67 specifies more than one residue! The simulation can still
    14031 run, but this will probably cause problems later if not rectified by
    14032 renumbering. 
    14033 
    14034 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14035 bonded heavy atom. 
    14036 
    14037 > select #8
    14038 
    14039 109253 atoms, 111453 bonds, 14 pseudobonds, 5349 residues, 22 models selected 
    14040 
    14041 > close #6
    14042 
    14043 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14044 
    14045 > volume subtract #8.1.1.1 #5 new t
    14046 
    14047 Expected a keyword 
    14048 
    14049 > volume subtract #8.1.1.1 #5 inPlace true
    14050 
    14051 Can't modify volume in place: class1b_26A.mrc 
    14052 
    14053 > volume subtract #8.1.1.1 #5 inPlace false
    14054 
    14055 > close #5
    14056 
    14057 > select clear
    14058 
    14059 > save working.cxs
    14060 
    14061 Taking snapshot of stepper: working_2.pdb 
    14062 
    14063 > isolde add ligand LMT
    14064 
    14065 > hide #!6 models
    14066 
    14067 > ui mousemode right "translate selected atoms"
    14068 
    14069 > isolde add ligand LMT
    14070 
    14071 > ui mousemode right "rotate selected models"
    14072 
    14073 > ui mousemode right "translate selected atoms"
    14074 
    14075 > isolde add ligand LMT
    14076 
    14077 > ui mousemode right "translate selected atoms"
    14078 
    14079 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14080 bonded heavy atom. 
    14081 
    14082 > isolde add ligand LMT
    14083 
    14084 > ui mousemode right "translate selected atoms"
    14085 
    14086 > ui mousemode right "translate selected atoms"
    14087 
    14088 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14089 bonded heavy atom. 
    14090 
    14091 > show #!6 models
    14092 
    14093 > isolde add ligand LMT
    14094 
    14095 > ui mousemode right "translate selected atoms"
    14096 
    14097 > hide #!6 models
    14098 
    14099 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14100 bonded heavy atom. 
    14101 
    14102 > select clear
    14103 
    14104 > show #!6 models
    14105 
    14106 > isolde add ligand LMT
    14107 
    14108 > ui mousemode right "translate selected atoms"
    14109 
    14110 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14111 bonded heavy atom. 
    14112 
    14113 > close #6
    14114 
    14115 > select #8
    14116 
    14117 109739 atoms, 111945 bonds, 14 pseudobonds, 5355 residues, 22 models selected 
    14118 
    14119 > select clear
    14120 
    14121 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14122 
    14123 > volume subtract #8.1.1.1 #5 inPlace false
    14124 
    14125 > close #5
    14126 
    14127 > select ~BCL
    14128 
    14129 Expected an objects specifier or a keyword 
    14130 
    14131 > select :BCL
    14132 
    14133 11900 atoms, 12580 bonds, 85 residues, 1 model selected 
    14134 
    14135 > select down
    14136 
    14137 2 atoms, 1 bond, 1 residue, 1 model selected 
    14138 
    14139 > select up
    14140 
    14141 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14142 
    14143 > select /AG:10-40@CA
    14144 
    14145 31 atoms, 31 residues, 1 model selected 
    14146 
    14147 > select /AH:10-40@CA
    14148 
    14149 31 atoms, 31 residues, 1 model selected 
    14150 
    14151 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14152 run, but this will probably cause problems later if not rectified by
    14153 renumbering. 
    14154 
    14155 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14156 run, but this will probably cause problems later if not rectified by
    14157 renumbering. 
    14158 
    14159 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14160 run, but this will probably cause problems later if not rectified by
    14161 renumbering. 
    14162 
    14163 > isolde add ligand LMT
    14164 
    14165 > ui mousemode right "translate selected atoms"
    14166 
    14167 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14168 run, but this will probably cause problems later if not rectified by
    14169 renumbering. 
    14170 
    14171 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14172 bonded heavy atom. 
    14173 
    14174 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14175 bonded heavy atom. 
    14176 
    14177 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14178 bonded heavy atom. 
    14179 
    14180 > ui mousemode right "translate selected atoms"
    14181 
    14182 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14183 run, but this will probably cause problems later if not rectified by
    14184 renumbering. 
    14185 
    14186 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14187 bonded heavy atom. 
    14188 
    14189 > select /AJ:10-40@CA
    14190 
    14191 31 atoms, 31 residues, 1 model selected 
    14192 
    14193 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14194 run, but this will probably cause problems later if not rectified by
    14195 renumbering. 
    14196 
    14197 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14198 run, but this will probably cause problems later if not rectified by
    14199 renumbering. 
    14200 
    14201 > select /AK:10-40@CA
    14202 
    14203 31 atoms, 31 residues, 1 model selected 
    14204 
    14205 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14206 run, but this will probably cause problems later if not rectified by
    14207 renumbering. 
    14208 
    14209 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14210 run, but this will probably cause problems later if not rectified by
    14211 renumbering. 
    14212 
    14213 Chain BK, residue 60 specifies more than one residue! The simulation can still
    14214 run, but this will probably cause problems later if not rectified by
    14215 renumbering. 
    14216 
    14217 > select /AM:10-40@CA
    14218 
    14219 31 atoms, 31 residues, 1 model selected 
    14220 
    14221 Chain BL, residue 60 specifies more than one residue! The simulation can still
    14222 run, but this will probably cause problems later if not rectified by
    14223 renumbering. 
    14224 
    14225 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14226 run, but this will probably cause problems later if not rectified by
    14227 renumbering. 
    14228 
    14229 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14230 run, but this will probably cause problems later if not rectified by
    14231 renumbering. 
    14232 
    14233 > select clear
    14234 
    14235 > select /AN:10-40@CA
    14236 
    14237 31 atoms, 31 residues, 1 model selected 
    14238 
    14239 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14240 run, but this will probably cause problems later if not rectified by
    14241 renumbering. 
    14242 
    14243 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14244 run, but this will probably cause problems later if not rectified by
    14245 renumbering. 
    14246 
    14247 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14248 run, but this will probably cause problems later if not rectified by
    14249 renumbering. 
    14250 
    14251 > select /AP:10-40@CA
    14252 
    14253 31 atoms, 31 residues, 1 model selected 
    14254 
    14255 Chain BO, residue 60 specifies more than one residue! The simulation can still
    14256 run, but this will probably cause problems later if not rectified by
    14257 renumbering. 
    14258 
    14259 Chain BP, residue 60 specifies more than one residue! The simulation can still
    14260 run, but this will probably cause problems later if not rectified by
    14261 renumbering. 
    14262 
    14263 > select /AQ:10-40@CA
    14264 
    14265 31 atoms, 31 residues, 1 model selected 
    14266 
    14267 > select up
    14268 
    14269 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14270 
    14271 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14272 run, but this will probably cause problems later if not rectified by
    14273 renumbering. 
    14274 
    14275 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    14276 run, but this will probably cause problems later if not rectified by
    14277 renumbering. 
    14278 
    14279 > select clear
    14280 
    14281 > select /AS:10-40@CA
    14282 
    14283 31 atoms, 31 residues, 1 model selected 
    14284 
    14285 > select up
    14286 
    14287 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14288 
    14289 Chain BS, residue 60 specifies more than one residue! The simulation can still
    14290 run, but this will probably cause problems later if not rectified by
    14291 renumbering. 
    14292 
    14293 > select clear
    14294 
    14295 > select /AT:10-40@CA
    14296 
    14297 31 atoms, 31 residues, 1 model selected 
    14298 
    14299 > select up
    14300 
    14301 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14302 
    14303 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14304 run, but this will probably cause problems later if not rectified by
    14305 renumbering. 
    14306 
    14307 Chain BS, residue 60 specifies more than one residue! The simulation can still
    14308 run, but this will probably cause problems later if not rectified by
    14309 renumbering. 
    14310 
    14311 Chain BT, residue 60 specifies more than one residue! The simulation can still
    14312 run, but this will probably cause problems later if not rectified by
    14313 renumbering. 
    14314 
    14315 > select clear
    14316 
    14317 > select /AV:10-40@CA
    14318 
    14319 31 atoms, 31 residues, 1 model selected 
    14320 
    14321 > hide #!6 models
    14322 
    14323 Chain BU, residue 60 specifies more than one residue! The simulation can still
    14324 run, but this will probably cause problems later if not rectified by
    14325 renumbering. 
    14326 
    14327 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14328 run, but this will probably cause problems later if not rectified by
    14329 renumbering. 
    14330 
    14331 > select clear
    14332 
    14333 > show #!6 models
    14334 
    14335 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14336 run, but this will probably cause problems later if not rectified by
    14337 renumbering. 
    14338 
    14339 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14340 run, but this will probably cause problems later if not rectified by
    14341 renumbering. 
    14342 
    14343 > select /AW:10-40@CA
    14344 
    14345 31 atoms, 31 residues, 1 model selected 
    14346 
    14347 > select ~protein
    14348 
    14349 31499 atoms, 32362 bonds, 14 pseudobonds, 291 residues, 39 models selected 
    14350 
    14351 > select clear
    14352 
    14353 > select up
    14354 
    14355 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14356 
    14357 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14358 run, but this will probably cause problems later if not rectified by
    14359 renumbering. 
    14360 
    14361 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14362 run, but this will probably cause problems later if not rectified by
    14363 renumbering. 
    14364 
    14365 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14366 run, but this will probably cause problems later if not rectified by
    14367 renumbering. 
    14368 
    14369 > select clear
    14370 
    14371 > select /AA:10-40@CA
    14372 
    14373 31 atoms, 31 residues, 1 model selected 
    14374 
    14375 Chain BA, residue 60 specifies more than one residue! The simulation can still
    14376 run, but this will probably cause problems later if not rectified by
    14377 renumbering. 
    14378 
    14379 Chain BB, residue 60 specifies more than one residue! The simulation can still
    14380 run, but this will probably cause problems later if not rectified by
    14381 renumbering. 
    14382 
    14383 Chain BX, residue 60 specifies more than one residue! The simulation can still
    14384 run, but this will probably cause problems later if not rectified by
    14385 renumbering. 
    14386 
    14387 > select /AD:10-40@CA
    14388 
    14389 31 atoms, 31 residues, 1 model selected 
    14390 
    14391 Chain BC, residue 60 specifies more than one residue! The simulation can still
    14392 run, but this will probably cause problems later if not rectified by
    14393 renumbering. 
    14394 
    14395 Chain BD, residue 60 specifies more than one residue! The simulation can still
    14396 run, but this will probably cause problems later if not rectified by
    14397 renumbering. 
    14398 
    14399 > select /AE:10-40@CA
    14400 
    14401 31 atoms, 31 residues, 1 model selected 
    14402 
    14403 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14404 run, but this will probably cause problems later if not rectified by
    14405 renumbering. 
    14406 
    14407 Chain BE, residue 60 specifies more than one residue! The simulation can still
    14408 run, but this will probably cause problems later if not rectified by
    14409 renumbering. 
    14410 
    14411 > isolde add ligand LMT
    14412 
    14413 > ui mousemode right "translate selected atoms"
    14414 
    14415 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14416 run, but this will probably cause problems later if not rectified by
    14417 renumbering. 
    14418 
    14419 > isolde ignore ~se;
    14420 
    14421 Expected a residues specifier or a keyword 
    14422 
    14423 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14424 run, but this will probably cause problems later if not rectified by
    14425 renumbering. 
    14426 
    14427 > isolde ignore ~sel
    14428 
    14429 ISOLDE: currently ignoring 5370 residues in model 8.2 
    14430 ISOLDE: currently ignoring 1 residues in model 2 
    14431 ISOLDE: currently ignoring 1 residues in model 1.2 
    14432 
    14433 > isolde ~ignore
    14434 
    14435 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14436 run, but this will probably cause problems later if not rectified by
    14437 renumbering. 
    14438 
    14439 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14440 run, but this will probably cause problems later if not rectified by
    14441 renumbering. 
    14442 
    14443 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14444 run, but this will probably cause problems later if not rectified by
    14445 renumbering. 
    14446 
    14447 > select clear
    14448 
    14449 > select clear
    14450 
    14451 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14452 run, but this will probably cause problems later if not rectified by
    14453 renumbering. 
    14454 
    14455 Chain BG, residue 60 specifies more than one residue! The simulation can still
    14456 run, but this will probably cause problems later if not rectified by
    14457 renumbering. 
    14458 
    14459 > save working.cxs
    14460 
    14461 Taking snapshot of stepper: working_2.pdb 
    14462 
    14463 > select ~protein
    14464 
    14465 32000 atoms, 32888 bonds, 14 pseudobonds, 295 residues, 39 models selected 
    14466 
    14467 > select clear
    14468 
    14469 > hide #!6 models
    14470 
    14471 > hide #!8.1 models
    14472 
    14473 > hide protein
    14474 
    14475 > ~cartoon
    14476 
    14477 > show ~HC
    14478 
    14479 > show #!8.1 models
    14480 
    14481 > cartoon
    14482 
    14483 > select clear
    14484 
    14485 > close #6
    14486 
    14487 > select #8
    14488 
    14489 111861 atoms, 114181 bonds, 14 pseudobonds, 5371 residues, 22 models selected 
    14490 
    14491 > select clear
    14492 
    14493 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    14494 
    14495 > volume subtract #8.1.1.1 #5 inPlace false
    14496 
    14497 > close #5
    14498 
    14499 > select clear
    14500 
    14501 > select clear
    14502 
    14503 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14504 run, but this will probably cause problems later if not rectified by
    14505 renumbering. 
    14506 
    14507 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14508 run, but this will probably cause problems later if not rectified by
    14509 renumbering. 
    14510 
    14511 > isolde add ligand LMT
    14512 
    14513 > ui mousemode right "translate selected atoms"
    14514 
    14515 > isolde ignore ~sel
    14516 
    14517 ISOLDE: currently ignoring 5371 residues in model 8.2 
    14518 ISOLDE: currently ignoring 1 residues in model 2 
    14519 ISOLDE: currently ignoring 1 residues in model 1.2 
    14520 Traceback (most recent call last): 
    14521 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14522 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    14523 self.start_sim() 
    14524 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14525 packages/chimerax/isolde/isolde.py", line 2727, in start_sim 
    14526 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    14527 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14528 packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__ 
    14529 self._prepare_mdff_managers() 
    14530 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14531 packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    14532 _prepare_mdff_managers 
    14533 focus = False) 
    14534 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14535 packages/chimerax/clipper/symmetry.py", line 982, in
    14536 isolate_and_cover_selection 
    14537 extra_padding=extra_padding) 
    14538 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14539 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    14540 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    14541 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14542 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    14543 self.structure = self._unique_structure(atoms) 
    14544 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14545 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    14546 _unique_structure 
    14547 raise TypeError('All atoms for zone mask must be from a single model!') 
    14548 TypeError: All atoms for zone mask must be from a single model! 
    14549  
    14550 TypeError: All atoms for zone mask must be from a single model! 
    14551  
    14552 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    14553 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    14554 _unique_structure 
    14555 raise TypeError('All atoms for zone mask must be from a single model!') 
    14556  
    14557 See log for complete Python traceback. 
    14558  
    14559 
    14560 > isolde ~ignore
    14561 
    14562 > show ~HC
    14563 
    14564 > color bychain
    14565 
    14566 > color byhetero
    14567 
    14568 > cartoon
    14569 
    14570 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14571 run, but this will probably cause problems later if not rectified by
    14572 renumbering. 
    14573 
    14574 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14575 run, but this will probably cause problems later if not rectified by
    14576 renumbering. 
    14577 
    14578 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14579 run, but this will probably cause problems later if not rectified by
    14580 renumbering. 
    14581 
    14582 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14583 bonded heavy atom. 
    14584 
    14585 > isolde add ligand LMT
    14586 
    14587 > ui mousemode right "translate selected atoms"
    14588 
    14589 > isolde ignore ~sel
    14590 
    14591 ISOLDE: currently ignoring 5372 residues in model 8.2 
    14592 ISOLDE: currently ignoring 1 residues in model 2 
    14593 ISOLDE: currently ignoring 1 residues in model 1.2 
    14594 
    14595 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14596 bonded heavy atom. 
    14597 
    14598 > isolde ~ignore
    14599 
    14600 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14601 run, but this will probably cause problems later if not rectified by
    14602 renumbering. 
    14603 
    14604 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14605 run, but this will probably cause problems later if not rectified by
    14606 renumbering. 
    14607 
    14608 > isolde ignore sel
    14609 
    14610 ISOLDE: currently ignoring 1 residues in model 8.2 
    14611 
    14612 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14613 run, but this will probably cause problems later if not rectified by
    14614 renumbering. 
    14615 
    14616 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14617 run, but this will probably cause problems later if not rectified by
    14618 renumbering. 
    14619 
    14620 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14621 run, but this will probably cause problems later if not rectified by
    14622 renumbering. 
    14623 
    14624 > isolde ~ignore
    14625 
    14626 Chain AW, residue 62 specifies more than one residue! The simulation can still
    14627 run, but this will probably cause problems later if not rectified by
    14628 renumbering. 
    14629 
    14630 Chain BV, residue 60 specifies more than one residue! The simulation can still
    14631 run, but this will probably cause problems later if not rectified by
    14632 renumbering. 
    14633 
    14634 Chain BW, residue 60 specifies more than one residue! The simulation can still
    14635 run, but this will probably cause problems later if not rectified by
    14636 renumbering. 
    14637 
    14638 > select :LMT
    14639 
    14640 9072 atoms, 9184 bonds, 112 residues, 1 model selected 
    14641 
    14642 > isolde add ligand LMT
    14643 
    14644 > ui mousemode right "translate selected atoms"
    14645 
    14646 > isolde ignore ~sel
    14647 
    14648 ISOLDE: currently ignoring 5373 residues in model 8.2 
    14649 ISOLDE: currently ignoring 1 residues in model 2 
    14650 ISOLDE: currently ignoring 1 residues in model 1.2 
    14651 
    14652 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14653 bonded heavy atom. 
    14654 
    14655 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14656 bonded heavy atom. 
    14657 
    14658 > isolde ~ignore
    14659 
    14660 > isolde ignore sel
    14661 
    14662 ISOLDE: currently ignoring 1 residues in model 8.2 
    14663 
    14664 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14665 run, but this will probably cause problems later if not rectified by
    14666 renumbering. 
    14667 
    14668 Chain BT, residue 60 specifies more than one residue! The simulation can still
    14669 run, but this will probably cause problems later if not rectified by
    14670 renumbering. 
    14671 
    14672 > isolde ~ignore
    14673 
    14674 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14675 run, but this will probably cause problems later if not rectified by
    14676 renumbering. 
    14677 
    14678 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14679 bonded heavy atom. 
    14680 
    14681 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14682 bonded heavy atom. 
    14683 
    14684 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14685 bonded heavy atom. 
    14686 
    14687 > isolde add ligand LMT
    14688 
    14689 > ui mousemode right "translate selected atoms"
    14690 
    14691 > isolde ~ignore
    14692 
    14693 > isolde ignore ~sel
    14694 
    14695 ISOLDE: currently ignoring 5374 residues in model 8.2 
    14696 ISOLDE: currently ignoring 1 residues in model 2 
    14697 ISOLDE: currently ignoring 1 residues in model 1.2 
    14698 
    14699 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14700 bonded heavy atom. 
    14701 
    14702 > isolde ~ignore
    14703 
    14704 Chain AT, residue 62 specifies more than one residue! The simulation can still
    14705 run, but this will probably cause problems later if not rectified by
    14706 renumbering. 
    14707 
    14708 > select ~protein
    14709 
    14710 32324 atoms, 33216 bonds, 14 pseudobonds, 299 residues, 39 models selected 
    14711 
    14712 > select clear
    14713 
    14714 > isolde add ligand LMT
    14715 
    14716 > ui mousemode right "translate selected atoms"
    14717 
    14718 > isolde ignore ~sel
    14719 
    14720 ISOLDE: currently ignoring 5375 residues in model 8.2 
    14721 ISOLDE: currently ignoring 1 residues in model 2 
    14722 ISOLDE: currently ignoring 1 residues in model 1.2 
    14723 
    14724 > isolde ~ignore
    14725 
    14726 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    14727 run, but this will probably cause problems later if not rectified by
    14728 renumbering. 
    14729 
    14730 > select clear
    14731 
    14732 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14733 run, but this will probably cause problems later if not rectified by
    14734 renumbering. 
    14735 
    14736 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14737 run, but this will probably cause problems later if not rectified by
    14738 renumbering. 
    14739 
    14740 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14741 run, but this will probably cause problems later if not rectified by
    14742 renumbering. 
    14743 
    14744 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14745 bonded heavy atom. 
    14746 
    14747 > isolde add ligand LMT
    14748 
    14749 > ui mousemode right "translate selected atoms"
    14750 
    14751 > isolde ignore ~sel
    14752 
    14753 ISOLDE: currently ignoring 5376 residues in model 8.2 
    14754 ISOLDE: currently ignoring 1 residues in model 2 
    14755 ISOLDE: currently ignoring 1 residues in model 1.2 
    14756 
    14757 > isolde ~ignore
    14758 
    14759 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14760 run, but this will probably cause problems later if not rectified by
    14761 renumbering. 
    14762 
    14763 Chain BN, residue 60 specifies more than one residue! The simulation can still
    14764 run, but this will probably cause problems later if not rectified by
    14765 renumbering. 
    14766 
    14767 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14768 run, but this will probably cause problems later if not rectified by
    14769 renumbering. 
    14770 
    14771 Chain BL, residue 60 specifies more than one residue! The simulation can still
    14772 run, but this will probably cause problems later if not rectified by
    14773 renumbering. 
    14774 
    14775 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14776 run, but this will probably cause problems later if not rectified by
    14777 renumbering. 
    14778 
    14779 > isolde add ligand LMT
    14780 
    14781 > ui mousemode right "translate selected atoms"
    14782 
    14783 > isolde ignore ~sel
    14784 
    14785 ISOLDE: currently ignoring 5377 residues in model 8.2 
    14786 ISOLDE: currently ignoring 1 residues in model 2 
    14787 ISOLDE: currently ignoring 1 residues in model 1.2 
    14788 
    14789 > isolde ~ignore
    14790 
    14791 Chain AN, residue 62 specifies more than one residue! The simulation can still
    14792 run, but this will probably cause problems later if not rectified by
    14793 renumbering. 
    14794 
    14795 Chain BM, residue 60 specifies more than one residue! The simulation can still
    14796 run, but this will probably cause problems later if not rectified by
    14797 renumbering. 
    14798 
    14799 > isolde add ligand LMT
    14800 
    14801 > ui mousemode right "translate selected atoms"
    14802 
    14803 > isolde ignore ~sel
    14804 
    14805 ISOLDE: currently ignoring 5378 residues in model 8.2 
    14806 ISOLDE: currently ignoring 1 residues in model 2 
    14807 ISOLDE: currently ignoring 1 residues in model 1.2 
    14808 
    14809 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14810 bonded heavy atom. 
    14811 
    14812 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14813 bonded heavy atom. 
    14814 
    14815 > isolde ~ignore
    14816 
    14817 > select up
    14818 
    14819 81 atoms, 82 bonds, 1 residue, 1 model selected 
    14820 
    14821 > isolde ignore sel
    14822 
    14823 ISOLDE: currently ignoring 1 residues in model 8.2 
    14824 
    14825 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14826 run, but this will probably cause problems later if not rectified by
    14827 renumbering. 
    14828 
    14829 > isolde ~ignore
    14830 
    14831 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14832 run, but this will probably cause problems later if not rectified by
    14833 renumbering. 
    14834 
    14835 Chain BK, residue 60 specifies more than one residue! The simulation can still
    14836 run, but this will probably cause problems later if not rectified by
    14837 renumbering. 
    14838 
    14839 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14840 bonded heavy atom. 
    14841 
    14842 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14843 bonded heavy atom. 
    14844 
    14845 > isolde ~ignore
    14846 
    14847 > select up
    14848 
    14849 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14850 
    14851 > isolde ignore ~sel
    14852 
    14853 ISOLDE: currently ignoring 5378 residues in model 8.2 
    14854 ISOLDE: currently ignoring 1 residues in model 2 
    14855 ISOLDE: currently ignoring 1 residues in model 1.2 
    14856 
    14857 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14858 bonded heavy atom. 
    14859 
    14860 > isolde ~ignore
    14861 
    14862 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14863 run, but this will probably cause problems later if not rectified by
    14864 renumbering. 
    14865 
    14866 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14867 run, but this will probably cause problems later if not rectified by
    14868 renumbering. 
    14869 
    14870 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14871 run, but this will probably cause problems later if not rectified by
    14872 renumbering. 
    14873 
    14874 > select clear
    14875 
    14876 > isolde add ligand LMT
    14877 
    14878 > ui mousemode right "translate selected atoms"
    14879 
    14880 > isolde ignore ~sel
    14881 
    14882 ISOLDE: currently ignoring 5379 residues in model 8.2 
    14883 ISOLDE: currently ignoring 1 residues in model 2 
    14884 ISOLDE: currently ignoring 1 residues in model 1.2 
    14885 
    14886 > isolde ~ignore
    14887 
    14888 Chain AK, residue 62 specifies more than one residue! The simulation can still
    14889 run, but this will probably cause problems later if not rectified by
    14890 renumbering. 
    14891 
    14892 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    14893 run, but this will probably cause problems later if not rectified by
    14894 renumbering. 
    14895 
    14896 > save working.cxs
    14897 
    14898 Taking snapshot of stepper: working_2.pdb 
    14899 
    14900 > isolde add ligand LMT
    14901 
    14902 > ui mousemode right "translate selected atoms"
    14903 
    14904 > isolde ignore ~sel
    14905 
    14906 ISOLDE: currently ignoring 5380 residues in model 8.2 
    14907 ISOLDE: currently ignoring 1 residues in model 2 
    14908 ISOLDE: currently ignoring 1 residues in model 1.2 
    14909 
    14910 > isolde ~ignore
    14911 
    14912 > isolde ignore sel
    14913 
    14914 ISOLDE: currently ignoring 1 residues in model 8.2 
    14915 
    14916 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14917 run, but this will probably cause problems later if not rectified by
    14918 renumbering. 
    14919 
    14920 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14921 run, but this will probably cause problems later if not rectified by
    14922 renumbering. 
    14923 
    14924 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14925 run, but this will probably cause problems later if not rectified by
    14926 renumbering. 
    14927 
    14928 > isolde ~ignore
    14929 
    14930 Chain BH, residue 60 specifies more than one residue! The simulation can still
    14931 run, but this will probably cause problems later if not rectified by
    14932 renumbering. 
    14933 
    14934 Chain BI, residue 60 specifies more than one residue! The simulation can still
    14935 run, but this will probably cause problems later if not rectified by
    14936 renumbering. 
    14937 
    14938 > isolde add ligand LMT
    14939 
    14940 > ui mousemode right "translate selected atoms"
    14941 
    14942 > isolde ignore ~sel
    14943 
    14944 ISOLDE: currently ignoring 5381 residues in model 8.2 
    14945 ISOLDE: currently ignoring 1 residues in model 2 
    14946 ISOLDE: currently ignoring 1 residues in model 1.2 
    14947 
    14948 > isolde ~ignore
    14949 
    14950 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14951 run, but this will probably cause problems later if not rectified by
    14952 renumbering. 
    14953 
    14954 Chain AH, residue 62 specifies more than one residue! The simulation can still
    14955 run, but this will probably cause problems later if not rectified by
    14956 renumbering. 
    14957 
    14958 > isolde add ligand LMT
    14959 
    14960 > ui mousemode right "rotate selected models"
    14961 
    14962 > ui mousemode right "translate selected atoms"
    14963 
    14964 > isolde ignore ~sel
    14965 
    14966 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14967 ISOLDE: currently ignoring 1 residues in model 2 
    14968 ISOLDE: currently ignoring 1 residues in model 1.2 
    14969 
    14970 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14971 bonded heavy atom. 
    14972 
    14973 > isolde ~ignore
    14974 
    14975 Chain AE, residue 62 specifies more than one residue! The simulation can still
    14976 run, but this will probably cause problems later if not rectified by
    14977 renumbering. 
    14978 
    14979 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14980 bonded heavy atom. 
    14981 
    14982 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    14983 bonded heavy atom. 
    14984 
    14985 > select up
    14986 
    14987 140 atoms, 148 bonds, 1 residue, 1 model selected 
    14988 
    14989 > isolde ignore ~sel
    14990 
    14991 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14992 ISOLDE: currently ignoring 1 residues in model 2 
    14993 ISOLDE: currently ignoring 1 residues in model 1.2 
    14994 
    14995 > isolde ignore ~sel
    14996 
    14997 ISOLDE: currently ignoring 5382 residues in model 8.2 
    14998 ISOLDE: currently ignoring 1 residues in model 2 
    14999 ISOLDE: currently ignoring 1 residues in model 1.2 
    15000 
    15001 > isolde add ligand LMT
    15002 
    15003 > ui mousemode right "translate selected atoms"
    15004 
    15005 > isolde ignore ~sel
    15006 
    15007 ISOLDE: currently ignoring 5383 residues in model 8.2 
    15008 ISOLDE: currently ignoring 1 residues in model 2 
    15009 ISOLDE: currently ignoring 1 residues in model 1.2 
    15010 
    15011 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15012 bonded heavy atom. 
    15013 
    15014 > isolde ~ignore
    15015 
    15016 Chain AE, residue 62 specifies more than one residue! The simulation can still
    15017 run, but this will probably cause problems later if not rectified by
    15018 renumbering. 
    15019 
    15020 Chain BC, residue 60 specifies more than one residue! The simulation can still
    15021 run, but this will probably cause problems later if not rectified by
    15022 renumbering. 
    15023 
    15024 Chain BD, residue 60 specifies more than one residue! The simulation can still
    15025 run, but this will probably cause problems later if not rectified by
    15026 renumbering. 
    15027 
    15028 Chain AE, residue 62 specifies more than one residue! The simulation can still
    15029 run, but this will probably cause problems later if not rectified by
    15030 renumbering. 
    15031 
    15032 Chain BC, residue 60 specifies more than one residue! The simulation can still
    15033 run, but this will probably cause problems later if not rectified by
    15034 renumbering. 
    15035 
    15036 Chain BD, residue 60 specifies more than one residue! The simulation can still
    15037 run, but this will probably cause problems later if not rectified by
    15038 renumbering. 
    15039 
    15040 > setattr #8 bonds radius 0.05
    15041 
    15042 Assigning radius attribute to 115247 items 
    15043 
    15044 > setattr #8 bonds radius 0.2
    15045 
    15046 Assigning radius attribute to 115247 items 
    15047 
    15048 > save working.cxs
    15049 
    15050 Taking snapshot of stepper: working_2.pdb 
    15051 
    15052 > close #6
    15053 
    15054 > select #8
    15055 
    15056 112914 atoms, 115247 bonds, 14 pseudobonds, 5384 residues, 22 models selected 
    15057 
    15058 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    15059 
    15060 > volume subtract #8.1.1.1 #5
    15061 
    15062 > close #5
    15063 
    15064 > select clear
    15065 
    15066 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    15067 run, but this will probably cause problems later if not rectified by
    15068 renumbering. 
    15069 
    15070 > isolde add ligand LMT
    15071 
    15072 > ui mousemode right "translate selected atoms"
    15073 
    15074 > isolde ignore ~sel
    15075 
    15076 ISOLDE: currently ignoring 5384 residues in model 8.2 
    15077 ISOLDE: currently ignoring 1 residues in model 2 
    15078 ISOLDE: currently ignoring 1 residues in model 1.2 
    15079 
    15080 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15081 bonded heavy atom. 
    15082 
    15083 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15084 bonded heavy atom. 
    15085 
    15086 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15087 bonded heavy atom. 
    15088 
    15089 > isolde ~ignore
    15090 
    15091 Chain AQ, residue 62 specifies more than one residue! The simulation can 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 > select up
    15099 
    15100 81 atoms, 82 bonds, 1 residue, 1 model selected 
    15101 
    15102 > delete sel
    15103 
    15104 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    15105 run, but this will probably cause problems later if not rectified by
    15106 renumbering. 
    15107 
    15108 Chain BQ, residue 60 specifies more than one residue! The simulation can still
    15109 run, but this will probably cause problems later if not rectified by
    15110 renumbering. 
    15111 
    15112 > isolde add ligand PEE
    15113 
    15114 Deleted the following atoms from residue PEE AQ63: H83 
    15115 
    15116 > ui mousemode right "translate selected atoms"
    15117 
    15118 > isolde ignore ~sel
    15119 
    15120 ISOLDE: currently ignoring 5384 residues in model 8.2 
    15121 ISOLDE: currently ignoring 1 residues in model 2 
    15122 ISOLDE: currently ignoring 1 residues in model 1.2 
    15123 
    15124 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15125 bonded heavy atom. 
    15126 
    15127 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15128 bonded heavy atom. 
    15129 
    15130 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15131 bonded heavy atom. 
    15132 
    15133 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15134 bonded heavy atom. 
    15135 
    15136 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15137 bonded heavy atom. 
    15138 
    15139 > isolde ~ignore
    15140 
    15141 Chain AQ, residue 62 specifies more than one residue! The simulation can still
    15142 run, but this will probably cause problems later if not rectified by
    15143 renumbering. 
    15144 
    15145 > save working.cxs
    15146 
    15147 Taking snapshot of stepper: working_2.pdb 
    15148 
    15149 > isolde add ligand LMT
    15150 
    15151 > ui mousemode right "translate selected atoms"
    15152 
    15153 > select ~protein
    15154 
    15155 33267 atoms, 34168 bonds, 14 pseudobonds, 310 residues, 39 models selected 
    15156 
    15157 > select clear
    15158 
    15159 > isolde add ligand P5S
    15160 
    15161 Deleted the following atoms from residue P5S M705: HXT, HO15 
    15162 
    15163 > ui mousemode right "translate selected atoms"
    15164 
    15165 > isolde ignore ~sel
    15166 
    15167 ISOLDE: currently ignoring 5386 residues in model 8.2 
    15168 ISOLDE: currently ignoring 1 residues in model 2 
    15169 ISOLDE: currently ignoring 1 residues in model 1.2 
    15170 
    15171 > hide #!6 models
    15172 
    15173 > select up
    15174 
    15175 135 atoms, 134 bonds, 1 residue, 1 model selected 
    15176 
    15177 > delete sel
    15178 
    15179 > isolde add ligand PSF
    15180 
    15181 Fetching CCD PSF from http://ligand-expo.rcsb.org/reports/P/PSF/PSF.cif 
    15182 Deleted the following atoms from residue PSF M705: HO3, HXT 
    15183 
    15184 > ui mousemode right "translate selected atoms"
    15185 
    15186 > isolde ignore ~sel
    15187 
    15188 ISOLDE: currently ignoring 5386 residues in model 8.2 
    15189 ISOLDE: currently ignoring 1 residues in model 2 
    15190 ISOLDE: currently ignoring 1 residues in model 1.2 
    15191 
    15192 > isolde add ligand PSF
    15193 
    15194 Deleted the following atoms from residue PSF ai68: HO3, HXT 
    15195 
    15196 > isolde ignore ~sel
    15197 
    15198 ISOLDE: currently ignoring 5387 residues in model 8.2 
    15199 ISOLDE: currently ignoring 1 residues in model 2 
    15200 ISOLDE: currently ignoring 1 residues in model 1.2 
    15201 
    15202 > ui mousemode right "translate selected atoms"
    15203 
    15204 > isolde ~ignore
    15205 
    15206 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15207 run, but this will probably cause problems later if not rectified by
    15208 renumbering. 
    15209 
    15210 > select up
    15211 
    15212 62 atoms, 61 bonds, 1 residue, 1 model selected 
    15213 
    15214 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15215 bonded heavy atom. 
    15216 
    15217 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15218 bonded heavy atom. 
    15219 
    15220 > show #!6 models
    15221 
    15222 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15223 run, but this will probably cause problems later if not rectified by
    15224 renumbering. 
    15225 
    15226 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15227 run, but this will probably cause problems later if not rectified by
    15228 renumbering. 
    15229 
    15230 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15231 run, but this will probably cause problems later if not rectified by
    15232 renumbering. 
    15233 
    15234 > select up
    15235 
    15236 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15237 
    15238 > isolde ignore ~sel
    15239 
    15240 ISOLDE: currently ignoring 5387 residues in model 8.2 
    15241 ISOLDE: currently ignoring 1 residues in model 2 
    15242 ISOLDE: currently ignoring 1 residues in model 1.2 
    15243 
    15244 > isolde ~ignore
    15245 
    15246 > isolde ignore se
    15247 
    15248 Expected a residues specifier or a keyword 
    15249 
    15250 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15251 run, but this will probably cause problems later if not rectified by
    15252 renumbering. 
    15253 
    15254 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15255 run, but this will probably cause problems later if not rectified by
    15256 renumbering. 
    15257 
    15258 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15259 run, but this will probably cause problems later if not rectified by
    15260 renumbering. 
    15261 
    15262 > select up
    15263 
    15264 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15265 
    15266 > isolde ignore sel
    15267 
    15268 ISOLDE: currently ignoring 1 residues in model 8.2 
    15269 
    15270 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15271 run, but this will probably cause problems later if not rectified by
    15272 renumbering. 
    15273 
    15274 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15275 run, but this will probably cause problems later if not rectified by
    15276 renumbering. 
    15277 
    15278 Chain BJ, residue 60 specifies more than one residue! The simulation can still
    15279 run, but this will probably cause problems later if not rectified by
    15280 renumbering. 
    15281 
    15282 > isolde ~ignore
    15283 
    15284 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15285 run, but this will probably cause problems later if not rectified by
    15286 renumbering. 
    15287 
    15288 Chain AK, residue 62 specifies more than one residue! The simulation can still
    15289 run, but this will probably cause problems later if not rectified by
    15290 renumbering. 
    15291 
    15292 > isolde add ligand LMT
    15293 
    15294 > ui mousemode right "translate selected atoms"
    15295 
    15296 > isolde ignore ~sel
    15297 
    15298 ISOLDE: currently ignoring 5388 residues in model 8.2 
    15299 ISOLDE: currently ignoring 1 residues in model 2 
    15300 ISOLDE: currently ignoring 1 residues in model 1.2 
    15301 
    15302 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    15303 bonded heavy atom. 
    15304 
    15305 > isolde ~ignore
    15306 
    15307 > save working.cxs
    15308 
    15309 Taking snapshot of stepper: working_2.pdb 
    15310 
    15311 > select ~protein
    15312 
    15313 33472 atoms, 34372 bonds, 14 pseudobonds, 313 residues, 39 models selected 
    15314 
    15315 > select clear
    15316 
    15317 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15318 run, but this will probably cause problems later if not rectified by
    15319 renumbering. 
    15320 
    15321 Chain AN, residue 62 specifies more than one residue! The simulation can still
    15322 run, but this will probably cause problems later if not rectified by
    15323 renumbering. 
    15324 
    15325 > select clear
    15326 
    15327 Chain AW, residue 62 specifies more than one residue! The simulation can still
    15328 run, but this will probably cause problems later if not rectified by
    15329 renumbering. 
    15330 
    15331 Chain BA, residue 60 specifies more than one residue! The simulation can still
    15332 run, but this will probably cause problems later if not rectified by
    15333 renumbering. 
    15334 
    15335 Chain BX, residue 60 specifies more than one residue! The simulation can still
    15336 run, but this will probably cause problems later if not rectified by
    15337 renumbering. 
    15338 
    15339 > select clear
    15340 
    15341 Chain AH, residue 62 specifies more than one residue! The simulation can still
    15342 run, but this will probably cause problems later if not rectified by
    15343 renumbering. 
    15344 
    15345 > save working.cxs
    15346 
    15347 Taking snapshot of stepper: working_2.pdb 
    15348 
    15349 > save working.cif #8
    15350 
    15351 Not saving entity_poly_seq for non-authoritative sequences 
    15352 
    15353 > select #1
    15354 
    15355 256 atoms, 255 bonds, 1 residue, 8 models selected 
    15356 
    15357 > select #8
    15358 
    15359 113333 atoms, 115665 bonds, 14 pseudobonds, 5389 residues, 22 models selected 
    15360 
    15361 > select clear
    15362 
    15363 > view sel
    15364 
    15365 > select /ak:67&~protein
    15366 
    15367 140 atoms, 148 bonds, 1 residue, 1 model selected 
    15368 
    15369 > view sel
    15370 
    15371 > select clear
    15372 
    15373 > view sel
    15374 
    15375 > select clear
    15376 
    15377 > view sel
    15378 
    15379 > select clear
    15380 
    15381 > view sel
    15382 
    15383 > select clear
    15384 
    15385 > view sel
    15386 
    15387 > select clear
    15388 
    15389 > view sel
    15390 
    15391 > select clear
    15392 
    15393 > view sel
    15394 
    15395 > select clear
    15396 
    15397 > view sel
    15398 
    15399 > select clear
    15400 
    15401 > view sel
    15402 
    15403 > select clear
    15404 
    15405 > view sel
    15406 
    15407 > select clear
    15408 
    15409 > view sel
    15410 
    15411 > view sel
    15412 
    15413 > select clear
    15414 
    15415 > select clear
    15416 
    15417 > select clear
    15418 
    15419 > select clear
    15420 
    15421 > select clear
    15422 
    15423 > select clear
    15424 
    15425 > select clear
    15426 
    15427 > select clear
    15428 
    15429 > select clear
    15430 
    15431 > select clear
    15432 
    15433 > select clear
    15434 
    15435 > select clear
    15436 
    15437 > select clear
    15438 
    15439 > select clear
    15440 
    15441 > select clear
    15442 
    15443 > select clear
    15444 
    15445 > select clear
    15446 
    15447 > select clear
    15448 
    15449 > select clear
    15450 
    15451 > select clear
    15452 
    15453 > select clear
    15454 
    15455 > select clear
    15456 
    15457 > select clear
    15458 
    15459 > save working.cif #8
    15460 
    15461 Not saving entity_poly_seq for non-authoritative sequences 
    15462 
    15463 > select ~H
    15464 
    15465 55527 atoms, 116032 bonds, 14 pseudobonds, 5391 residues, 39 models selected 
    15466 
    15467 > save working_noh.cif #8 selectedOnly true
    15468 
    15469 Not saving entity_poly_seq for non-authoritative sequences 
    15470 
    15471 > select clear
    15472 
    15473 > save working.pdb #8
    15474 
    15475 > view /CG:1
    15476 
    15477 > select /C
    15478 
    15479 4865 atoms, 4968 bonds, 4 pseudobonds, 303 residues, 2 models selected 
    15480 
    15481 > select up
    15482 
    15483 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15484 
    15485 > view /MG:MAN
    15486 
    15487 > select up
    15488 
    15489 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15490 
    15491 > save working.cif #8
    15492 
    15493 Not saving entity_poly_seq for non-authoritative sequences 
    15494 
    15495 > select clear
    15496 
    15497 > hide #!6 models
    15498 
    15499 > select up
    15500 
    15501 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15502 
    15503 > save working.cif #8
    15504 
    15505 Not saving entity_poly_seq for non-authoritative sequences 
    15506 
    15507 > ui mousemode right "translate selected atoms"
    15508 
    15509 > select /C:1010-1020
    15510 
    15511 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15512 
    15513 > delete sel
    15514 
    15515 > select /C:1010-1020
    15516 
    15517 78 atoms, 81 bonds, 4 residues, 1 model selected 
    15518 
    15519 > delete sel
    15520 
    15521 > select /M:20-50
    15522 
    15523 435 atoms, 440 bonds, 31 residues, 1 model selected 
    15524 
    15525 > select /D:20-50
    15526 
    15527 Nothing selected 
    15528 
    15529 > open
    15530 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    15531 
    15532 Summary of feedback from opening
    15533 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif 
    15534 --- 
    15535 warnings | Unknown polymer entity '1' near line 475 
    15536 Unknown polymer entity '2' near line 2593 
    15537 Unknown polymer entity '3' near line 5781 
    15538 Unknown polymer entity '4' near line 26370 
    15539 Unknown polymer entity '5' near line 27136 
    15540 10 messages similar to the above omitted 
    15541 Atom H is not in the residue template for MET /AA:1 
    15542 Atom C1 is not in the residue template for GPC /AA:60 
    15543 Atom H is not in the residue template for MET /AB:1 
    15544 Atom C1 is not in the residue template for GPC /AB:60 
    15545 Atom H is not in the residue template for MET /AC:1 
    15546 Atom C1 is not in the residue template for GPC /AC:60 
    15547 Atom H is not in the residue template for MET /AD:1 
    15548 Atom C1 is not in the residue template for GPC /AD:60 
    15549 Atom H is not in the residue template for MET /AE:1 
    15550 Atom C1 is not in the residue template for GPC /AE:60 
    15551 Atom H is not in the residue template for MET /AF:1 
    15552 Atom C1 is not in the residue template for GPC /AF:60 
    15553 Atom H is not in the residue template for MET /AG:1 
    15554 Atom C1 is not in the residue template for GPC /AG:60 
    15555 Atom H is not in the residue template for MET /AH:1 
    15556 Atom C1 is not in the residue template for GPC /AH:60 
    15557 Atom H is not in the residue template for MET /AI:1 
    15558 Atom C1 is not in the residue template for GPC /AI:60 
    15559 Atom H is not in the residue template for MET /AJ:1 
    15560 Atom C1 is not in the residue template for GPC /AJ:60 
    15561 Atom H is not in the residue template for MET /AK:1 
    15562 Atom C1 is not in the residue template for GPC /AK:60 
    15563 Atom C26 is not in the residue template for PEX /AK:62 
    15564 Atom H is not in the residue template for MET /AL:1 
    15565 Atom C1 is not in the residue template for GPC /AL:60 
    15566 Atom H is not in the residue template for MET /AM:1 
    15567 Atom C1 is not in the residue template for GPC /AM:60 
    15568 Atom H is not in the residue template for MET /AN:1 
    15569 Atom C1 is not in the residue template for GPC /AN:60 
    15570 Atom H is not in the residue template for MET /AO:1 
    15571 Atom C1 is not in the residue template for GPC /AO:60 
    15572 Atom H is not in the residue template for MET /AP:1 
    15573 Atom C1 is not in the residue template for GPC /AP:60 
    15574 Atom H is not in the residue template for MET /AQ:1 
    15575 Atom C1 is not in the residue template for GPC /AQ:60 
    15576 Atom H is not in the residue template for MET /AR:1 
    15577 Atom C1 is not in the residue template for GPC /AR:60 
    15578 Atom H is not in the residue template for MET /AS:1 
    15579 Atom C1 is not in the residue template for GPC /AS:60 
    15580 Atom H is not in the residue template for MET /AT:1 
    15581 Atom C1 is not in the residue template for GPC /AT:60 
    15582 Atom H is not in the residue template for MET /AU:1 
    15583 Atom C1 is not in the residue template for GPC /AU:60 
    15584 Atom H is not in the residue template for MET /AV:1 
    15585 Atom C1 is not in the residue template for GPC /AV:60 
    15586 Atom H is not in the residue template for MET /AW:1 
    15587 Atom C1 is not in the residue template for GPC /AW:60 
    15588 Atom H is not in the residue template for MET /AX:1 
    15589 Atom C1 is not in the residue template for GPC /AX:60 
    15590 Atom H is not in the residue template for GLY /BQ:5 
    15591 Atom H is not in the residue template for GLY /BR:5 
    15592 Atom H is not in the residue template for GLY /BS:5 
    15593 Atom H is not in the residue template for GLY /BT:5 
    15594 Atom H11 is not in the residue template for BPH /L:606 
    15595 Atom H11 is not in the residue template for BPH /M:605 
    15596 Atom C1 is not in the residue template for RCC /M:701 
    15597 Atom HN2 is not in the residue template for ARG /ak:71 
    15598 Atom H is not in the residue template for GLY /C1:32 
    15599 Atom C1 is not in the residue template for GPC /Ba:60 
    15600 Atom C1 is not in the residue template for GPC /Bb:60 
    15601 Atom C1 is not in the residue template for GPC /Bc:60 
    15602 Atom C1 is not in the residue template for GPC /Bd:60 
    15603 Atom C1 is not in the residue template for GPC /Be:60 
    15604 11 messages similar to the above omitted 
    15605 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    15606  
    15607 Chain information for model1a.cif #5 
    15608 --- 
    15609 Chain | Description 
    15610 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    15611 AC AD | ? 
    15612 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 bl
    15613 bm bo bp | ? 
    15614 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    15615 C | ? 
    15616 C1 | ? 
    15617 H1 | ? 
    15618 H2 | ? 
    15619 L | ? 
    15620 M | ? 
    15621 aa | ? 
    15622 ab ad ae af ag ah ai aj al am an ao ap | ? 
    15623 ac | ? 
    15624 ak | ? 
    15625  
    15626 
    15627 > cartoon #5
    15628 
    15629 > hide #5
    15630 
    15631 > select /M:20-50
    15632 
    15633 736 atoms, 744 bonds, 2 pseudobonds, 52 residues, 3 models selected 
    15634 
    15635 > view /C:1010
    15636 
    15637 No objects specified. 
    15638 
    15639 > view /C:1001
    15640 
    15641 > dssp
    15642 
    15643 > select :BCL
    15644 
    15645 25620 atoms, 26748 bonds, 336 pseudobonds, 183 residues, 3 models selected 
    15646 
    15647 > close #5
    15648 
    15649 > clipper spotlight radius 13.00
    15650 
    15651 > clipper spotlight radius 14.00
    15652 
    15653 > clipper spotlight radius 15.00
    15654 
    15655 > clipper spotlight radius 16.00
    15656 
    15657 > clipper spotlight radius 17.00
    15658 
    15659 > select /ak
    15660 
    15661 1347 atoms, 1369 bonds, 73 residues, 2 models selected 
    15662 
    15663 > view /C:117
    15664 
    15665 > select #8&~protein
    15666 
    15667 33103 atoms, 34005 bonds, 14 pseudobonds, 311 residues, 22 models selected 
    15668 
    15669 > select LMG
    15670 
    15671 Expected an objects specifier or a keyword 
    15672 
    15673 > select :LMG
    15674 
    15675 141 atoms, 141 bonds, 1 residue, 1 model selected 
    15676 
    15677 > view :LMG
    15678 
    15679 > select :LMX
    15680 
    15681 129 atoms, 129 bonds, 1 residue, 1 model selected 
    15682 
    15683 > view sel
    15684 
    15685 > select clear
    15686 
    15687 > save working.cxs
    15688 
    15689 Taking snapshot of stepper: working_2.pdb 
    15690 opened ChimeraX session 
    15691 
    15692 > show #!6 models
    15693 
    15694 > volume #6 level 0.03545
    15695 
    15696 > ui tool show Shell
    15697 
    15698 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    15699 UserWarning: IPython History requires SQLite, your history will not be saved 
    15700 warn("IPython History requires SQLite, your history will not be saved") 
    15701 
    15702 > isolde start
    15703 
    15704 > set selectionWidth 4
    15705 
    15706 Done loading forcefield 
    15707 
    15708 > select #6
    15709 
    15710 4 models selected 
    15711 
    15712 > select :HOH
    15713 
    15714 15 atoms, 10 bonds, 5 residues, 1 model selected 
    15715 
    15716 > hide #!6 models
    15717 
    15718 > select :HOH
    15719 
    15720 3309 atoms, 2206 bonds, 1103 residues, 2 models selected 
    15721 
    15722 > delete sel
    15723 
    15724 > select :HOH
    15725 
    15726 2505 atoms, 1670 bonds, 835 residues, 1 model selected 
    15727 
    15728 > show #!6 models
    15729 
    15730 > hide #!6 models
    15731 
    15732 > delete :HOH
    15733 
    15734 > select :HOH
    15735 
    15736 498 atoms, 332 bonds, 166 residues, 1 model selected 
    15737 
    15738 > show #!6 models
    15739 
    15740 > hide #!6 models
    15741 
    15742 > select :HOH
    15743 
    15744 498 atoms, 332 bonds, 166 residues, 1 model selected 
    15745 
    15746 > show #!6 models
    15747 
    15748 > delete :HOH
    15749 
    15750 > select :HOH
    15751 
    15752 1497 atoms, 998 bonds, 499 residues, 1 model selected 
    15753 
    15754 > hide #!6 models
    15755 
    15756 > show #!6 models
    15757 
    15758 > hide #!6 models
    15759 
    15760 > show #!6 models
    15761 
    15762 > select :HOH
    15763 
    15764 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15765 
    15766 > hide #!6 models
    15767 
    15768 Loading residue template for LMG from internal database 
    15769 Loading residue template for PEE from internal database 
    15770 Loading residue template for PEX from internal database 
    15771 Loading residue template for PSF from internal database 
    15772 
    15773 > select :HOH
    15774 
    15775 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15776 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15777 more memory-efficient implementation. 
    15778 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15779 more memory-efficient implementation. 
    15780 
    15781 > select clear
    15782 
    15783 > select clear
    15784 
    15785 > select clear
    15786 
    15787 > select :HOH
    15788 
    15789 1926 atoms, 1284 bonds, 642 residues, 1 model selected 
    15790 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15791 more memory-efficient implementation. 
    15792 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15793 more memory-efficient implementation. 
    15794 
    15795 > select clear
    15796 
    15797 > select #8.1.1.1
    15798 
    15799 3 models selected 
    15800 
    15801 > select clear
    15802 
    15803 > select :HOH
    15804 
    15805 2085 atoms, 1390 bonds, 695 residues, 1 model selected 
    15806 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15807 more memory-efficient implementation. 
    15808 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15809 more memory-efficient implementation. 
    15810 
    15811 > select clear
    15812 
    15813 > close #6
    15814 
    15815 > select #1
    15816 
    15817 256 atoms, 255 bonds, 1 residue, 8 models selected 
    15818 Traceback (most recent call last): 
    15819 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15820 packages/chimerax/isolde/isolde.py", line 2580, in _xtal_mask_to_selection 
    15821 self._xtal_mask_to_atoms(sel, focus) 
    15822 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15823 packages/chimerax/isolde/isolde.py", line 2589, in _xtal_mask_to_atoms 
    15824 atoms, 0, context, cutoff, focus=focus) 
    15825 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15826 packages/chimerax/clipper/symmetry.py", line 982, in
    15827 isolate_and_cover_selection 
    15828 extra_padding=extra_padding) 
    15829 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15830 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    15831 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    15832 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15833 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    15834 self.structure = self._unique_structure(atoms) 
    15835 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15836 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15837 _unique_structure 
    15838 raise TypeError('All atoms for zone mask must be from a single model!') 
    15839 TypeError: All atoms for zone mask must be from a single model! 
    15840  
    15841 TypeError: All atoms for zone mask must be from a single model! 
    15842  
    15843 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    15844 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    15845 _unique_structure 
    15846 raise TypeError('All atoms for zone mask must be from a single model!') 
    15847  
    15848 See log for complete Python traceback. 
    15849  
    15850 
    15851 > select #8
    15852 
    15853 115418 atoms, 117055 bonds, 14 pseudobonds, 6084 residues, 22 models selected 
    15854 
    15855 > select clear
    15856 
    15857 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    15858 
    15859 > volume subtract #8.1.1.1 #5
    15860 
    15861 > close #5
    15862 
    15863 > select clear
    15864 
    15865 > select clear
    15866 
    15867 > select :HOH
    15868 
    15869 2085 atoms, 1390 bonds, 695 residues, 1 model selected 
    15870 
    15871 > select clear
    15872 
    15873 > hide #!6 models
    15874 
    15875 > show #!6 models
    15876 
    15877 > select clear
    15878 
    15879 > select #6
    15880 
    15881 4 models selected 
    15882 
    15883 > select :HOH
    15884 
    15885 1494 atoms, 996 bonds, 498 residues, 1 model selected 
    15886 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15887 more memory-efficient implementation. 
    15888 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    15889 more memory-efficient implementation. 
    15890 
    15891 > hide #!6 models
    15892 
    15893 > select clear
    15894 
    15895 > select :HOH
    15896 
    15897 1494 atoms, 996 bonds, 498 residues, 1 model selected 
    15898 
    15899 > isolde add water
    15900 
    15901 > isolde sim start sel
    15902 
    15903 > select :HOH
    15904 
    15905 1095 atoms, 730 bonds, 365 residues, 1 model selected 
    15906 
    15907 > select clear
    15908 
    15909 > save working.cxs
    15910 
    15911 Taking snapshot of stepper: working_2.pdb 
    15912 
    15913 > delete sel
    15914 
    15915 > delete sel
    15916 
    15917 > isolde add water
    15918 
    15919 > isolde sim start sel
    15920 
    15921 > isolde add water
    15922 
    15923 > isolde sim start sel
    15924 
    15925 > isolde add water
    15926 
    15927 > isolde sim start sel
    15928 
    15929 > isolde add water
    15930 
    15931 > isolde sim start sel
    15932 
    15933 > delete sel
    15934 
    15935 > setattr sel atoms name H
    15936 
    15937 Assigning name attribute to 1 item 
    15938 
    15939 > isolde add water
    15940 
    15941 > isolde sim start sel
    15942 
    15943 > select up
    15944 
    15945 3 atoms, 2 bonds, 1 residue, 1 model selected 
    15946 
    15947 > delete sel
    15948 
    15949 > isolde add water
    15950 
    15951 > isolde sim start sel
    15952 
    15953 > isolde add water
    15954 
    15955 > isolde sim start sel
    15956 
    15957 > isolde add water
    15958 
    15959 > isolde sim start sel
    15960 
    15961 > isolde add water simSettle false
    15962 
    15963 > isolde add water simSettle false
    15964 
    15965 > show #!6 models
    15966 
    15967 > hide #!6 models
    15968 
    15969 > show #!6 models
    15970 
    15971 > isolde add water
    15972 
    15973 > isolde sim start sel
    15974 
    15975 > hide #!6 models
    15976 
    15977 > isolde add water
    15978 
    15979 > isolde sim start sel
    15980 
    15981 > isolde add water simSettle false
    15982 
    15983 > isolde add water simSettle false
    15984 
    15985 > isolde add water simSettle false
    15986 
    15987 > isolde add water
    15988 
    15989 > isolde sim start sel
    15990 
    15991 > isolde add water
    15992 
    15993 > isolde sim start sel
    15994 
    15995 > isolde add water simSettle false
    15996 
    15997 > isolde add water simSettle false
    15998 
    15999 > isolde add water simSettle false
    16000 
    16001 > isolde add water
    16002 
    16003 > isolde sim start sel
    16004 
    16005 > isolde add water
    16006 
    16007 > isolde sim start sel
    16008 
    16009 > show #!6 models
    16010 
    16011 > hide #!6 models
    16012 
    16013 > show #!6 models
    16014 
    16015 > hide #!6 models
    16016 
    16017 > isolde add water simSettle false
    16018 
    16019 > isolde add water simSettle false
    16020 
    16021 > isolde add water
    16022 
    16023 > isolde sim start sel
    16024 
    16025 > show #!6 models
    16026 
    16027 > volume #6 level 0.02957
    16028 
    16029 > volume #6 level 0.02196
    16030 
    16031 > volume #6 level 0.02872
    16032 
    16033 > hide #!6 models
    16034 
    16035 > isolde add water
    16036 
    16037 > isolde sim start sel
    16038 
    16039 > isolde add water
    16040 
    16041 > isolde sim start sel
    16042 
    16043 > isolde add water simSettle false
    16044 
    16045 > isolde add water simSettle false
    16046 
    16047 > select /ak
    16048 
    16049 1380 atoms, 1391 bonds, 84 residues, 2 models selected 
    16050 
    16051 > isolde add water simSettle false
    16052 
    16053 > select /ak
    16054 
    16055 1380 atoms, 1391 bonds, 84 residues, 2 models selected 
    16056 
    16057 > select up
    16058 
    16059 114625 atoms, 116562 bonds, 5784 residues, 2 models selected 
    16060 
    16061 > select clear
    16062 
    16063 > isolde add water simSettle false
    16064 
    16065 > select /ak
    16066 
    16067 1383 atoms, 1393 bonds, 85 residues, 2 models selected 
    16068 
    16069 > select /ak
    16070 
    16071 1383 atoms, 1393 bonds, 85 residues, 2 models selected 
    16072 
    16073 > isolde add water simSettle false
    16074 
    16075 > isolde add water simSettle false
    16076 
    16077 > isolde add water simSettle false
    16078 
    16079 > isolde add water simSettle false
    16080 
    16081 > select clear
    16082 
    16083 > isolde add water simSettle false
    16084 
    16085 > select clear
    16086 
    16087 > view /aa:45
    16088 
    16089 > view /ab:45
    16090 
    16091 > isolde add water simSettle false
    16092 
    16093 > isolde add water simSettle false
    16094 
    16095 > view /ac:45
    16096 
    16097 > select clear
    16098 
    16099 > view /ad:45
    16100 
    16101 > view /ae:45
    16102 
    16103 > view /af:45
    16104 
    16105 > view /ag:45
    16106 
    16107 > view /ah:45
    16108 
    16109 > isolde add water simSettle false
    16110 
    16111 > select clear
    16112 
    16113 > view /ai:45
    16114 
    16115 > view /aj:45
    16116 
    16117 > view /ak:45
    16118 
    16119 > view /al:45
    16120 
    16121 > isolde add water simSettle false
    16122 
    16123 > isolde add water simSettle false
    16124 
    16125 > select clear
    16126 
    16127 > view /am:45
    16128 
    16129 > isolde add water simSettle false
    16130 
    16131 > select clear
    16132 
    16133 > view /an:45
    16134 
    16135 > isolde add water simSettle false
    16136 
    16137 > select clear
    16138 
    16139 > view /ao:45
    16140 
    16141 > view /ap:45
    16142 
    16143 > isolde add water simSettle false
    16144 
    16145 > select clear
    16146 
    16147 > view /aa:5
    16148 
    16149 > view /AA:45
    16150 
    16151 > view /AB:4
    16152 
    16153 > view /AB:43
    16154 
    16155 > view /AC:43
    16156 
    16157 > view /AD:43
    16158 
    16159 > view /AE:43
    16160 
    16161 > select clear
    16162 
    16163 > view /AF:43
    16164 
    16165 > view /AG:43
    16166 
    16167 > view /AH:43
    16168 
    16169 > view /AI:43
    16170 
    16171 > save working.cxs
    16172 
    16173 Taking snapshot of stepper: working_2.pdb 
    16174 
    16175 > close #8.1
    16176 
    16177 > clipper associate #3 toModel #8
    16178 
    16179 > volume gaussian #8 bfactor 50
    16180 
    16181 > clipper associate #3 toModel #1
    16182 
    16183 > close #1.1
    16184 
    16185 > volume gaussian #8 bfactor 50
    16186 
    16187 > clipper associate #3 toModel #8
    16188 
    16189 > clipper set contourSensitivity 0.25
    16190 
    16191 > select /D1
    16192 
    16193 Nothing selected 
    16194 
    16195 > delete /C2
    16196 
    16197 > select /H1
    16198 
    16199 1580 atoms, 1586 bonds, 75 residues, 1 model selected 
    16200 
    16201 > select /M
    16202 
    16203 6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected 
    16204 
    16205 > select clear
    16206 
    16207 > isolde restrain distances #8
    16208 
    16209 > select :HOH
    16210 
    16211 1218 atoms, 812 bonds, 406 residues, 1 model selected 
    16212 
    16213 > select /M
    16214 
    16215 6670 atoms, 6741 bonds, 6 pseudobonds, 404 residues, 2 models selected 
    16216 
    16217 > select clear
    16218 
    16219 > select /M:20-50
    16220 
    16221 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16222 
    16223 > isolde release distances sel
    16224 
    16225 > select clear
    16226 
    16227 > select #8
    16228 
    16229 112951 atoms, 114855 bonds, 14 pseudobonds, 5695 residues, 22 models selected 
    16230 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16231 more memory-efficient implementation. 
    16232 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16233 more memory-efficient implementation. 
    16234 
    16235 > select clear
    16236 
    16237 > close #8.2.10
    16238 
    16239 > select clear
    16240 
    16241 > select /M:20-50
    16242 
    16243 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16244 
    16245 > open
    16246 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif
    16247 
    16248 Summary of feedback from opening
    16249 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/model1a.cif 
    16250 --- 
    16251 warnings | Unknown polymer entity '1' near line 475 
    16252 Unknown polymer entity '2' near line 2593 
    16253 Unknown polymer entity '3' near line 5781 
    16254 Unknown polymer entity '4' near line 26370 
    16255 Unknown polymer entity '5' near line 27136 
    16256 10 messages similar to the above omitted 
    16257 Atom H is not in the residue template for MET /AA:1 
    16258 Atom C1 is not in the residue template for GPC /AA:60 
    16259 Atom H is not in the residue template for MET /AB:1 
    16260 Atom C1 is not in the residue template for GPC /AB:60 
    16261 Atom H is not in the residue template for MET /AC:1 
    16262 Atom C1 is not in the residue template for GPC /AC:60 
    16263 Atom H is not in the residue template for MET /AD:1 
    16264 Atom C1 is not in the residue template for GPC /AD:60 
    16265 Atom H is not in the residue template for MET /AE:1 
    16266 Atom C1 is not in the residue template for GPC /AE:60 
    16267 Atom H is not in the residue template for MET /AF:1 
    16268 Atom C1 is not in the residue template for GPC /AF:60 
    16269 Atom H is not in the residue template for MET /AG:1 
    16270 Atom C1 is not in the residue template for GPC /AG:60 
    16271 Atom H is not in the residue template for MET /AH:1 
    16272 Atom C1 is not in the residue template for GPC /AH:60 
    16273 Atom H is not in the residue template for MET /AI:1 
    16274 Atom C1 is not in the residue template for GPC /AI:60 
    16275 Atom H is not in the residue template for MET /AJ:1 
    16276 Atom C1 is not in the residue template for GPC /AJ:60 
    16277 Atom H is not in the residue template for MET /AK:1 
    16278 Atom C1 is not in the residue template for GPC /AK:60 
    16279 Atom C26 is not in the residue template for PEX /AK:62 
    16280 Atom H is not in the residue template for MET /AL:1 
    16281 Atom C1 is not in the residue template for GPC /AL:60 
    16282 Atom H is not in the residue template for MET /AM:1 
    16283 Atom C1 is not in the residue template for GPC /AM:60 
    16284 Atom H is not in the residue template for MET /AN:1 
    16285 Atom C1 is not in the residue template for GPC /AN:60 
    16286 Atom H is not in the residue template for MET /AO:1 
    16287 Atom C1 is not in the residue template for GPC /AO:60 
    16288 Atom H is not in the residue template for MET /AP:1 
    16289 Atom C1 is not in the residue template for GPC /AP:60 
    16290 Atom H is not in the residue template for MET /AQ:1 
    16291 Atom C1 is not in the residue template for GPC /AQ:60 
    16292 Atom H is not in the residue template for MET /AR:1 
    16293 Atom C1 is not in the residue template for GPC /AR:60 
    16294 Atom H is not in the residue template for MET /AS:1 
    16295 Atom C1 is not in the residue template for GPC /AS:60 
    16296 Atom H is not in the residue template for MET /AT:1 
    16297 Atom C1 is not in the residue template for GPC /AT:60 
    16298 Atom H is not in the residue template for MET /AU:1 
    16299 Atom C1 is not in the residue template for GPC /AU:60 
    16300 Atom H is not in the residue template for MET /AV:1 
    16301 Atom C1 is not in the residue template for GPC /AV:60 
    16302 Atom H is not in the residue template for MET /AW:1 
    16303 Atom C1 is not in the residue template for GPC /AW:60 
    16304 Atom H is not in the residue template for MET /AX:1 
    16305 Atom C1 is not in the residue template for GPC /AX:60 
    16306 Atom H is not in the residue template for GLY /BQ:5 
    16307 Atom H is not in the residue template for GLY /BR:5 
    16308 Atom H is not in the residue template for GLY /BS:5 
    16309 Atom H is not in the residue template for GLY /BT:5 
    16310 Atom H11 is not in the residue template for BPH /L:606 
    16311 Atom H11 is not in the residue template for BPH /M:605 
    16312 Atom C1 is not in the residue template for RCC /M:701 
    16313 Atom HN2 is not in the residue template for ARG /ak:71 
    16314 Atom H is not in the residue template for GLY /C1:32 
    16315 Atom C1 is not in the residue template for GPC /Ba:60 
    16316 Atom C1 is not in the residue template for GPC /Bb:60 
    16317 Atom C1 is not in the residue template for GPC /Bc:60 
    16318 Atom C1 is not in the residue template for GPC /Bd:60 
    16319 Atom C1 is not in the residue template for GPC /Be:60 
    16320 11 messages similar to the above omitted 
    16321 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    16322  
    16323 Chain information for model1a.cif #3 
    16324 --- 
    16325 Chain | Description 
    16326 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    16327 AC AD | ? 
    16328 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 bl
    16329 bm bo bp | ? 
    16330 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    16331 C | ? 
    16332 C1 | ? 
    16333 H1 | ? 
    16334 H2 | ? 
    16335 L | ? 
    16336 M | ? 
    16337 aa | ? 
    16338 ab ad ae af ag ah ai aj al am an ao ap | ? 
    16339 ac | ? 
    16340 ak | ? 
    16341  
    16342 
    16343 > delete #3&~/M
    16344 
    16345 > select #3/M
    16346 
    16347 5881 atoms, 5992 bonds, 16 pseudobonds, 333 residues, 3 models selected 
    16348 
    16349 > style sel stick
    16350 
    16351 Changed 5881 atom styles 
    16352 
    16353 > hide HC
    16354 
    16355 > color sel green
    16356 
    16357 > color sel byhetero
    16358 
    16359 > select clear
    16360 
    16361 > select #8/M:20-50
    16362 
    16363 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16364 
    16365 > select clear
    16366 
    16367 > hide #!3 models
    16368 
    16369 > select #8/M:20-50
    16370 
    16371 435 atoms, 440 bonds, 31 residues, 1 model selected 
    16372 
    16373 > delete #8/M:22-35
    16374 
    16375 > select #8/M:20-50
    16376 
    16377 242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected 
    16378 
    16379 > select #8/M:20-50
    16380 
    16381 242 atoms, 244 bonds, 1 pseudobond, 17 residues, 2 models selected 
    16382 
    16383 > isolde add water simSettle false
    16384 
    16385 > select clear
    16386 
    16387 > save working.cxs
    16388 
    16389 Taking snapshot of stepper: working_2.pdb 
    16390 
    16391 > close #6
    16392 
    16393 > close #4
    16394 
    16395 > close #3
    16396 
    16397 > close #2
    16398 
    16399 > close #1
    16400 
    16401 > save working.cxs
    16402 
    16403 Taking snapshot of stepper: working_2.pdb 
    16404 
    16405 > select #8
    16406 
    16407 112761 atoms, 114661 bonds, 15 pseudobonds, 5682 residues, 23 models selected 
    16408 
    16409 > select clear
    16410 
    16411 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    16412 
    16413 > volume subtract #8.1.1.1 #1
    16414 
    16415 > close #1
    16416 
    16417 > select /M:4-12
    16418 
    16419 162 atoms, 163 bonds, 9 residues, 1 model selected 
    16420 
    16421 > select clear
    16422 
    16423 > select up
    16424 
    16425 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16426 
    16427 > select up
    16428 
    16429 215 atoms, 216 bonds, 12 residues, 1 model selected 
    16430 
    16431 > select clear
    16432 
    16433 > select clear
    16434 
    16435 > select /AA/AX:BCL
    16436 
    16437 1311 atoms, 1345 bonds, 57 residues, 1 model selected 
    16438 
    16439 > select /AA-AX:BCL
    16440 
    16441 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16442 
    16443 > select /AA-AX:BCL
    16444 
    16445 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16446 
    16447 > isolde add water sel f
    16448 
    16449 Expected a keyword 
    16450 
    16451 > isolde add water simSettle false
    16452 
    16453 > select /AA-AX:BCL
    16454 
    16455 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16456 
    16457 > select /AA-AX:BCL
    16458 
    16459 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16460 
    16461 > select /AA-AX:BCL
    16462 
    16463 5460 atoms, 5772 bonds, 39 residues, 1 model selected 
    16464 
    16465 > select up
    16466 
    16467 140 atoms, 148 bonds, 1 residue, 1 model selected 
    16468 
    16469 > select /AD:10-40@CA
    16470 
    16471 31 atoms, 31 residues, 1 model selected 
    16472 
    16473 > select /AB:10-40@CA
    16474 
    16475 31 atoms, 31 residues, 1 model selected 
    16476 
    16477 > select /AB
    16478 
    16479 1212 atoms, 1234 bonds, 53 residues, 1 model selected 
    16480 
    16481 > select /AA-AX:BCL
    16482 
    16483 5600 atoms, 5920 bonds, 40 residues, 1 model selected 
    16484 
    16485 > select clear
    16486 
    16487 > select /AB
    16488 
    16489 1352 atoms, 1382 bonds, 54 residues, 1 model selected 
    16490 
    16491 > select /AA-AX:BCL
    16492 
    16493 5600 atoms, 5920 bonds, 40 residues, 1 model selected 
    16494 
    16495 > select /AX:10-40@CA
    16496 
    16497 31 atoms, 31 residues, 1 model selected 
    16498 
    16499 > select /AX
    16500 
    16501 1302 atoms, 1322 bonds, 57 residues, 1 model selected 
    16502 
    16503 > delete /AX:73
    16504 
    16505 > select /AX:10-40@CA
    16506 
    16507 31 atoms, 31 residues, 1 model selected 
    16508 
    16509 > select /AA-AX:BCL
    16510 
    16511 5740 atoms, 6068 bonds, 41 residues, 1 model selected 
    16512 
    16513 > select up
    16514 
    16515 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16516 
    16517 > delete sel
    16518 
    16519 > select /AA-AX:BCL
    16520 
    16521 5740 atoms, 6068 bonds, 41 residues, 1 model selected 
    16522 
    16523 > select /AU:10-40@CA
    16524 
    16525 31 atoms, 31 residues, 1 model selected 
    16526 
    16527 > select /AU
    16528 
    16529 1218 atoms, 1238 bonds, 55 residues, 1 model selected 
    16530 
    16531 > select /AA-AX:BCL
    16532 
    16533 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16534 
    16535 > select /AA-AX:BCL
    16536 
    16537 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16538 
    16539 > select up
    16540 
    16541 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16542 
    16543 > delete sel
    16544 
    16545 > select /AA-AX:BCL
    16546 
    16547 5880 atoms, 6216 bonds, 42 residues, 1 model selected 
    16548 
    16549 > select /AR:10-40@CA
    16550 
    16551 31 atoms, 31 residues, 1 model selected 
    16552 
    16553 > select /AR
    16554 
    16555 1215 atoms, 1236 bonds, 54 residues, 1 model selected 
    16556 
    16557 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16558 bonded heavy atom. 
    16559 
    16560 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16561 bonded heavy atom. 
    16562 
    16563 > select /AA-AX:BCL
    16564 
    16565 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16566 
    16567 > select /AA-AX:BCL
    16568 
    16569 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16570 
    16571 > select /AA-AX:BCL
    16572 
    16573 6020 atoms, 6364 bonds, 43 residues, 1 model selected 
    16574 
    16575 > select /Ao:10-40@CA
    16576 
    16577 Nothing selected 
    16578 
    16579 > select /AO:10-40@CA
    16580 
    16581 31 atoms, 31 residues, 1 model selected 
    16582 
    16583 > select /AO
    16584 
    16585 1134 atoms, 1154 bonds, 53 residues, 1 model selected 
    16586 
    16587 > select up
    16588 
    16589 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16590 
    16591 > delete sel
    16592 
    16593 > select /AO
    16594 
    16595 1274 atoms, 1302 bonds, 54 residues, 1 model selected 
    16596 
    16597 > select /AA-AX:BCL
    16598 
    16599 6160 atoms, 6512 bonds, 44 residues, 1 model selected 
    16600 
    16601 > select /AL:10-40@CA
    16602 
    16603 31 atoms, 31 residues, 1 model selected 
    16604 
    16605 > select /AL
    16606 
    16607 1305 atoms, 1324 bonds, 58 residues, 1 model selected 
    16608 
    16609 > select /AL:10-40@CA
    16610 
    16611 31 atoms, 31 residues, 1 model selected 
    16612 
    16613 > select /AA-AX:BCL
    16614 
    16615 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16616 
    16617 > select clear
    16618 
    16619 > select up
    16620 
    16621 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16622 
    16623 > delete sel
    16624 
    16625 > select /AA-AX:BCL
    16626 
    16627 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16628 
    16629 > select /AA-AX:BCL
    16630 
    16631 6300 atoms, 6660 bonds, 45 residues, 1 model selected 
    16632 
    16633 > select clear
    16634 
    16635 > select up
    16636 
    16637 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16638 
    16639 > delete sel
    16640 
    16641 > select /AF:10-40@CA
    16642 
    16643 31 atoms, 31 residues, 1 model selected 
    16644 
    16645 > select /AF
    16646 
    16647 1389 atoms, 1408 bonds, 60 residues, 1 model selected 
    16648 
    16649 > select clear
    16650 
    16651 > select /AA-AX:BCL
    16652 
    16653 6440 atoms, 6808 bonds, 46 residues, 1 model selected 
    16654 
    16655 > select /AA-AX:BCL
    16656 
    16657 6440 atoms, 6808 bonds, 46 residues, 1 model selected 
    16658 
    16659 > select /AI:10-40@CA
    16660 
    16661 31 atoms, 31 residues, 1 model selected 
    16662 
    16663 > select /AI
    16664 
    16665 1464 atoms, 1486 bonds, 59 residues, 1 model selected 
    16666 
    16667 > select up
    16668 
    16669 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16670 
    16671 > delete sel
    16672 
    16673 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16674 bonded heavy atom. 
    16675 
    16676 > select /AA-AX:BCL
    16677 
    16678 6580 atoms, 6956 bonds, 47 residues, 1 model selected 
    16679 
    16680 > select /AC:10-40@CA
    16681 
    16682 31 atoms, 31 residues, 1 model selected 
    16683 
    16684 > select /AC
    16685 
    16686 1207 atoms, 1225 bonds, 55 residues, 1 model selected 
    16687 
    16688 > select up
    16689 
    16690 140 atoms, 148 bonds, 1 residue, 1 model selected 
    16691 
    16692 > isolde ignore sel
    16693 
    16694 ISOLDE: currently ignoring 1 residues in model 8.2 
    16695 
    16696 > isolde ~ignore
    16697 
    16698 > select /AA-AX:BCL
    16699 
    16700 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16701 
    16702 > select /AA-AX:BCL
    16703 
    16704 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16705 
    16706 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    16707 bonded heavy atom. 
    16708 
    16709 > select /AA-AX:BCL
    16710 
    16711 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    16712 
    16713 > select clear
    16714 
    16715 > save working.cxs
    16716 
    16717 Taking snapshot of stepper: working_2.pdb 
    16718 
    16719 > select /ba-bp:BCL
    16720 
    16721 2240 atoms, 2368 bonds, 16 residues, 1 model selected 
    16722 
    16723 > select /ba-bp,aa-ap:BCL
    16724 
    16725 4480 atoms, 4736 bonds, 32 residues, 1 model selected 
    16726 
    16727 > select clear
    16728 
    16729 > select clear
    16730 
    16731 > isolde add water simSettle false
    16732 
    16733 > view /aa:26
    16734 
    16735 > view /ab:26
    16736 
    16737 > select clear
    16738 
    16739 > view /ac:26
    16740 
    16741 > view /ad:26
    16742 
    16743 > view /ae:26
    16744 
    16745 > view /af:26
    16746 
    16747 > view /ag:26
    16748 
    16749 > view /ah:26
    16750 
    16751 > view /ai:26
    16752 
    16753 > view /ap:26
    16754 
    16755 > view /aj:26
    16756 
    16757 > select clear
    16758 
    16759 > select clear
    16760 
    16761 > save working.cxs
    16762 
    16763 Taking snapshot of stepper: working_2.pdb 
    16764 
    16765 > isolde add water simSettle false
    16766 
    16767 > select :HOH
    16768 
    16769 1218 atoms, 812 bonds, 406 residues, 1 model selected 
    16770 
    16771 > select #8.1.1.1
    16772 
    16773 3 models selected 
    16774 
    16775 > select clear
    16776 
    16777 > close #2
    16778 
    16779 > select #8
    16780 
    16781 113595 atoms, 115653 bonds, 15 pseudobonds, 5601 residues, 23 models selected 
    16782 
    16783 > volume zone #8.1.1.1 nearAtoms #8 range 1.5 newMap true
    16784 
    16785 > volume subtract #8.1.1.1 #1
    16786 
    16787 > close #1
    16788 
    16789 > select clear
    16790 
    16791 > select #2
    16792 
    16793 4 models selected 
    16794 
    16795 > select clear
    16796 
    16797 > select :HOH
    16798 
    16799 2655 atoms, 1770 bonds, 885 residues, 1 model selected 
    16800 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16801 more memory-efficient implementation. 
    16802 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16803 more memory-efficient implementation. 
    16804 
    16805 > select clear
    16806 
    16807 > select clear
    16808 
    16809 > select :HOH
    16810 
    16811 2655 atoms, 1770 bonds, 885 residues, 1 model selected 
    16812 
    16813 > select clear
    16814 
    16815 > select :HOH
    16816 
    16817 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16818 
    16819 > select clear
    16820 
    16821 > style sel sphere
    16822 
    16823 Changed 672 atom styles 
    16824 
    16825 > select :HOH
    16826 
    16827 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16828 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16829 more memory-efficient implementation. 
    16830 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    16831 more memory-efficient implementation. 
    16832 
    16833 > select clear
    16834 
    16835 > select :HOH
    16836 
    16837 2799 atoms, 1866 bonds, 933 residues, 1 model selected 
    16838 
    16839 > style sel stick
    16840 
    16841 Changed 2799 atom styles 
    16842 
    16843 > select :HOH
    16844 
    16845 2334 atoms, 1556 bonds, 778 residues, 1 model selected 
    16846 
    16847 > select clear
    16848 
    16849 > hide #!2 models
    16850 
    16851 > select ~:HOH&~H
    16852 
    16853 55004 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 27 models selected 
    16854 
    16855 > select up
    16856 
    16857 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16858 
    16859 > delete sel
    16860 
    16861 > select up
    16862 
    16863 9 atoms, 6 bonds, 3 residues, 1 model selected 
    16864 
    16865 > delete sel
    16866 
    16867 > delete sel
    16868 
    16869 > select up
    16870 
    16871 9 atoms, 6 bonds, 3 residues, 1 model selected 
    16872 
    16873 > delete sel
    16874 
    16875 > select #8
    16876 
    16877 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16878 
    16879 > select clear
    16880 
    16881 > select #8
    16882 
    16883 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16884 
    16885 > select clear
    16886 
    16887 > select #8
    16888 
    16889 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16890 
    16891 > select clear
    16892 
    16893 > select clear
    16894 
    16895 > select #8
    16896 
    16897 114906 atoms, 116527 bonds, 15 pseudobonds, 6038 residues, 23 models selected 
    16898 
    16899 > select clear
    16900 
    16901 > select up
    16902 
    16903 405 atoms, 410 bonds, 5 residues, 1 model selected 
    16904 
    16905 > style sel sphere
    16906 
    16907 Changed 405 atom styles 
    16908 
    16909 > style sel ball
    16910 
    16911 Changed 405 atom styles 
    16912 
    16913 > style sel stick
    16914 
    16915 Changed 405 atom styles 
    16916 
    16917 > color sel lightgreen
    16918 
    16919 > color sel byhetero
    16920 
    16921 > color ~sel lightgrey
    16922 
    16923 > color ~sel byhetero
    16924 
    16925 > color sel green
    16926 
    16927 > color sel byhetero
    16928 
    16929 > select clear
    16930 
    16931 > hide :HOH
    16932 
    16933 > select clear
    16934 
    16935 > save sideways_detergents.jpg
    16936 
    16937 > save sideways_detergents.jpg
    16938 
    16939 > color bychain
    16940 
    16941 > color byhetero
    16942 
    16943 > save working.cxs
    16944 
    16945 Taking snapshot of stepper: working_2.pdb 
    16946 opened ChimeraX session 
    16947 
    16948 > select /aa-ap,ba-bp&~protein
    16949 
    16950 6585 atoms, 6636 bonds, 253 residues, 1 model selected 
    16951 
    16952 > isolde start
    16953 
    16954 > set selectionWidth 4
    16955 
    16956 Done loading forcefield 
    16957 
    16958 > ui tool show Shell
    16959 
    16960 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    16961 UserWarning: IPython History requires SQLite, your history will not be saved 
    16962 warn("IPython History requires SQLite, your history will not be saved") 
    16963 
    16964 > select /aa-ap,ba-bp&~protein
    16965 
    16966 6585 atoms, 6636 bonds, 253 residues, 1 model selected 
    16967 
    16968 > select up
    16969 
    16970 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16971 
    16972 > select /aa-ap,ba-bp,AA-AX,BA-BX
    16973 
    16974 89079 atoms, 90638 bonds, 4388 residues, 1 model selected 
    16975 
    16976 > select clear
    16977 
    16978 > select up
    16979 
    16980 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16981 
    16982 > select /AH
    16983 
    16984 1463 atoms, 1484 bonds, 65 residues, 1 model selected 
    16985 
    16986 > select up
    16987 
    16988 81 atoms, 82 bonds, 1 residue, 1 model selected 
    16989 
    16990 > select up
    16991 
    16992 3 atoms, 2 bonds, 1 residue, 1 model selected 
    16993 
    16994 > delete sel
    16995 
    16996 Loading residue template for PEE from internal database 
    16997 Loading residue template for PEX from internal database 
    16998 Loading residue template for LMG from internal database 
    16999 Loading residue template for PSF from internal database 
    17000 
    17001 > select /aa-ap,ba-bp,AA-AX,BA-BX
    17002 
    17003 89076 atoms, 90636 bonds, 4387 residues, 1 model selected 
    17004 
    17005 > select /aa-ap,ba-bp,AA-AX,BA-BX&~protein
    17006 
    17007 30204 atoms, 30692 bonds, 676 residues, 1 model selected 
    17008 
    17009 > hide protein
    17010 
    17011 > select /aa-ap,ba-bp&~protein
    17012 
    17013 6501 atoms, 6552 bonds, 251 residues, 1 model selected 
    17014 
    17015 > select clear
    17016 
    17017 > select up
    17018 
    17019 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17020 
    17021 > select /NA
    17022 
    17023 Nothing selected 
    17024 
    17025 > select /AN
    17026 
    17027 1364 atoms, 1390 bonds, 58 residues, 1 model selected 
    17028 
    17029 > select up
    17030 
    17031 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17032 
    17033 > select /AT
    17034 
    17035 1367 atoms, 1392 bonds, 59 residues, 1 model selected 
    17036 
    17037 > select up
    17038 
    17039 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17040 
    17041 > select up
    17042 
    17043 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17044 
    17045 > select /AE
    17046 
    17047 1370 atoms, 1394 bonds, 60 residues, 1 model selected 
    17048 
    17049 > select up
    17050 
    17051 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17052 
    17053 > select /aa-ap,ba-bp&~protein
    17054 
    17055 6258 atoms, 6306 bonds, 248 residues, 1 model selected 
    17056 
    17057 > select clear
    17058 
    17059 > select /AK
    17060 
    17061 1361 atoms, 1388 bonds, 57 residues, 1 model selected 
    17062 
    17063 > select up
    17064 
    17065 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17066 
    17067 > select up
    17068 
    17069 419 atoms, 426 bonds, 27 residues, 1 model selected 
    17070 
    17071 > select /AS
    17072 
    17073 1251 atoms, 1278 bonds, 57 residues, 1 model selected 
    17074 
    17075 > select up
    17076 
    17077 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17078 
    17079 > select /AT
    17080 
    17081 1448 atoms, 1474 bonds, 60 residues, 1 model selected 
    17082 
    17083 > select up
    17084 
    17085 81 atoms, 82 bonds, 1 residue, 1 model selected 
    17086 
    17087 > select /aa-ap,ba-bp&~protein&~:HOH
    17088 
    17089 5391 atoms, 5644 bonds, 37 residues, 1 model selected 
    17090 
    17091 > select clear
    17092 
    17093 > select /AA-AX,BA-BX&~protein&~:HOH
    17094 
    17095 23574 atoms, 24222 bonds, 226 residues, 1 model selected 
    17096 
    17097 > select clear
    17098 
    17099 > select /aa-ap,ba-bp
    17100 
    17101 31156 atoms, 31603 bonds, 1836 residues, 1 model selected 
    17102 
    17103 > select /aa-ap,ba-bp&protein
    17104 
    17105 25141 atoms, 25543 bonds, 1591 residues, 1 model selected 
    17106 
    17107 > select clear
    17108 
    17109 > select /AA-AX,BA-BX&~protein&~:HOH
    17110 
    17111 23574 atoms, 24222 bonds, 226 residues, 1 model selected 
    17112 
    17113 > select zone /aa-ap,ba-bp range 4 & sel
    17114 
    17115 Missing or invalid "range" argument: Expected a number 
    17116 
    17117 > select zone /aa-ap,ba-bp range 4
    17118 
    17119 Missing or invalid "range" argument: Expected a number 
    17120 
    17121 > select zone /aa-ap,ba-bp 4
    17122 
    17123 Selected 10127 atoms, 2 surfaces 
    17124 
    17125 > select sel&/AA-AX,BA-BX&~protein&~:HOH
    17126 
    17127 4211 atoms, 3646 bonds, 114 residues, 1 model selected 
    17128 
    17129 > select zone /aa-ap,ba-bp&protein 4
    17130 
    17131 Selected 13233 atoms, 2 surfaces 
    17132 
    17133 > select sel&/AA-AX,BA-BX&~protein&~:HOH
    17134 
    17135 3584 atoms, 2961 bonds, 107 residues, 1 model selected 
    17136 
    17137 > select sel&:PEX,LMT
    17138 
    17139 2797 atoms, 2354 bonds, 57 residues, 1 model selected 
    17140 
    17141 > select up
    17142 
    17143 2638 atoms, 2181 bonds, 57 residues, 1 model selected 
    17144 
    17145 > select up
    17146 
    17147 2634 atoms, 2173 bonds, 57 residues, 1 model selected 
    17148 
    17149 > select down
    17150 
    17151 2218 atoms, 1914 bonds, 57 residues, 1 model selected 
    17152 
    17153 > select up
    17154 
    17155 2560 atoms, 2075 bonds, 57 residues, 1 model selected 
    17156 
    17157 > select down
    17158 
    17159 1819 atoms, 1586 bonds, 57 residues, 1 model selected 
    17160 
    17161 > show sel
    17162 
    17163 > select up
    17164 
    17165 849 atoms, 659 bonds, 44 residues, 1 model selected 
    17166 
    17167 > select up
    17168 
    17169 4076 atoms, 4088 bonds, 44 residues, 1 model selected 
    17170 
    17171 > save reassigning_ligands.cxs
    17172 
    17173 Taking snapshot of stepper: working_2.pdb 
    17174 
    17175 > select /AA-AX,BA-BX&~protein&~:HOH
    17176 
    17177 19498 atoms, 20134 bonds, 182 residues, 1 model selected 
    17178 
    17179 > save reassigning_ligands.cxs
    17180 
    17181 Taking snapshot of stepper: working_2.pdb 
    17182 Restoring stepper: working_2.pdb 
    17183 opened ChimeraX session 
    17184 
    17185 > select :GPC
    17186 
    17187 4000 atoms, 3960 bonds, 40 residues, 1 model selected 
    17188 
    17189 > select /Ba-Bp
    17190 
    17191 1603 atoms, 1586 bonds, 17 residues, 1 model selected 
    17192 
    17193 > select /Ba-Bp
    17194 
    17195 Nothing selected 
    17196 
    17197 > select /Aa-Ap
    17198 
    17199 Nothing selected 
    17200 
    17201 > save reassigning_ligands.cxs
    17202 
    17203 Taking snapshot of stepper: working_2.pdb 
    17204 Restoring stepper: working_2.pdb 
    17205 opened ChimeraX session 
    17206 Traceback (most recent call last): 
    17207 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17208 packages/chimerax/map/volume_viewer.py", line 1530, in <lambda> 
    17209 QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50)) 
    17210 RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted 
    17211  
    17212 RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted 
    17213  
    17214 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17215 packages/chimerax/map/volume_viewer.py", line 1530, in 
    17216 QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50)) 
    17217  
    17218 See log for complete Python traceback. 
    17219  
    17220 
    17221 > select ~:HOH
    17222 
    17223 112638 atoms, 115015 bonds, 15 pseudobonds, 5282 residues, 24 models selected 
    17224 
    17225 > select zone sel 3
    17226 
    17227 Selected 1994 atoms 
    17228 
    17229 > select up
    17230 
    17231 2145 atoms, 1430 bonds, 715 residues, 1 model selected 
    17232 
    17233 > select :HOH&~sel
    17234 
    17235 120 atoms, 80 bonds, 40 residues, 1 model selected 
    17236 
    17237 > delete sel
    17238 
    17239 > view /L:40
    17240 
    17241 > select up
    17242 
    17243 6 atoms, 4 bonds, 2 residues, 1 model selected 
    17244 
    17245 > delete sel
    17246 
    17247 > isolde add ligand MQ9
    17248 
    17249 > delete sel
    17250 
    17251 > isolde add ligand MQ8
    17252 
    17253 > ui mousemode right "translate selected atoms"
    17254 
    17255 > isolde ignore ~sel
    17256 
    17257 ISOLDE: currently ignoring 5995 residues in model 8.2 
    17258 
    17259 > isolde ~ignore
    17260 
    17261 > save working.cxs
    17262 
    17263 Taking snapshot of stepper: working_2.pdb 
    17264 
    17265 > select #8
    17266 
    17267 114902 atoms, 116567 bonds, 15 pseudobonds, 5996 residues, 23 models selected 
    17268 
    17269 > show #!2 models
    17270 
    17271 > select /aa-ap
    17272 
    17273 18677 atoms, 18860 bonds, 1123 residues, 1 model selected 
    17274 
    17275 > select clear
    17276 
    17277 > select /aa-ap
    17278 
    17279 18677 atoms, 18860 bonds, 1123 residues, 1 model selected 
    17280 
    17281 > select clear
    17282 
    17283 > select #8
    17284 
    17285 114902 atoms, 116567 bonds, 15 pseudobonds, 5996 residues, 23 models selected 
    17286 
    17287 > select /aa-ap
    17288 
    17289 18677 atoms, 18860 bonds, 1123 residues, 1 model selected 
    17290 
    17291 > select clear
    17292 
    17293 > select clear
    17294 
    17295 > select /aa-ap
    17296 
    17297 18677 atoms, 18860 bonds, 1123 residues, 1 model selected 
    17298 
    17299 > swapaa mousemode sel MET
    17300 
    17301 > swapaa mousemode sel SER
    17302 
    17303 > swapaa mousemode sel PRO
    17304 
    17305 > swapaa mousemode sel LEU
    17306 
    17307 > swapaa mousemode sel GLY
    17308 
    17309 > delete sel
    17310 
    17311 > hide #!2 models
    17312 
    17313 > select up
    17314 
    17315 14 atoms, 14 bonds, 1 residue, 1 model selected 
    17316 
    17317 > select up
    17318 
    17319 159 atoms, 161 bonds, 12 residues, 1 model selected 
    17320 
    17321 > swapaa mousemode sel ARG
    17322 
    17323 > swapaa mousemode sel ARG
    17324 
    17325 Traceback (most recent call last): 
    17326 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17327 packages/chimerax/atomic/molarray.py", line 112, in __init__ 
    17328 pointers = numpy.array([i._c_pointer.value for i in items], cptr) 
    17329 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17330 packages/chimerax/atomic/molarray.py", line 112, in <listcomp> 
    17331 pointers = numpy.array([i._c_pointer.value for i in items], cptr) 
    17332 AttributeError: 'Rotamer' object has no attribute '_c_pointer' 
    17333  
    17334 During handling of the above exception, another exception occurred: 
    17335  
    17336 Traceback (most recent call last): 
    17337 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17338 packages/chimerax/isolde/isolde.py", line 2089, in _commit_rotamer 
    17339 rrm.commit_preview(rot) 
    17340 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17341 packages/chimerax/isolde/molobject.py", line 4169, in commit_preview 
    17342 rr = self.add_restraint(rotamer) 
    17343 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17344 packages/chimerax/isolde/molobject.py", line 4077, in add_restraint 
    17345 rr = self._get_restraints(_rotamers([r]), True) 
    17346 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17347 packages/chimerax/isolde/molobject.py", line 78, in _rotamers 
    17348 return Rotamers(p) 
    17349 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17350 packages/chimerax/isolde/molarray.py", line 269, in __init__ 
    17351 super().__init__(c_pointers, Rotamer, Rotamers) 
    17352 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17353 packages/chimerax/atomic/molarray.py", line 117, in __init__ 
    17354 raise ValueError('Collection items of unrecognized type "%s"' % t) 
    17355 ValueError: Collection items of unrecognized type "<class 'list'>" 
    17356  
    17357 ValueError: Collection items of unrecognized type "" 
    17358  
    17359 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
    17360 packages/chimerax/atomic/molarray.py", line 117, in __init__ 
    17361 raise ValueError('Collection items of unrecognized type "%s"' % t) 
    17362  
    17363 See log for complete Python traceback. 
    17364  
    17365 
    17366 No rotamer preview selected! Ignoring command. 
    17367 
    17368 > isolde ignore ~sel
    17369 
    17370 ISOLDE: currently ignoring 5994 residues in model 8.2 
    17371 Traceback (most recent call last): 
    17372 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17373 packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause 
    17374 self.start_sim() 
    17375 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17376 packages/chimerax/isolde/isolde.py", line 2727, in start_sim 
    17377 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    17378 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17379 packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__ 
    17380 self._prepare_mdff_managers() 
    17381 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17382 packages/chimerax/isolde/openmm/openmm_interface.py", line 869, in
    17383 _prepare_mdff_managers 
    17384 focus = False) 
    17385 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17386 packages/chimerax/clipper/symmetry.py", line 982, in
    17387 isolate_and_cover_selection 
    17388 extra_padding=extra_padding) 
    17389 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17390 packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms 
    17391 zm.set_symmetry_map(atoms, transforms, transform_indices) 
    17392 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17393 packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map 
    17394 self.structure = self._unique_structure(atoms) 
    17395 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17396 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    17397 _unique_structure 
    17398 raise TypeError('All atoms for zone mask must be from a single model!') 
    17399 TypeError: All atoms for zone mask must be from a single model! 
    17400  
    17401 TypeError: All atoms for zone mask must be from a single model! 
    17402  
    17403 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    17404 packages/chimerax/clipper/maps/mask_handler.py", line 185, in
    17405 _unique_structure 
    17406 raise TypeError('All atoms for zone mask must be from a single model!') 
    17407  
    17408 See log for complete Python traceback. 
    17409  
    17410 
    17411 > isolde ~ignore
    17412 
    17413 > color bychain
    17414 
    17415 > color byhetero
    17416 
    17417 > cartoon
    17418 
    17419 > select up
    17420 
    17421 24 atoms, 23 bonds, 1 residue, 1 model selected 
    17422 
    17423 > isolde ignore ~sel
    17424 
    17425 ISOLDE: currently ignoring 5993 residues in model 8.2 
    17426 
    17427 > isolde ~ignore
    17428 
    17429 Added a C-terminal OXT to chain C1 
    17430 
    17431 > select up
    17432 
    17433 24 atoms, 23 bonds, 1 residue, 1 model selected 
    17434 
    17435 > show sel
    17436 
    17437 > swapaa sel mousem GLU
    17438 
    17439 Expected a keyword 
    17440 
    17441 > swapaa mousemode sel GLU
    17442 
    17443 > swapaa mousemode sel ALA
    17444 
    17445 > swapaa mousemode sel ALA
    17446 
    17447 > select up
    17448 
    17449 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17450 
    17451 > delete sel
    17452 
    17453 > select up
    17454 
    17455 10 atoms, 9 bonds, 1 residue, 1 model selected 
    17456 
    17457 > select up
    17458 
    17459 162 atoms, 164 bonds, 12 residues, 1 model selected 
    17460 
    17461 > select /ap:50-100
    17462 
    17463 291 atoms, 295 bonds, 23 residues, 1 model selected 
    17464 
    17465 Chain ap, residue 60 specifies more than one residue! The simulation can still
    17466 run, but this will probably cause problems later if not rectified by
    17467 renumbering. 
    17468 
    17469 > select clear
    17470 
    17471 > swapaa mousemode sel ALA
    17472 
    17473 > select up
    17474 
    17475 10 atoms, 9 bonds, 1 residue, 1 model selected 
    17476 
    17477 > delete sel
    17478 
    17479 > select /ap:50-100
    17480 
    17481 294 atoms, 298 bonds, 23 residues, 1 model selected 
    17482 
    17483 > select clear
    17484 
    17485 Residue ALA ap61 is not a C-terminal residue! 
    17486 Residue ALA ap61 is not a C-terminal residue! 
    17487 
    17488 > isolde add ligand TRP
    17489 
    17490 place_ligand() was called with use_md_template=True, but no suitable template
    17491 was found. This command has been ignored. 
    17492 
    17493 > select up
    17494 
    17495 27 atoms, 28 bonds, 1 residue, 1 model selected 
    17496 
    17497 > delete sel
    17498 
    17499 > select :MQ8
    17500 
    17501 125 atoms, 126 bonds, 1 residue, 1 model selected 
    17502 
    17503 > select clear
    17504 
    17505 > select /ap
    17506 
    17507 1268 atoms, 1283 bonds, 81 residues, 1 model selected 
    17508 Added a C-terminal OXT to chain ap 
    17509 
    17510 > isolde add water
    17511 
    17512 > isolde sim start sel
    17513 
    17514 > select up
    17515 
    17516 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17517 
    17518 > style sel stick
    17519 
    17520 Changed 3 atom styles 
    17521 
    17522 > color sel byhetero
    17523 
    17524 > select clear
    17525 
    17526 > isolde add water simSettle false
    17527 
    17528 > isolde add water simSettle false
    17529 
    17530 > isolde add water simSettle false
    17531 
    17532 > select clear
    17533 
    17534 > clipper spotlight radius 19.00
    17535 
    17536 > clipper spotlight radius 20.00
    17537 
    17538 > select up
    17539 
    17540 17 atoms, 16 bonds, 1 residue, 1 model selected 
    17541 
    17542 > select up
    17543 
    17544 159 atoms, 161 bonds, 11 residues, 1 model selected 
    17545 
    17546 Chain bk, residue 100 specifies more than one residue! The simulation can
    17547 still run, but this will probably cause problems later if not rectified by
    17548 renumbering. 
    17549 
    17550 Deleted the following atoms from residue GLU an63: HN2 
    17551 Deleted the following atoms from residue SER an65: HN2 
    17552 Deleted the following atoms from residue LEU an67: HN2 
    17553 Deleted the following atoms from residue ARG an71: HN2 
    17554 
    17555 Chain bk, residue 100 specifies more than one residue! The simulation can
    17556 still run, but this will probably cause problems later if not rectified by
    17557 renumbering. 
    17558 
    17559 > select up
    17560 
    17561 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17562 
    17563 > select up
    17564 
    17565 155 atoms, 157 bonds, 11 residues, 1 model selected 
    17566 
    17567 > select clear
    17568 
    17569 > show #!2 models
    17570 
    17571 > hide #!2 models
    17572 
    17573 > isolde add ligand LMT chain ba
    17574 
    17575 > ui mousemode right "translate selected atoms"
    17576 
    17577 > select clear
    17578 
    17579 > select up
    17580 
    17581 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17582 
    17583 > delete sel
    17584 
    17585 > select up
    17586 
    17587 9 atoms, 6 bonds, 3 residues, 1 model selected 
    17588 
    17589 > select up
    17590 
    17591 12 atoms, 8 bonds, 4 residues, 1 model selected 
    17592 
    17593 > delete sel
    17594 
    17595 > select up
    17596 
    17597 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17598 
    17599 > select up
    17600 
    17601 6 atoms, 4 bonds, 2 residues, 1 model selected 
    17602 
    17603 > select up
    17604 
    17605 9 atoms, 6 bonds, 3 residues, 1 model selected 
    17606 
    17607 > select up
    17608 
    17609 15 atoms, 10 bonds, 5 residues, 1 model selected 
    17610 
    17611 > select up
    17612 
    17613 18 atoms, 12 bonds, 6 residues, 1 model selected 
    17614 
    17615 > select up
    17616 
    17617 27 atoms, 18 bonds, 9 residues, 1 model selected 
    17618 
    17619 > delete sel
    17620 
    17621 > select clear
    17622 
    17623 > select ~:HOH
    17624 
    17625 112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 27 models selected 
    17626 
    17627 > usage sel
    17628 
    17629 select [objects] [residues true or false] [polymer an atoms specifier]
    17630 [minimumLength a number] [maximumLength a number] [sequence a text string] 
    17631 — select specified objects 
    17632 Subcommands are:
    17633 
    17634   * select add
    17635   * select clear
    17636   * select down
    17637   * select intersect
    17638   * select subtract
    17639   * select up
    17640   * select zone
    17641 
    17642  
    17643 
    17644 > select #8.2&~:HOH
    17645 
    17646 112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models selected 
    17647 
    17648 > select zone sel 3
    17649 
    17650 Selected 1954 atoms, 5 surfaces 
    17651 
    17652 > select up
    17653 
    17654 2103 atoms, 1402 bonds, 701 residues, 6 models selected 
    17655 
    17656 > select :HOH&~sel
    17657 
    17658 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17659 
    17660 > select clear
    17661 
    17662 > select #8.2&~:HOH
    17663 
    17664 112976 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models selected 
    17665 
    17666 > select zone sel 3
    17667 
    17668 Selected 1954 atoms, 5 surfaces 
    17669 
    17670 > select up
    17671 
    17672 2103 atoms, 1402 bonds, 701 residues, 6 models selected 
    17673 
    17674 > select down
    17675 
    17676 1954 atoms, 701 residues, 6 models selected 
    17677 
    17678 > select clear
    17679 
    17680 > select #8.2&~:HOH&~H
    17681 
    17682 55156 atoms, 115358 bonds, 15 pseudobonds, 5293 residues, 13 models selected 
    17683 
    17684 > select zone sel 3
    17685 
    17686 Selected 59310 atoms, 5 surfaces 
    17687 
    17688 > select up
    17689 
    17690 114877 atoms, 116626 bonds, 5926 residues, 6 models selected 
    17691 
    17692 > select :HOH&~sel
    17693 
    17694 204 atoms, 136 bonds, 68 residues, 1 model selected 
    17695 
    17696 > delete sel
    17697 
    17698 > isolde add ligand MQ8
    17699 
    17700 > ui mousemode right "translate selected atoms"
    17701 
    17702 > isolde ignore ~sel
    17703 
    17704 ISOLDE: currently ignoring 5927 residues in model 8.2 
    17705 
    17706 > isolde ~ignore
    17707 
    17708 Chain bk, residue 100 specifies more than one residue! The simulation can
    17709 still run, but this will probably cause problems later if not rectified by
    17710 renumbering. 
    17711 
    17712 > select clear
    17713 
    17714 > select up
    17715 
    17716 125 atoms, 126 bonds, 1 residue, 1 model selected 
    17717 
    17718 > show sel
    17719 
    17720 > select clear
    17721 
    17722 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17723 bonded heavy atom. 
    17724 
    17725 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    17726 bonded heavy atom. 
    17727 
    17728 Chain bk, residue 100 specifies more than one residue! The simulation can
    17729 still run, but this will probably cause problems later if not rectified by
    17730 renumbering. 
    17731 
    17732 > select :MQ9
    17733 
    17734 138 atoms, 139 bonds, 1 residue, 1 model selected 
    17735 
    17736 > select :MQ8,MQ9
    17737 
    17738 388 atoms, 391 bonds, 3 residues, 1 model selected 
    17739 
    17740 > select up
    17741 
    17742 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17743 
    17744 > delete sel
    17745 
    17746 > select up
    17747 
    17748 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17749 
    17750 > delete sel
    17751 
    17752 > select up
    17753 
    17754 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17755 
    17756 > delete sel
    17757 
    17758 > select clear
    17759 
    17760 > select clear
    17761 
    17762 > select up
    17763 
    17764 15 atoms, 10 bonds, 5 residues, 1 model selected 
    17765 
    17766 > delete sel
    17767 
    17768 > select clear
    17769 
    17770 > select up
    17771 
    17772 256 atoms, 255 bonds, 1 residue, 1 model selected 
    17773 
    17774 > select clear
    17775 
    17776 > isolde add water simSettle false
    17777 
    17778 > select up
    17779 
    17780 6 atoms, 4 bonds, 2 residues, 1 model selected 
    17781 
    17782 > delete sel
    17783 
    17784 > isolde add water simSettle false
    17785 
    17786 > isolde add water simSettle false
    17787 
    17788 > isolde add water simSettle false
    17789 
    17790 > isolde add water simSettle false
    17791 
    17792 > isolde add water simSettle false
    17793 
    17794 > isolde add water simSettle false
    17795 
    17796 > isolde add water simSettle false
    17797 
    17798 > isolde add water simSettle false
    17799 
    17800 No existing atoms found within the given distance cutoff of the target
    17801 position. You may repeat with a larger cutoff or explicitly specify the
    17802 B-factor and chain ID, but keep in mind that placing waters outside of
    17803 H-bonding distance to the model is generally inadvisable. 
    17804 
    17805 > isolde add water simSettle false
    17806 
    17807 > isolde add water simSettle false
    17808 
    17809 > isolde add water simSettle false
    17810 
    17811 > select clear
    17812 
    17813 > save working.cxs
    17814 
    17815 Taking snapshot of stepper: working_2.pdb 
    17816 opened ChimeraX session 
    17817 
    17818 > view /M:GCU
    17819 
    17820 > open
    17821 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/GUX.xml
    17822 
    17823 Opened GUX.xml 
    17824 
    17825 > open
    17826 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    17827 
    17828 > select #1
    17829 
    17830 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17831 
    17832 > ui mousemode right "translate selected atoms"
    17833 
    17834 > select up
    17835 
    17836 2 atoms, 1 bond, 1 residue, 1 model selected 
    17837 
    17838 > select up
    17839 
    17840 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17841 
    17842 > delete sel
    17843 
    17844 > isolde start
    17845 
    17846 > set selectionWidth 4
    17847 
    17848 Done loading forcefield 
    17849 
    17850 > pwd
    17851 
    17852 Current working directory is:
    17853 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a 
    17854 
    17855 > open
    17856 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    17857 
    17858 > select #1
    17859 
    17860 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17861 
    17862 > delete #1/M:GCU
    17863 
    17864 > open
    17865 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    17866 
    17867 > select #1
    17868 
    17869 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17870 
    17871 > delete #8/M:GCU
    17872 
    17873 > ui tool show Shell
    17874 
    17875 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    17876 UserWarning: IPython History requires SQLite, your history will not be saved 
    17877 warn("IPython History requires SQLite, your history will not be saved") 
    17878 
    17879 > hide #1 models
    17880 
    17881 > select up
    17882 
    17883 67 atoms, 69 bonds, 3 residues, 1 model selected 
    17884 
    17885 Chain bk, residue 100 specifies more than one residue! The simulation can
    17886 still run, but this will probably cause problems later if not rectified by
    17887 renumbering. 
    17888 
    17889 > select up
    17890 
    17891 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17892 
    17893 > select clear
    17894 
    17895 > select /C
    17896 
    17897 5190 atoms, 5214 bonds, 4 pseudobonds, 390 residues, 2 models selected 
    17898 
    17899 > select clear
    17900 
    17901 > view :GUX
    17902 
    17903 > select up
    17904 
    17905 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17906 
    17907 > save acetylated_gcu.jpg
    17908 
    17909 > select clear
    17910 
    17911 > view /M:GCU
    17912 
    17913 > view #8:GCU
    17914 
    17915 > view #8:GUX
    17916 
    17917 > close #1#2
    17918 
    17919 > view :GCU
    17920 
    17921 > open
    17922 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/ligands/glycans/gcx_o_acetyl.pdb
    17923 
    17924 > select #1
    17925 
    17926 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17927 
    17928 > ui mousemode right "translate selected atoms"
    17929 
    17930 > select up
    17931 
    17932 19 atoms, 19 bonds, 1 residue, 1 model selected 
    17933 
    17934 > delete sel
    17935 
    17936 > hide #1 models
    17937 
    17938 > select up
    17939 
    17940 67 atoms, 69 bonds, 3 residues, 1 model selected 
    17941 
    17942 Chain bk, residue 100 specifies more than one residue! The simulation can
    17943 still run, but this will probably cause problems later if not rectified by
    17944 renumbering. 
    17945 
    17946 > select up
    17947 
    17948 29 atoms, 29 bonds, 1 residue, 1 model selected 
    17949 
    17950 > select clear
    17951 
    17952 > save model1a_2020_11_02.pdb #1
    17953 
    17954 > save model1a_2020_11_02.pdb #8
    17955 
    17956 > view /M:GUX
    17957 
    17958 > select clear
    17959 
    17960 > isolde add water simSettle false
    17961 
    17962 > save model1a_2020_11_02.pdb #8
    17963 
    17964 > isolde add water simSettle false
    17965 
    17966 > isolde add water simSettle false
    17967 
    17968 > select up
    17969 
    17970 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17971 
    17972 > delete sel
    17973 
    17974 > isolde add water simSettle false
    17975 
    17976 > isolde add water simSettle false
    17977 
    17978 > select up
    17979 
    17980 3 atoms, 2 bonds, 1 residue, 1 model selected 
    17981 
    17982 > delete sel
    17983 
    17984 > isolde add water simSettle false
    17985 
    17986 > isolde add water simSettle false
    17987 
    17988 > isolde add water simSettle false
    17989 
    17990 > isolde add water simSettle false
    17991 
    17992 > isolde add water simSettle false
    17993 
    17994 > isolde add water simSettle false
    17995 
    17996 > isolde add water simSettle false
    17997 
    17998 > isolde add water simSettle false
    17999 
    18000 > isolde add water simSettle false
    18001 
    18002 > isolde add water simSettle false
    18003 
    18004 > select clear
    18005 
    18006 > isolde add water simSettle false
    18007 
    18008 > isolde add water simSettle false
    18009 
    18010 > isolde add water simSettle false
    18011 
    18012 > isolde add water simSettle false
    18013 
    18014 > isolde add water simSettle false
    18015 
    18016 > isolde add water simSettle false
    18017 
    18018 > isolde add water simSettle false
    18019 
    18020 > isolde add water simSettle false
    18021 
    18022 > isolde add water simSettle false
    18023 
    18024 > isolde add water simSettle false
    18025 
    18026 > select clear
    18027 
    18028 > isolde add water simSettle false
    18029 
    18030 > isolde add water simSettle false
    18031 
    18032 > select clear
    18033 
    18034 > isolde add water simSettle false
    18035 
    18036 > select clear
    18037 
    18038 > isolde add water simSettle false
    18039 
    18040 > select clear
    18041 
    18042 > isolde add water simSettle false
    18043 
    18044 > isolde add water simSettle false
    18045 
    18046 > isolde add water simSettle false
    18047 
    18048 > isolde add water simSettle false
    18049 
    18050 > isolde add water simSettle false
    18051 
    18052 > select up
    18053 
    18054 3 atoms, 2 bonds, 1 residue, 1 model selected 
    18055 
    18056 > delete sel
    18057 
    18058 > select /a*:50-60
    18059 
    18060 2020 atoms, 2035 bonds, 172 residues, 1 model selected 
    18061 
    18062 > select clear
    18063 
    18064 > isolde add water simSettle false
    18065 
    18066 > select clear
    18067 
    18068 > select clear
    18069 
    18070 > select clear
    18071 
    18072 > isolde add water simSettle false
    18073 
    18074 > select clear
    18075 
    18076 > isolde add water simSettle false
    18077 
    18078 > isolde add water simSettle false
    18079 
    18080 > select clear
    18081 
    18082 > isolde add water simSettle false
    18083 
    18084 > select clear
    18085 
    18086 > isolde add water simSettle false
    18087 
    18088 > isolde add water simSettle false
    18089 
    18090 > isolde add water simSettle false
    18091 
    18092 > select up
    18093 
    18094 6 atoms, 4 bonds, 2 residues, 1 model selected 
    18095 
    18096 > delete sel
    18097 
    18098 > select up
    18099 
    18100 3 atoms, 2 bonds, 1 residue, 1 model selected 
    18101 
    18102 > delete sel
    18103 
    18104 > select up
    18105 
    18106 3 atoms, 2 bonds, 1 residue, 1 model selected 
    18107 
    18108 > delete sel
    18109 
    18110 > select clear
    18111 
    18112 > save model1a_2020_11_02.cxs
    18113 
    18114 Taking snapshot of stepper: Model 1a 
    18115 
    18116 > save model1a_2020_11_02.pdb #8
    18117 
    18118 > select clear
    18119 
    18120 > delete sel
    18121 
    18122 > dssp
    18123 
    18124 > save model1a_2020_11_02.cxs
    18125 
    18126 Taking snapshot of stepper: Model 1a 
    18127 opened ChimeraX session 
    18128 
    18129 > close #8.1.1.2
    18130 
    18131 > open
    18132 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1a/class1a_r_2.35A.mrc
    18133 
    18134 Opened class1a_r_2.35A.mrc, grid size 400,400,400, pixel 0.999, shown at level
    18135 0.0164, step 2, values float32 
    18136 
    18137 > clipper associate #2 toModel #8
    18138 
    18139 > close #1
    18140 
    18141 > isolde start
    18142 
    18143 > set selectionWidth 4
    18144 
    18145 Done loading forcefield 
    18146 
    18147 > view /M:MAN
    18148 
    18149 > select clear
    18150 
    18151 > clipper spotlight radius 11.00
    18152 
    18153 > clipper spotlight radius 10.00
    18154 
    18155 > clipper spotlight radius 9.00
    18156 
    18157 > clipper spotlight radius 8.00
    18158 
    18159 > clipper spotlight radius 7.00
    18160 
    18161 > clipper spotlight radius 6.00
    18162 
    18163 > clipper spotlight radius 5.00
    18164 
    18165 > clipper spotlight radius 6.00
    18166 
    18167 > clipper spotlight radius 7.00
    18168 
    18169 > clipper spotlight radius 8.00
    18170 
    18171 > clipper spotlight radius 9.00
    18172 
    18173 > clipper spotlight radius 10.00
    18174 
    18175 > clipper spotlight radius 11.00
    18176 
    18177 > clipper spotlight radius 12.00
    18178 
    18179 > clipper spotlight radius 13.00
    18180 
    18181 > clipper spotlight radius 14.00
    18182 
    18183 > clipper spotlight radius 15.00
    18184 
    18185 > clipper spotlight radius 16.00
    18186 
    18187 > select clear
    18188 
    18189 > select clear
    18190 
    18191 > save man.jpg
    18192 
    18193 > select clear
    18194 
    18195 > save model1a_2020_11_04.cxs
    18196 
    18197 Taking snapshot of stepper: Model 1a 
    18198 opened ChimeraX session 
    18199 
    18200 > ui tool show Shell
    18201 
    18202 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    18203 UserWarning: IPython History requires SQLite, your history will not be saved 
    18204 warn("IPython History requires SQLite, your history will not be saved") 
    18205 
    18206 > open class4b_r_2.35A_postprocess_masked.mrc
    18207 
    18208 Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400, pixel
    18209 0.999, shown at level 0.0164, step 2, values float32 
    18210 
    18211 > volume gaussian #1 bfactor 50
    18212 
    18213 > close #8.1
    18214 
    18215 > clipper associate #1,2 toModel #8
    18216 
    18217 > isolde start
    18218 
    18219 > set selectionWidth 4
    18220 
    18221 Done loading forcefield 
    18222 
    18223 > clipper set contourSensitivity 0.25
    18224 
    18225 > select clear
    18226 
    18227 > ui tool show Shell
    18228 
    18229 > alias keep setattr sel residues isolde_keep true
    18230 
    18231 > alias st isolde step $*
    18232 
    18233 > alias aw isolde add water $*
    18234 
    18235 > keep
    18236 
    18237 Assigning isolde_keep attribute to 1 item 
    18238 
    18239 > keep
    18240 
    18241 Assigning isolde_keep attribute to 1 item 
    18242 
    18243 > keep
    18244 
    18245 Assigning isolde_keep attribute to 1 item 
    18246 
    18247 > keep
    18248 
    18249 Assigning isolde_keep attribute to 1 item 
    18250 
    18251 > keep
    18252 
    18253 Assigning isolde_keep attribute to 1 item 
    18254 
    18255 > keep
    18256 
    18257 Assigning isolde_keep attribute to 1 item 
    18258 
    18259 > keep
    18260 
    18261 Assigning isolde_keep attribute to 1 item 
    18262 
    18263 > select clear
    18264 
    18265 > keep
    18266 
    18267 Assigning isolde_keep attribute to 1 item 
    18268 
    18269 > keep
    18270 
    18271 Assigning isolde_keep attribute to 1 item 
    18272 
    18273 > keep
    18274 
    18275 Assigning isolde_keep attribute to 1 item 
    18276 
    18277 > keep
    18278 
    18279 Assigning isolde_keep attribute to 1 item 
    18280 
    18281 > keep
    18282 
    18283 Assigning isolde_keep attribute to 1 item 
    18284 
    18285 > keep
    18286 
    18287 Assigning isolde_keep attribute to 1 item 
    18288 
    18289 > keep
    18290 
    18291 Assigning isolde_keep attribute to 1 item 
    18292 
    18293 > keep
    18294 
    18295 Assigning isolde_keep attribute to 1 item 
    18296 
    18297 > keep
    18298 
    18299 Assigning isolde_keep attribute to 1 item 
    18300 
    18301 > keep
    18302 
    18303 Assigning isolde_keep attribute to 1 item 
    18304 
    18305 > keep
    18306 
    18307 Assigning isolde_keep attribute to 1 item 
    18308 
    18309 > keep
    18310 
    18311 Assigning isolde_keep attribute to 1 item 
    18312 
    18313 > keep
    18314 
    18315 Assigning isolde_keep attribute to 1 item 
    18316 
    18317 > keep
    18318 
    18319 Assigning isolde_keep attribute to 1 item 
    18320 
    18321 > keep
    18322 
    18323 Assigning isolde_keep attribute to 1 item 
    18324 
    18325 > keep
    18326 
    18327 Assigning isolde_keep attribute to 1 item 
    18328 
    18329 > select clear
    18330 
    18331 > select clear
    18332 
    18333 > select clear
    18334 
    18335 > select up
    18336 
    18337 3 atoms, 2 bonds, 1 residue, 1 model selected 
    18338 
    18339 > keep
    18340 
    18341 Assigning isolde_keep attribute to 1 item 
    18342 
    18343 > keep
    18344 
    18345 Assigning isolde_keep attribute to 1 item 
    18346 
    18347 > keep
    18348 
    18349 Assigning isolde_keep attribute to 1 item 
    18350 
    18351 > keep
    18352 
    18353 Assigning isolde_keep attribute to 1 item 
    18354 
    18355 > keep
    18356 
    18357 Assigning isolde_keep attribute to 1 item 
    18358 
    18359 > keep
    18360 
    18361 Assigning isolde_keep attribute to 1 item 
    18362 
    18363 > keep
    18364 
    18365 Assigning isolde_keep attribute to 1 item 
    18366 
    18367 > keep
    18368 
    18369 Assigning isolde_keep attribute to 1 item 
    18370 
    18371 > keep
    18372 
    18373 Assigning isolde_keep attribute to 1 item 
    18374 
    18375 > keep
    18376 
    18377 Assigning isolde_keep attribute to 1 item 
    18378 
    18379 > keep
    18380 
    18381 Assigning isolde_keep attribute to 1 item 
    18382 
    18383 > keep
    18384 
    18385 Assigning isolde_keep attribute to 1 item 
    18386 
    18387 > keep
    18388 
    18389 Assigning isolde_keep attribute to 1 item 
    18390 
    18391 > keep
    18392 
    18393 Assigning isolde_keep attribute to 1 item 
    18394 
    18395 > aw
    18396 
    18397 > isolde sim start sel
    18398 
    18399 > keep
    18400 
    18401 Assigning isolde_keep attribute to 1 item 
    18402 
    18403 > keep
    18404 
    18405 Assigning isolde_keep attribute to 1 item 
    18406 
    18407 > select clear
    18408 
    18409 > keep
    18410 
    18411 Assigning isolde_keep attribute to 1 item 
    18412 
    18413 > keep
    18414 
    18415 Assigning isolde_keep attribute to 1 item 
    18416 
    18417 > keep
    18418 
    18419 Assigning isolde_keep attribute to 1 item 
    18420 
    18421 > keep
    18422 
    18423 Assigning isolde_keep attribute to 1 item 
    18424 
    18425 > keep
    18426 
    18427 Assigning isolde_keep attribute to 1 item 
    18428 
    18429 > keep
    18430 
    18431 Assigning isolde_keep attribute to 1 item 
    18432 
    18433 > keep
    18434 
    18435 Assigning isolde_keep attribute to 1 item 
    18436 
    18437 > keep
    18438 
    18439 Assigning isolde_keep attribute to 1 item 
    18440 
    18441 > keep
    18442 
    18443 Assigning isolde_keep attribute to 1 item 
    18444 
    18445 > keep
    18446 
    18447 Assigning isolde_keep attribute to 1 item 
    18448 
    18449 > keep
    18450 
    18451 Assigning isolde_keep attribute to 1 item 
    18452 
    18453 > keep
    18454 
    18455 Assigning isolde_keep attribute to 1 item 
    18456 
    18457 > keep
    18458 
    18459 Assigning isolde_keep attribute to 1 item 
    18460 
    18461 > save working.cxs
    18462 
    18463 Taking snapshot of stepper: Model 1a 
    18464 
    18465 > keep
    18466 
    18467 Assigning isolde_keep attribute to 1 item 
    18468 
    18469 > keep
    18470 
    18471 Assigning isolde_keep attribute to 1 item 
    18472 
    18473 > keep
    18474 
    18475 Assigning isolde_keep attribute to 1 item 
    18476 
    18477 > keep
    18478 
    18479 Assigning isolde_keep attribute to 1 item 
    18480 
    18481 > keep
    18482 
    18483 Assigning isolde_keep attribute to 1 item 
    18484 
    18485 > keep
    18486 
    18487 Assigning isolde_keep attribute to 1 item 
    18488 
    18489 > keep
    18490 
    18491 Assigning isolde_keep attribute to 1 item 
    18492 
    18493 > keep
    18494 
    18495 Assigning isolde_keep attribute to 1 item 
    18496 
    18497 > keep
    18498 
    18499 Assigning isolde_keep attribute to 1 item 
    18500 
    18501 > keep
    18502 
    18503 Assigning isolde_keep attribute to 1 item 
    18504 
    18505 > keep
    18506 
    18507 Assigning isolde_keep attribute to 1 item 
    18508 
    18509 > keep
    18510 
    18511 Assigning isolde_keep attribute to 1 item 
    18512 
    18513 > keep
    18514 
    18515 Assigning isolde_keep attribute to 1 item 
    18516 
    18517 > keep
    18518 
    18519 Assigning isolde_keep attribute to 1 item 
    18520 
    18521 > keep
    18522 
    18523 Assigning isolde_keep attribute to 1 item 
    18524 
    18525 > keep
    18526 
    18527 Assigning isolde_keep attribute to 1 item 
    18528 
    18529 > select clear
    18530 
    18531 > keep
    18532 
    18533 Assigning isolde_keep attribute to 1 item 
    18534 
    18535 > keep
    18536 
    18537 Assigning isolde_keep attribute to 1 item 
    18538 
    18539 > keep
    18540 
    18541 Assigning isolde_keep attribute to 1 item 
    18542 
    18543 > keep
    18544 
    18545 Assigning isolde_keep attribute to 1 item 
    18546 
    18547 > select clear
    18548 
    18549 > keep
    18550 
    18551 Assigning isolde_keep attribute to 1 item 
    18552 
    18553 > keep
    18554 
    18555 Assigning isolde_keep attribute to 1 item 
    18556 
    18557 > keep
    18558 
    18559 Assigning isolde_keep attribute to 1 item 
    18560 
    18561 > keep
    18562 
    18563 Assigning isolde_keep attribute to 1 item 
    18564 
    18565 > keep
    18566 
    18567 Assigning isolde_keep attribute to 1 item 
    18568 
    18569 > keep
    18570 
    18571 Assigning isolde_keep attribute to 1 item 
    18572 
    18573 > keep
    18574 
    18575 Assigning isolde_keep attribute to 1 item 
    18576 
    18577 > keep
    18578 
    18579 Assigning isolde_keep attribute to 1 item 
    18580 
    18581 > keep
    18582 
    18583 Assigning isolde_keep attribute to 1 item 
    18584 
    18585 > keep
    18586 
    18587 Assigning isolde_keep attribute to 1 item 
    18588 
    18589 > keep
    18590 
    18591 Assigning isolde_keep attribute to 1 item 
    18592 
    18593 > keep
    18594 
    18595 Assigning isolde_keep attribute to 1 item 
    18596 
    18597 > keep
    18598 
    18599 Assigning isolde_keep attribute to 1 item 
    18600 
    18601 > keep
    18602 
    18603 Assigning isolde_keep attribute to 1 item 
    18604 
    18605 > select clear
    18606 
    18607 > keep
    18608 
    18609 Assigning isolde_keep attribute to 1 item 
    18610 
    18611 > keep
    18612 
    18613 Assigning isolde_keep attribute to 1 item 
    18614 
    18615 > keep
    18616 
    18617 Assigning isolde_keep attribute to 1 item 
    18618 
    18619 > keep
    18620 
    18621 Assigning isolde_keep attribute to 1 item 
    18622 
    18623 > select clear
    18624 
    18625 > keep
    18626 
    18627 Assigning isolde_keep attribute to 1 item 
    18628 
    18629 > keep
    18630 
    18631 Assigning isolde_keep attribute to 1 item 
    18632 
    18633 > keep
    18634 
    18635 Assigning isolde_keep attribute to 1 item 
    18636 
    18637 > keep
    18638 
    18639 Assigning isolde_keep attribute to 1 item 
    18640 
    18641 > keep
    18642 
    18643 Assigning isolde_keep attribute to 1 item 
    18644 
    18645 > keep
    18646 
    18647 Assigning isolde_keep attribute to 1 item 
    18648 
    18649 > keep
    18650 
    18651 Assigning isolde_keep attribute to 1 item 
    18652 
    18653 > keep
    18654 
    18655 Assigning isolde_keep attribute to 1 item 
    18656 
    18657 > keep
    18658 
    18659 Assigning isolde_keep attribute to 1 item 
    18660 
    18661 > keep
    18662 
    18663 Assigning isolde_keep attribute to 1 item 
    18664 
    18665 > keep
    18666 
    18667 Assigning isolde_keep attribute to 1 item 
    18668 
    18669 > keep
    18670 
    18671 Assigning isolde_keep attribute to 1 item 
    18672 
    18673 > keep
    18674 
    18675 Assigning isolde_keep attribute to 1 item 
    18676 
    18677 > select clear
    18678 
    18679 > keep
    18680 
    18681 Assigning isolde_keep attribute to 1 item 
    18682 
    18683 > keep
    18684 
    18685 Assigning isolde_keep attribute to 1 item 
    18686 
    18687 > keep
    18688 
    18689 Assigning isolde_keep attribute to 1 item 
    18690 
    18691 > keep
    18692 
    18693 Assigning isolde_keep attribute to 1 item 
    18694 
    18695 > keep
    18696 
    18697 Assigning isolde_keep attribute to 1 item 
    18698 
    18699 > keep
    18700 
    18701 Assigning isolde_keep attribute to 1 item 
    18702 
    18703 > keep
    18704 
    18705 Assigning isolde_keep attribute to 1 item 
    18706 
    18707 > keep
    18708 
    18709 Assigning isolde_keep attribute to 1 item 
    18710 
    18711 > keep
    18712 
    18713 Assigning isolde_keep attribute to 1 item 
    18714 
    18715 > keep
    18716 
    18717 Assigning isolde_keep attribute to 1 item 
    18718 
    18719 > keep
    18720 
    18721 Assigning isolde_keep attribute to 1 item 
    18722 
    18723 > keep
    18724 
    18725 Assigning isolde_keep attribute to 1 item 
    18726 
    18727 > keep
    18728 
    18729 Assigning isolde_keep attribute to 1 item 
    18730 
    18731 > keep
    18732 
    18733 Assigning isolde_keep attribute to 1 item 
    18734 
    18735 > keep
    18736 
    18737 Assigning isolde_keep attribute to 1 item 
    18738 
    18739 > keep
    18740 
    18741 Assigning isolde_keep attribute to 1 item 
    18742 
    18743 > keep
    18744 
    18745 Assigning isolde_keep attribute to 1 item 
    18746 
    18747 > select clear
    18748 
    18749 > keep
    18750 
    18751 Assigning isolde_keep attribute to 1 item 
    18752 
    18753 > select clear
    18754 
    18755 > keep
    18756 
    18757 Assigning isolde_keep attribute to 1 item 
    18758 
    18759 > keep
    18760 
    18761 Assigning isolde_keep attribute to 1 item 
    18762 
    18763 > keep
    18764 
    18765 Assigning isolde_keep attribute to 1 item 
    18766 
    18767 > keep
    18768 
    18769 Assigning isolde_keep attribute to 1 item 
    18770 
    18771 > view /aa:4
    18772 
    18773 > view /aa:47
    18774 
    18775 > view /ab:47
    18776 
    18777 > view /ac:47
    18778 
    18779 > view /ad:47
    18780 
    18781 > view /ae:47
    18782 
    18783 > view /af:47
    18784 
    18785 > view /ag:47
    18786 
    18787 > view /ah:47
    18788 
    18789 > view /ai:47
    18790 
    18791 > view /aj:47
    18792 
    18793 > view /ak:47
    18794 
    18795 > view /al:47
    18796 
    18797 > view /am:47
    18798 
    18799 > view /an:47
    18800 
    18801 > view /ao:47
    18802 
    18803 > view /ap:47
    18804 
    18805 > view /aq:47
    18806 
    18807 No objects specified. 
    18808 
    18809 > keep
    18810 
    18811 Assigning isolde_keep attribute to 1 item 
    18812 
    18813 > keep
    18814 
    18815 Assigning isolde_keep attribute to 1 item 
    18816 
    18817 > select clear
    18818 
    18819 > keep
    18820 
    18821 Assigning isolde_keep attribute to 1 item 
    18822 
    18823 > keep
    18824 
    18825 Assigning isolde_keep attribute to 1 item 
    18826 
    18827 > keep
    18828 
    18829 Assigning isolde_keep attribute to 1 item 
    18830 
    18831 > setattr sel residues isolde_keep false
    18832 
    18833 Assigning isolde_keep attribute to 1 item 
    18834 
    18835 > keep
    18836 
    18837 Assigning isolde_keep attribute to 1 item 
    18838 
    18839 > keep
    18840 
    18841 Assigning isolde_keep attribute to 1 item 
    18842 
    18843 > keep
    18844 
    18845 Assigning isolde_keep attribute to 1 item 
    18846 
    18847 > keep
    18848 
    18849 Assigning isolde_keep attribute to 1 item 
    18850 
    18851 > keep
    18852 
    18853 Assigning isolde_keep attribute to 1 item 
    18854 
    18855 > keep
    18856 
    18857 Assigning isolde_keep attribute to 1 item 
    18858 
    18859 > keep
    18860 
    18861 Assigning isolde_keep attribute to 1 item 
    18862 
    18863 > keep
    18864 
    18865 Assigning isolde_keep attribute to 1 item 
    18866 
    18867 > keep
    18868 
    18869 Assigning isolde_keep attribute to 1 item 
    18870 
    18871 > keep
    18872 
    18873 Assigning isolde_keep attribute to 1 item 
    18874 
    18875 > select clear
    18876 
    18877 > keep
    18878 
    18879 Assigning isolde_keep attribute to 1 item 
    18880 
    18881 > select up
    18882 
    18883 3 atoms, 2 bonds, 1 residue, 1 model selected 
    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 > keep
    18906 
    18907 Assigning isolde_keep attribute to 1 item 
    18908 
    18909 > setattr sel residues isolde_keep false
    18910 
    18911 Assigning isolde_keep attribute to 1 item 
    18912 
    18913 > keep
    18914 
    18915 Assigning isolde_keep attribute to 1 item 
    18916 
    18917 > keep
    18918 
    18919 Assigning isolde_keep attribute to 1 item 
    18920 
    18921 > keep
    18922 
    18923 Assigning isolde_keep attribute to 1 item 
    18924 
    18925 > keep
    18926 
    18927 Assigning isolde_keep attribute to 1 item 
    18928 
    18929 > keep
    18930 
    18931 Assigning isolde_keep attribute to 1 item 
    18932 
    18933 > keep
    18934 
    18935 Assigning isolde_keep attribute to 1 item 
    18936 
    18937 > select clear
    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 > setattr sel residues isolde_keep false
    18964 
    18965 Assigning isolde_keep attribute to 1 item 
    18966 
    18967 > keep
    18968 
    18969 Assigning isolde_keep attribute to 1 item 
    18970 
    18971 > keep
    18972 
    18973 Assigning isolde_keep attribute to 1 item 
    18974 
    18975 > keep
    18976 
    18977 Assigning isolde_keep attribute to 1 item 
    18978 
    18979 > keep
    18980 
    18981 Assigning isolde_keep attribute to 1 item 
    18982 
    18983 > select clear
    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 > keep
    19038 
    19039 Assigning isolde_keep attribute to 1 item 
    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 up
    19050 
    19051 5218 atoms, 5236 bonds, 396 residues, 1 model selected 
    19052 
    19053 > keep
    19054 
    19055 Assigning isolde_keep attribute to 1 item 
    19056 
    19057 > keep
    19058 
    19059 Assigning isolde_keep attribute to 1 item 
    19060 
    19061 > keep
    19062 
    19063 Assigning isolde_keep attribute to 1 item 
    19064 
    19065 > keep
    19066 
    19067 Assigning isolde_keep attribute to 1 item 
    19068 
    19069 > keep
    19070 
    19071 Assigning isolde_keep attribute to 1 item 
    19072 
    19073 > keep
    19074 
    19075 Assigning isolde_keep attribute to 1 item 
    19076 
    19077 > keep
    19078 
    19079 Assigning isolde_keep attribute to 1 item 
    19080 
    19081 > keep
    19082 
    19083 Assigning isolde_keep attribute to 1 item 
    19084 
    19085 > keep
    19086 
    19087 Assigning isolde_keep attribute to 1 item 
    19088 
    19089 > keep
    19090 
    19091 Assigning isolde_keep attribute to 1 item 
    19092 
    19093 > keep
    19094 
    19095 Assigning isolde_keep attribute to 1 item 
    19096 
    19097 > keep
    19098 
    19099 Assigning isolde_keep attribute to 1 item 
    19100 
    19101 > keep
    19102 
    19103 Assigning isolde_keep attribute to 1 item 
    19104 
    19105 > keep
    19106 
    19107 Assigning isolde_keep attribute to 1 item 
    19108 
    19109 > keep
    19110 
    19111 Assigning isolde_keep attribute to 1 item 
    19112 
    19113 > keep
    19114 
    19115 Assigning isolde_keep attribute to 1 item 
    19116 
    19117 > keep
    19118 
    19119 Assigning isolde_keep attribute to 1 item 
    19120 
    19121 > keep
    19122 
    19123 Assigning isolde_keep attribute to 1 item 
    19124 
    19125 > keep
    19126 
    19127 Assigning isolde_keep attribute to 1 item 
    19128 
    19129 > keep
    19130 
    19131 Assigning isolde_keep attribute to 1 item 
    19132 
    19133 > select up
    19134 
    19135 3 atoms, 2 bonds, 1 residue, 1 model selected 
    19136 
    19137 > keep
    19138 
    19139 Assigning isolde_keep attribute to 1 item 
    19140 
    19141 > keep
    19142 
    19143 Assigning isolde_keep attribute to 1 item 
    19144 
    19145 > keep
    19146 
    19147 Assigning isolde_keep attribute to 1 item 
    19148 
    19149 > keep
    19150 
    19151 Assigning isolde_keep attribute to 1 item 
    19152 
    19153 > select clear
    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 > keep
    19172 
    19173 Assigning isolde_keep attribute to 1 item 
    19174 
    19175 > aw sim f
    19176 
    19177 > aw sim f
    19178 
    19179 > keep
    19180 
    19181 Assigning isolde_keep attribute to 2 items 
    19182 
    19183 > keep
    19184 
    19185 Assigning isolde_keep attribute to 1 item 
    19186 
    19187 > keep
    19188 
    19189 Assigning isolde_keep attribute to 1 item 
    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 > select up
    19236 
    19237 3 atoms, 2 bonds, 1 residue, 1 model selected 
    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 > keep
    19248 
    19249 Assigning isolde_keep attribute to 1 item 
    19250 
    19251 > keep
    19252 
    19253 Assigning isolde_keep attribute to 1 item 
    19254 
    19255 > keep
    19256 
    19257 Assigning isolde_keep attribute to 1 item 
    19258 
    19259 > setattr sel residues isolde_keep false
    19260 
    19261 Assigning isolde_keep attribute to 1 item 
    19262 
    19263 > keep
    19264 
    19265 Assigning isolde_keep attribute to 1 item 
    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 > setattr sel residues isolde_keep false
    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 > keep
    19320 
    19321 Assigning isolde_keep attribute to 1 item 
    19322 
    19323 > keep
    19324 
    19325 Assigning isolde_keep attribute to 1 item 
    19326 
    19327 > keep
    19328 
    19329 Assigning isolde_keep attribute to 1 item 
    19330 
    19331 > keep
    19332 
    19333 Assigning isolde_keep attribute to 1 item 
    19334 
    19335 > keep
    19336 
    19337 Assigning isolde_keep attribute to 1 item 
    19338 
    19339 > keep
    19340 
    19341 Assigning isolde_keep attribute to 1 item 
    19342 
    19343 > keep
    19344 
    19345 Assigning isolde_keep attribute to 1 item 
    19346 
    19347 > keep
    19348 
    19349 Assigning isolde_keep attribute to 1 item 
    19350 
    19351 > keep
    19352 
    19353 Assigning isolde_keep attribute to 1 item 
    19354 
    19355 > keep
    19356 
    19357 Assigning isolde_keep attribute to 1 item 
    19358 
    19359 > keep
    19360 
    19361 Assigning isolde_keep attribute to 1 item 
    19362 
    19363 > keep
    19364 
    19365 Assigning isolde_keep attribute to 1 item 
    19366 
    19367 > keep
    19368 
    19369 Assigning isolde_keep attribute to 1 item 
    19370 
    19371 > keep
    19372 
    19373 Assigning isolde_keep attribute to 1 item 
    19374 
    19375 > keep
    19376 
    19377 Assigning isolde_keep attribute to 1 item 
    19378 
    19379 > keep
    19380 
    19381 Assigning isolde_keep attribute to 1 item 
    19382 
    19383 > keep
    19384 
    19385 Assigning isolde_keep attribute to 1 item 
    19386 
    19387 > keep
    19388 
    19389 Assigning isolde_keep attribute to 1 item 
    19390 
    19391 > aw
    19392 
    19393 > isolde sim start sel
    19394 
    19395 > select up
    19396 
    19397 6 atoms, 4 bonds, 2 residues, 1 model selected 
    19398 
    19399 > aw
    19400 
    19401 > isolde sim start sel
    19402 
    19403 > select up
    19404 
    19405 3 atoms, 2 bonds, 1 residue, 1 model selected 
    19406 
    19407 > delete sel
    19408 
    19409 > select up
    19410 
    19411 6 atoms, 4 bonds, 2 residues, 1 model selected 
    19412 
    19413 > keep
    19414 
    19415 Assigning isolde_keep attribute to 2 items 
    19416 
    19417 > keep
    19418 
    19419 Assigning isolde_keep attribute to 1 item 
    19420 
    19421 > keep
    19422 
    19423 Assigning isolde_keep attribute to 1 item 
    19424 
    19425 > keep
    19426 
    19427 Assigning isolde_keep attribute to 1 item 
    19428 
    19429 > keep
    19430 
    19431 Assigning isolde_keep attribute to 1 item 
    19432 
    19433 > keep
    19434 
    19435 Assigning isolde_keep attribute to 1 item 
    19436 
    19437 > keep
    19438 
    19439 Assigning isolde_keep attribute to 1 item 
    19440 
    19441 > keep
    19442 
    19443 Assigning isolde_keep attribute to 1 item 
    19444 
    19445 > keep
    19446 
    19447 Assigning isolde_keep attribute to 1 item 
    19448 
    19449 > keep
    19450 
    19451 Assigning isolde_keep attribute to 1 item 
    19452 
    19453 > keep
    19454 
    19455 Assigning isolde_keep attribute to 1 item 
    19456 
    19457 > keep
    19458 
    19459 Assigning isolde_keep attribute to 1 item 
    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 > select clear
    19470 
    19471 > select up
    19472 
    19473 1257 atoms, 1282 bonds, 59 residues, 1 model selected 
    19474 
    19475 > keep
    19476 
    19477 Assigning isolde_keep attribute to 1 item 
    19478 
    19479 > select clear
    19480 
    19481 > keep
    19482 
    19483 Assigning isolde_keep attribute to 1 item 
    19484 
    19485 > select clear
    19486 
    19487 > keep
    19488 
    19489 Assigning isolde_keep attribute to 1 item 
    19490 
    19491 > keep
    19492 
    19493 Assigning isolde_keep attribute to 1 item 
    19494 
    19495 > keep
    19496 
    19497 Assigning isolde_keep attribute to 1 item 
    19498 
    19499 > keep
    19500 
    19501 Assigning isolde_keep attribute to 1 item 
    19502 
    19503 > select clear
    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 > keep
    19518 
    19519 Assigning isolde_keep attribute to 1 item 
    19520 
    19521 > select clear
    19522 
    19523 > select clear
    19524 
    19525 > save working.cxs
    19526 
    19527 Taking snapshot of stepper: Model 1a 
    19528 
    19529 > select :HOH
    19530 
    19531 828 atoms, 552 bonds, 276 residues, 1 model selected 
    19532 
    19533 > select #1
    19534 
    19535 Nothing selected 
    19536 
    19537 > select #8
    19538 
    19539 113879 atoms, 115985 bonds, 15 pseudobonds, 5566 residues, 23 models selected 
    19540 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    19541 more memory-efficient implementation. 
    19542 Map is too large for fast cubic interpolation on the GPU! Switching to slower,
    19543 more memory-efficient implementation. 
    19544 
    19545 > select clear
    19546 
    19547 > select up
    19548 
    19549 215 atoms, 216 bonds, 12 residues, 1 model selected 
    19550 
    19551 > select clear
    19552 
    19553 > select clear
    19554 
    19555 > select clear
    19556 
    19557 > select clear
    19558 
    19559 > select clear
    19560 
    19561 > select clear
    19562 
    19563 > select clear
    19564 
    19565 > select clear
    19566 
    19567 > select clear
    19568 
    19569 > select clear
    19570 
    19571 > select clear
    19572 
    19573 > select clear
    19574 
    19575 > select clear
    19576 
    19577 > select clear
    19578 
    19579 > select clear
    19580 
    19581 > select clear
    19582 
    19583 > select clear
    19584 
    19585 > select clear
    19586 
    19587 > select clear
    19588 
    19589 > select clear
    19590 
    19591 > select clear
    19592 
    19593 > select clear
    19594 
    19595 > select clear
    19596 
    19597 > select clear
    19598 
    19599 > select clear
    19600 
    19601 > select clear
    19602 
    19603 > select clear
    19604 
    19605 > select clear
    19606 
    19607 > select clear
    19608 
    19609 > select clear
    19610 
    19611 > select clear
    19612 
    19613 > select clear
    19614 
    19615 > select clear
    19616 
    19617 > select clear
    19618 
    19619 > select clear
    19620 
    19621 > select clear
    19622 
    19623 > select clear
    19624 
    19625 > select clear
    19626 
    19627 > select clear
    19628 
    19629 > select clear
    19630 
    19631 > select clear
    19632 
    19633 > select clear
    19634 
    19635 > select clear
    19636 
    19637 > view /ba:32
    19638 
    19639 > view /bb:32
    19640 
    19641 > view /bc:32
    19642 
    19643 > view /bd:32
    19644 
    19645 > view /ba:32
    19646 
    19647 > view /bb:32
    19648 
    19649 > view /bc:32
    19650 
    19651 > view /bd:32
    19652 
    19653 > view /ba:27-32
    19654 
    19655 > view /bb:27-32
    19656 
    19657 > view /bc:27-32
    19658 
    19659 > view /be:27-32
    19660 
    19661 > select clear
    19662 
    19663 > view /bf:27-32
    19664 
    19665 > view /bg:27-32
    19666 
    19667 > view /bh:27-32
    19668 
    19669 > view /bi:27-32
    19670 
    19671 > select clear
    19672 
    19673 > view /bj:27-32
    19674 
    19675 > select clear
    19676 
    19677 > view /bk:27-32
    19678 
    19679 > select clear
    19680 
    19681 > view /bl:27-32
    19682 
    19683 > view /bl:27-32
    19684 
    19685 > view /bm:27-32
    19686 
    19687 > select clear
    19688 
    19689 > select clear
    19690 
    19691 > select clear
    19692 
    19693 > select clear
    19694 
    19695 > view /bn:27-32
    19696 
    19697 > select up
    19698 
    19699 16 atoms, 15 bonds, 1 residue, 1 model selected 
    19700 
    19701 > select up
    19702 
    19703 503 atoms, 512 bonds, 32 residues, 1 model selected 
    19704 
    19705 > select clear
    19706 
    19707 > select clear
    19708 
    19709 > view /bo:27-32
    19710 
    19711 > select up
    19712 
    19713 16 atoms, 15 bonds, 1 residue, 1 model selected 
    19714 
    19715 > select up
    19716 
    19717 503 atoms, 512 bonds, 32 residues, 1 model selected 
    19718 
    19719 > select clear
    19720 
    19721 > view /bp:27-32
    19722 
    19723 > select up
    19724 
    19725 16 atoms, 15 bonds, 1 residue, 1 model selected 
    19726 
    19727 > select up
    19728 
    19729 503 atoms, 512 bonds, 32 residues, 1 model selected 
    19730 
    19731 > select clear
    19732 
    19733 > select clear
    19734 
    19735 > view /bq:27-32
    19736 
    19737 No objects specified. 
    19738 
    19739 > save working.cxs
    19740 
    19741 Taking snapshot of stepper: Model 1a 
    19742 Restoring stepper: Model 1a 
    19743 opened ChimeraX session 
    19744 
    19745 > select :MAN
    19746 
    19747 40 atoms, 40 bonds, 2 residues, 1 model selected 
    19748 
    19749 > select clear
    19750 
    19751 > select :XYS
    19752 
    19753 36 atoms, 36 bonds, 2 residues, 1 model selected 
    19754 
    19755 > select :XYS
    19756 
    19757 36 atoms, 36 bonds, 2 residues, 1 model selected 
    19758 
    19759 > select clear
    19760 
    19761 > movie record
    19762 
    19763 > movie stop
    19764 
    19765 > movie reset
    19766 
    19767 > movie record
    19768 
    19769 > movie stop
    19770 
    19771 > movie encode glycan.mp4
    19772 
    19773 Movie saved to glycan.mp4 
    19774  
    19775 
    19776 > ui tool show "Change Substituents"
    19777 
    19778 > substitute sel substituents COCH3 guessAttachment true modify true minimize
    19779 > false
    19780 
    19781 > substitute sel substituents OH guessAttachment true modify true minimize
    19782 > false
    19783 
    19784 > substitute sel substituents COCH3 guessAttachment true modify true minimize
    19785 > false
    19786 
    19787 > select up
    19788 
    19789 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19790 
    19791 > setattr sel residues name XYX
    19792 
    19793 Assigning name attribute to 1 item 
    19794 
    19795 > show sel
    19796 
    19797 > setattr sel atoms name O2
    19798 
    19799 Assigning name attribute to 1 item 
    19800 
    19801 > select up
    19802 
    19803 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19804 
    19805 > show sel
    19806 
    19807 > select up
    19808 
    19809 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19810 
    19811 > show sel
    19812 
    19813 > open 3e80
    19814 
    19815 3e80 title: 
    19816 Structure of Heparinase II complexed with heparan sulfate degradation
    19817 disaccharide product [more info...] 
    19818  
    19819 Chain information for 3e80 #1 
    19820 --- 
    19821 Chain | Description 
    19822 A B C | Heparinase II protein 
    19823  
    19824 Non-standard residues in 3e80 #1 
    19825 --- 
    19826 GCD — 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid 
    19827 GCU — alpha-D-glucopyranuronic acid 
    19828 MAN — alpha-D-mannopyranose 
    19829 NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose 
    19830 PO4 — phosphate ion 
    19831 RAM — alpha-L-rhamnopyranose 
    19832 XYS — alpha-D-xylopyranose 
    19833 ZN — zinc ion 
    19834  
    19835 3e80 mmCIF Assemblies 
    19836 --- 
    19837 1| author_and_software_defined_assembly 
    19838 2| author_and_software_defined_assembly 
    19839 3| author_and_software_defined_assembly 
    19840  
    19841 
    19842 > select #1/A:RAM
    19843 
    19844 Nothing selected 
    19845 
    19846 > select #1/B:RAM
    19847 
    19848 Nothing selected 
    19849 
    19850 > select #1/C:RAM
    19851 
    19852 Nothing selected 
    19853 
    19854 > select #1/C:MAN
    19855 
    19856 Nothing selected 
    19857 
    19858 > select #1:MAN
    19859 
    19860 33 atoms, 33 bonds, 3 residues, 1 model selected 
    19861 
    19862 > select #1/F:MAN
    19863 
    19864 11 atoms, 11 bonds, 1 residue, 1 model selected 
    19865 
    19866 > align sel #8/M:MAN&~H
    19867 
    19868 Expected a keyword 
    19869 
    19870 > align sel toAtoms #8/M:MAN&~H
    19871 
    19872 RMSD between 11 atom pairs is 0.195 angstroms 
    19873 
    19874 > close #1
    19875 
    19876 > open 2fuq
    19877 
    19878 2fuq title: 
    19879 Crystal Structure of Heparinase II [more info...] 
    19880  
    19881 Chain information for 2fuq #1 
    19882 --- 
    19883 Chain | Description 
    19884 A B | heparinase II protein 
    19885  
    19886 Non-standard residues in 2fuq #1 
    19887 --- 
    19888 FMT — formic acid 
    19889 GCU — alpha-D-glucopyranuronic acid 
    19890 MAN — alpha-D-mannopyranose 
    19891 PO4 — phosphate ion 
    19892 RAM — alpha-L-rhamnopyranose 
    19893 XYS — alpha-D-xylopyranose 
    19894 ZN — zinc ion 
    19895  
    19896 
    19897 > select #1/C:MAN
    19898 
    19899 11 atoms, 11 bonds, 1 residue, 1 model selected 
    19900 
    19901 > align sel toAtoms #8/M:MAN&~H
    19902 
    19903 RMSD between 11 atom pairs is 0.151 angstroms 
    19904 
    19905 > hide #!8 models
    19906 
    19907 > show #1
    19908 
    19909 > hide #1&protein
    19910 
    19911 > delete #1&:HOH
    19912 
    19913 > show #!8 models
    19914 
    19915 > hide #!1 models
    19916 
    19917 > select up
    19918 
    19919 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19920 
    19921 > select clear
    19922 
    19923 > ui mousemode right "translate selected atoms"
    19924 
    19925 > setattr sel atoms name C2A
    19926 
    19927 Assigning name attribute to 1 item 
    19928 
    19929 > select clear
    19930 
    19931 > setattr sel atoms name O2A
    19932 
    19933 Assigning name attribute to 1 item 
    19934 
    19935 > setattr sel atoms name C2B
    19936 
    19937 Assigning name attribute to 1 item 
    19938 
    19939 > setattr sel atoms name H2B1
    19940 
    19941 Assigning name attribute to 1 item 
    19942 
    19943 > setattr sel atoms name H2B2
    19944 
    19945 Assigning name attribute to 1 item 
    19946 
    19947 > setattr sel atoms name H2B3
    19948 
    19949 Assigning name attribute to 1 item 
    19950 
    19951 > select :XYS
    19952 
    19953 34 atoms, 34 bonds, 3 residues, 2 models selected 
    19954 
    19955 > select #8:XYS
    19956 
    19957 18 atoms, 18 bonds, 1 residue, 1 model selected 
    19958 
    19959 > view sel
    19960 
    19961 > ui tool show "Change Substituents"
    19962 
    19963 > substitute sel substituents COCH3 newName XYX guessAttachment true modify
    19964 > true minimize false
    19965 
    19966 > select clear
    19967 
    19968 > setattr sel atoms name C2A
    19969 
    19970 Assigning name attribute to 1 item 
    19971 
    19972 > select up
    19973 
    19974 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19975 
    19976 > show sel
    19977 
    19978 > setattr sel atoms name O2A
    19979 
    19980 Assigning name attribute to 1 item 
    19981 
    19982 > setattr sel atoms name C2B
    19983 
    19984 Assigning name attribute to 1 item 
    19985 
    19986 > setattr sel atoms name H2B1
    19987 
    19988 Assigning name attribute to 1 item 
    19989 
    19990 > setattr sel atoms name H2B2
    19991 
    19992 Assigning name attribute to 1 item 
    19993 
    19994 > setattr sel atoms name H2B3
    19995 
    19996 Assigning name attribute to 1 item 
    19997 
    19998 > select clear
    19999 
    20000 > save working.cxs
    20001 
    20002 Taking snapshot of stepper: Model 1a 
    20003 
    20004 > select clear
    20005 
    20006 > select ~H
    20007 
    20008 67529 atoms, 128381 bonds, 21 pseudobonds, 7075 residues, 25 models selected 
    20009 
    20010 > save model1a_working_noh.cif #8 selectedOnly true
    20011 
    20012 Not saving entity_poly_seq for non-authoritative sequences 
    20013 
    20014 > select clear
    20015 
    20016 > isolde add ligand NDG
    20017 
    20018 Deleted the following atoms from residue NDG M1175: HO1, O1 
    20019 
    20020 > ui mousemode right "translate selected atoms"
    20021 
    20022 > show sel
    20023 
    20024 > isolde add ligand A2G
    20025 
    20026 Deleted the following atoms from residue A2G M1176: HO1, O1 
    20027 
    20028 > ui mousemode right "translate selected atoms"
    20029 
    20030 > show sel
    20031 
    20032 > delete sel
    20033 
    20034 > select up
    20035 
    20036 23 atoms, 23 bonds, 1 residue, 1 model selected 
    20037 
    20038 > delete sel
    20039 
    20040 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    20041 bonded heavy atom. 
    20042 
    20043 > select clear
    20044 
    20045 > view :XYX
    20046 
    20047 > select up
    20048 
    20049 23 atoms, 23 bonds, 1 residue, 1 model selected 
    20050 
    20051 > delete sel
    20052 
    20053 > isolde add ligand NDG
    20054 
    20055 Deleted the following atoms from residue NDG C1155: HO1, O1 
    20056 
    20057 > show sel
    20058 
    20059 > ui mousemode right "translate selected atoms"
    20060 
    20061 > view /M:NDG
    20062 
    20063 > select ~H
    20064 
    20065 67533 atoms, 128391 bonds, 21 pseudobonds, 7075 residues, 25 models selected 
    20066 
    20067 > save model1a_working_noh.cif #8 selectedOnly true
    20068 
    20069 Not saving entity_poly_seq for non-authoritative sequences 
    20070 
    20071 > select clear
    20072 
    20073 > save working.cxs
    20074 
    20075 Taking snapshot of stepper: Model 1a 
    20076 opened ChimeraX session 
    20077 
    20078 > close #1
    20079 
    20080 > isolde start
    20081 
    20082 > set selectionWidth 4
    20083 
    20084 Done loading forcefield 
    20085 
    20086 > select ~protein&~:HOH
    20087 
    20088 34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected 
    20089 
    20090 > select clear
    20091 
    20092 > st first
    20093 
    20094 > st
    20095 
    20096 > select clear
    20097 
    20098 > st
    20099 
    20100 > st interp 5
    20101 
    20102 > st interp 5
    20103 
    20104 > st
    20105 
    20106 > st
    20107 
    20108 > st
    20109 
    20110 > st
    20111 
    20112 > delete sel
    20113 
    20114 > aw
    20115 
    20116 > isolde sim start sel
    20117 
    20118 > st
    20119 
    20120 > st
    20121 
    20122 > st
    20123 
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    20229 
    20230 > st
    20231 
    20232 > isolde jumpto
    20233 
    20234 > isolde jumpto
    20235 
    20236 > isolde jumpto
    20237 
    20238 > isolde jumpto
    20239 
    20240 > isolde jumpto
    20241 
    20242 > isolde jumpto
    20243 
    20244 > isolde jumpto
    20245 
    20246 > isolde jumpto
    20247 
    20248 > isolde jumpto
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    20250 > isolde jumpto
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    20252 > isolde jumpto
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    20254 > isolde jumpto
    20255 
    20256 > isolde jumpto
    20257 
    20258 > isolde jumpto
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    20260 > isolde jumpto
    20261 
    20262 > isolde jumpto
    20263 
    20264 > isolde jumpto
    20265 
    20266 > isolde jumpto
    20267 
    20268 > isolde jumpto
    20269 
    20270 > isolde jumpto
    20271 
    20272 > isolde jumpto
    20273 
    20274 > isolde jumpto
    20275 
    20276 > isolde jumpto
    20277 
    20278 > isolde jumpto
    20279 
    20280 > isolde jumpto
    20281 
    20282 > isolde jumpto
    20283 
    20284 > isolde jumpto
    20285 
    20286 > isolde jumpto
    20287 
    20288 > isolde jumpto
    20289 
    20290 > isolde jumpto
    20291 
    20292 > isolde jumpto
    20293 
    20294 > isolde jumpto
    20295 
    20296 > isolde jumpto
    20297 
    20298 > isolde jumpto
    20299 
    20300 > isolde jumpto
    20301 
    20302 > isolde jumpto
    20303 
    20304 > isolde jumpto
    20305 
    20306 > isolde jumpto
    20307 
    20308 > isolde jumpto
    20309 
    20310 > isolde jumpto
    20311 
    20312 > isolde jumpto
    20313 
    20314 > isolde jumpto
    20315 
    20316 > isolde jumpto
    20317 
    20318 > isolde jumpto
    20319 
    20320 > isolde jumpto
    20321 
    20322 > isolde jumpto
    20323 
    20324 > isolde jumpto
    20325 
    20326 > st
    20327 
    20328 > st
    20329 
    20330 > st
    20331 
    20332 > st
    20333 
    20334 > st
    20335 
    20336 > awsf
    20337 
    20338 > awsf
    20339 
    20340 > awsf
    20341 
    20342 > awsf
    20343 
    20344 > aw
    20345 
    20346 > isolde sim start sel
    20347 
    20348 > aw
    20349 
    20350 > isolde sim start sel
    20351 
    20352 > st
    20353 
    20354 > st
    20355 
    20356 > st
    20357 
    20358 > st
    20359 
    20360 > aw
    20361 
    20362 > isolde sim start sel
    20363 
    20364 > aw
    20365 
    20366 > isolde sim start sel
    20367 
    20368 > aw
    20369 
    20370 > isolde sim start sel
    20371 
    20372 > st
    20373 
    20374 > st
    20375 
    20376 > st
    20377 
    20378 > st
    20379 
    20380 > st
    20381 
    20382 > st
    20383 
    20384 > st
    20385 
    20386 > st
    20387 
    20388 > aw
    20389 
    20390 > isolde sim start sel
    20391 
    20392 > st
    20393 
    20394 > awsf
    20395 
    20396 > awsf
    20397 
    20398 > awsf
    20399 
    20400 > awsf
    20401 
    20402 > awsf
    20403 
    20404 > awsf
    20405 
    20406 > awsf
    20407 
    20408 > awsf
    20409 
    20410 > st
    20411 
    20412 > aw
    20413 
    20414 > isolde sim start sel
    20415 
    20416 > st
    20417 
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    20419 
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    20421 
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    20424 > st
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    20428 > st
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    20432 > st
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    20434 > st
    20435 
    20436 > st
    20437 
    20438 > st
    20439 
    20440 > st
    20441 
    20442 > st
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    20445 
    20446 > st
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    20448 > st
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    20453 
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    20459 
    20460 > st
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    20462 > st
    20463 
    20464 > st
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    20466 > st
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    20468 > st
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    20470 > st
    20471 
    20472 > st
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    20474 > st
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    20476 > st
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    20478 > st
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    20480 > st
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    20496 > st
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    20498 > st
    20499 
    20500 > st
    20501 
    20502 > st
    20503 
    20504 > st
    20505 
    20506 > st
    20507 
    20508 > select clear
    20509 
    20510 > st
    20511 
    20512 > st
    20513 
    20514 > st
    20515 
    20516 > st
    20517 
    20518 > st
    20519 
    20520 > st
    20521 
    20522 > st
    20523 
    20524 > select clear
    20525 
    20526 > st
    20527 
    20528 > st
    20529 
    20530 > st
    20531 
    20532 > st
    20533 
    20534 > st
    20535 
    20536 > st
    20537 
    20538 > st
    20539 
    20540 > st
    20541 
    20542 > select clear
    20543 
    20544 > st
    20545 
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    20547 
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    20550 > st
    20551 
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    20571 
    20572 > st
    20573 
    20574 > st
    20575 
    20576 > st
    20577 
    20578 > st
    20579 
    20580 > select clear
    20581 
    20582 > st
    20583 
    20584 > st
    20585 
    20586 > st
    20587 
    20588 > st
    20589 
    20590 > st
    20591 
    20592 > st
    20593 
    20594 > select clear
    20595 
    20596 > st
    20597 
    20598 > st
    20599 
    20600 > st
    20601 
    20602 > st
    20603 
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    20619 
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    20621 
    20622 > st
    20623 
    20624 > st
    20625 
    20626 > st
    20627 
    20628 > aw
    20629 
    20630 > isolde sim start sel
    20631 
    20632 > st
    20633 
    20634 > st
    20635 
    20636 > st
    20637 
    20638 > st
    20639 
    20640 > st
    20641 
    20642 > st
    20643 
    20644 > st
    20645 
    20646 > st
    20647 
    20648 > st
    20649 
    20650 > st
    20651 
    20652 > awsf
    20653 
    20654 > select clear
    20655 
    20656 > select clear
    20657 
    20658 > st
    20659 
    20660 > st
    20661 
    20662 > st
    20663 
    20664 > st
    20665 
    20666 > st
    20667 
    20668 > st
    20669 
    20670 > st
    20671 
    20672 > st
    20673 
    20674 > aw
    20675 
    20676 > isolde sim start sel
    20677 
    20678 > aw
    20679 
    20680 > isolde sim start sel
    20681 
    20682 > st
    20683 
    20684 > st
    20685 
    20686 > st
    20687 
    20688 > st
    20689 
    20690 > st
    20691 
    20692 > st
    20693 
    20694 > st
    20695 
    20696 > awsf
    20697 
    20698 > awsf
    20699 
    20700 > st
    20701 
    20702 > st
    20703 
    20704 > st
    20705 
    20706 > aw
    20707 
    20708 > isolde sim start sel
    20709 
    20710 > select up
    20711 
    20712 3 atoms, 2 bonds, 1 residue, 1 model selected 
    20713 
    20714 > delete sel
    20715 
    20716 > st
    20717 
    20718 > awsf
    20719 
    20720 > awsf
    20721 
    20722 > awsf
    20723 
    20724 > select up
    20725 
    20726 6 atoms, 4 bonds, 2 residues, 1 model selected 
    20727 
    20728 > delete sel
    20729 
    20730 > st
    20731 
    20732 > awsf
    20733 
    20734 > awsf
    20735 
    20736 > st
    20737 
    20738 > st
    20739 
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    20751 
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    20753 
    20754 > st
    20755 
    20756 > st
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    20758 > st
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    20763 
    20764 > st
    20765 
    20766 > st
    20767 
    20768 > st
    20769 
    20770 > st
    20771 
    20772 > awsf
    20773 
    20774 > awsf
    20775 
    20776 > select up
    20777 
    20778 3 atoms, 2 bonds, 1 residue, 1 model selected 
    20779 
    20780 > delete sel
    20781 
    20782 > st
    20783 
    20784 > st
    20785 
    20786 > st
    20787 
    20788 > st
    20789 
    20790 > st
    20791 
    20792 > st
    20793 
    20794 > st
    20795 
    20796 > st
    20797 
    20798 > st
    20799 
    20800 > aw
    20801 
    20802 > isolde sim start sel
    20803 
    20804 > st
    20805 
    20806 > st
    20807 
    20808 > st
    20809 
    20810 > aw
    20811 
    20812 > isolde sim start sel
    20813 
    20814 > st
    20815 
    20816 > st
    20817 
    20818 > st
    20819 
    20820 > st
    20821 
    20822 > aw
    20823 
    20824 > isolde sim start sel
    20825 
    20826 > select up
    20827 
    20828 3 atoms, 2 bonds, 1 residue, 1 model selected 
    20829 
    20830 > delete sel
    20831 
    20832 > st
    20833 
    20834 > aw
    20835 
    20836 > isolde sim start sel
    20837 
    20838 > st
    20839 
    20840 > st
    20841 
    20842 > st
    20843 
    20844 > st
    20845 
    20846 > st
    20847 
    20848 > st
    20849 
    20850 > aw
    20851 
    20852 > isolde sim start sel
    20853 
    20854 > st
    20855 
    20856 > aw
    20857 
    20858 > isolde sim start sel
    20859 
    20860 > select up
    20861 
    20862 3 atoms, 2 bonds, 1 residue, 1 model selected 
    20863 
    20864 > delete sel
    20865 
    20866 > st
    20867 
    20868 > st
    20869 
    20870 > st
    20871 
    20872 > st
    20873 
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    20875 
    20876 > st
    20877 
    20878 > st
    20879 
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    20881 
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    20883 
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    20887 
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    20889 
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    20891 
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    20893 
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    20897 
    20898 > st
    20899 
    20900 > aw
    20901 
    20902 > isolde sim start sel
    20903 
    20904 > aw
    20905 
    20906 > isolde sim start sel
    20907 
    20908 > st
    20909 
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    20911 
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    20913 
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    20931 
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    20933 
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    20935 
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    20937 
    20938 > st
    20939 
    20940 > select clear
    20941 
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    20943 
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    20947 
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    20951 
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    20953 
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    20959 
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    20989 
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    20991 
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    20993 
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    20998 > st
    20999 
    21000 > st
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    21099 
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    21103 
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    21106 > st
    21107 
    21108 > st
    21109 
    21110 > st
    21111 
    21112 > aw
    21113 
    21114 > isolde sim start sel
    21115 
    21116 > st
    21117 
    21118 > st
    21119 
    21120 > st
    21121 
    21122 > st
    21123 
    21124 > st
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    21145 
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    21147 
    21148 > aw
    21149 
    21150 > isolde sim start sel
    21151 
    21152 > st
    21153 
    21154 > aw
    21155 
    21156 > isolde sim start sel
    21157 
    21158 > aw
    21159 
    21160 > isolde sim start sel
    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 > select clear
    21183 
    21184 > aw
    21185 
    21186 > isolde sim start sel
    21187 
    21188 > st
    21189 
    21190 > st
    21191 
    21192 > st
    21193 
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    21199 
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    21241 
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    21245 
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    21247 
    21248 > aw
    21249 
    21250 > isolde sim start sel
    21251 
    21252 > st
    21253 
    21254 > aw
    21255 
    21256 > isolde sim start sel
    21257 
    21258 > st
    21259 
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    21263 
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    21285 
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    21287 
    21288 > aw
    21289 
    21290 > isolde sim start sel
    21291 
    21292 > st
    21293 
    21294 > awsf
    21295 
    21296 > st
    21297 
    21298 > st
    21299 
    21300 > aw
    21301 
    21302 > isolde sim start sel
    21303 
    21304 > awsf
    21305 
    21306 > awsf
    21307 
    21308 > select clear
    21309 
    21310 > st
    21311 
    21312 > st
    21313 
    21314 > st
    21315 
    21316 > st
    21317 
    21318 > st
    21319 
    21320 > aw
    21321 
    21322 > isolde sim start sel
    21323 
    21324 > st
    21325 
    21326 > st
    21327 
    21328 > st
    21329 
    21330 > st
    21331 
    21332 > st
    21333 
    21334 > st
    21335 
    21336 > select clear
    21337 
    21338 > st
    21339 
    21340 > st
    21341 
    21342 > st
    21343 
    21344 > st
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    21367 
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    21387 
    21388 > st
    21389 
    21390 > st
    21391 
    21392 > st
    21393 
    21394 > st
    21395 
    21396 > select clear
    21397 
    21398 > st
    21399 
    21400 > st
    21401 
    21402 > aw
    21403 
    21404 > isolde sim start sel
    21405 
    21406 > st
    21407 
    21408 > st
    21409 
    21410 > st
    21411 
    21412 > st
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    21414 > st
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    21427 
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    21440 > st
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    21445 
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    21447 
    21448 > st
    21449 
    21450 > st
    21451 
    21452 > aw
    21453 
    21454 > isolde sim start sel
    21455 
    21456 > st
    21457 
    21458 > st
    21459 
    21460 > st
    21461 
    21462 > st
    21463 
    21464 > st
    21465 
    21466 > aw
    21467 
    21468 > isolde sim start sel
    21469 
    21470 > st
    21471 
    21472 > st
    21473 
    21474 > st
    21475 
    21476 > st
    21477 
    21478 > st
    21479 
    21480 > st
    21481 
    21482 > st
    21483 
    21484 > st
    21485 
    21486 > st
    21487 
    21488 > st
    21489 
    21490 > st
    21491 
    21492 > st
    21493 
    21494 > st
    21495 
    21496 > st
    21497 
    21498 > st
    21499 
    21500 > st
    21501 
    21502 > st
    21503 
    21504 > st
    21505 
    21506 > st
    21507 
    21508 > st
    21509 
    21510 > st
    21511 
    21512 > aw
    21513 
    21514 > isolde sim start 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 > awsf
    21543 
    21544 > awsf
    21545 
    21546 > st
    21547 
    21548 > st
    21549 
    21550 > st
    21551 
    21552 > st
    21553 
    21554 > st
    21555 
    21556 > aw
    21557 
    21558 > isolde sim start sel
    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 > st
    21591 
    21592 > st
    21593 
    21594 > st
    21595 
    21596 > st
    21597 
    21598 > st
    21599 
    21600 > st
    21601 
    21602 > aw
    21603 
    21604 > isolde sim start sel
    21605 
    21606 > st
    21607 
    21608 > st
    21609 
    21610 > st
    21611 
    21612 > st
    21613 
    21614 > st
    21615 
    21616 > st
    21617 
    21618 > select clear
    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 
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    21639 
    21640 > st
    21641 
    21642 > st
    21643 
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    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 > select clear
    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 > aw
    21697 
    21698 > isolde sim start sel
    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 > select clear
    21761 
    21762 > st
    21763 
    21764 > st
    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 > st
    21799 
    21800 > st
    21801 
    21802 > st
    21803 
    21804 > st
    21805 
    21806 > st
    21807 
    21808 > st
    21809 
    21810 > st
    21811 
    21812 > st
    21813 
    21814 > st
    21815 
    21816 > st
    21817 
    21818 > st
    21819 
    21820 > st
    21821 
    21822 > st
    21823 
    21824 > st
    21825 
    21826 > st
    21827 
    21828 > st
    21829 
    21830 > st
    21831 
    21832 > st
    21833 
    21834 > st
    21835 
    21836 > st
    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 > aw
    21879 
    21880 > isolde sim start sel
    21881 
    21882 > aw
    21883 
    21884 > isolde sim start sel
    21885 
    21886 > st
    21887 
    21888 > st
    21889 
    21890 > st
    21891 
    21892 > st
    21893 
    21894 > st
    21895 
    21896 > awsf
    21897 
    21898 > awsf
    21899 
    21900 > st
    21901 
    21902 > st
    21903 
    21904 > st
    21905 
    21906 > aw
    21907 
    21908 > isolde sim start sel
    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 > aw
    21929 
    21930 > isolde sim start sel
    21931 
    21932 > st
    21933 
    21934 > st
    21935 
    21936 > st
    21937 
    21938 > st
    21939 
    21940 > aw
    21941 
    21942 > isolde sim start sel
    21943 
    21944 > st
    21945 
    21946 > st
    21947 
    21948 > st
    21949 
    21950 > st
    21951 
    21952 > st
    21953 
    21954 > st
    21955 
    21956 > st
    21957 
    21958 > st
    21959 
    21960 > st
    21961 
    21962 > st
    21963 
    21964 > st
    21965 
    21966 > st
    21967 
    21968 > st
    21969 
    21970 > st
    21971 
    21972 > st
    21973 
    21974 > st
    21975 
    21976 > st
    21977 
    21978 > st
    21979 
    21980 > st
    21981 
    21982 > st
    21983 
    21984 > st
    21985 
    21986 > st
    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 > awsf
    22015 
    22016 > select clear
    22017 
    22018 > st
    22019 
    22020 > st
    22021 
    22022 > st
    22023 
    22024 > st
    22025 
    22026 > st
    22027 
    22028 > st
    22029 
    22030 > aw
    22031 
    22032 > isolde sim start sel
    22033 
    22034 > st
    22035 
    22036 > st
    22037 
    22038 > st
    22039 
    22040 > st
    22041 
    22042 > st
    22043 
    22044 > st
    22045 
    22046 > st
    22047 
    22048 > st
    22049 
    22050 > st
    22051 
    22052 > st
    22053 
    22054 > aw
    22055 
    22056 > isolde sim start sel
    22057 
    22058 > aw
    22059 
    22060 > isolde sim start sel
    22061 
    22062 > st
    22063 
    22064 > select clear
    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 > st
    22103 
    22104 > st
    22105 
    22106 > st
    22107 
    22108 > st
    22109 
    22110 > st
    22111 
    22112 > st
    22113 
    22114 > st
    22115 
    22116 > st
    22117 
    22118 > st
    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 > st
    22163 
    22164 > st
    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 > st
    22193 
    22194 > st
    22195 
    22196 > st
    22197 
    22198 > st
    22199 
    22200 > st
    22201 
    22202 > st
    22203 
    22204 > st
    22205 
    22206 > st
    22207 
    22208 > st
    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 > st
    22253 
    22254 > st
    22255 
    22256 > st
    22257 
    22258 > st
    22259 
    22260 > st
    22261 
    22262 > st
    22263 
    22264 > st
    22265 
    22266 > st
    22267 
    22268 > st
    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 > select clear
    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 > st
    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 > st
    22347 
    22348 > st
    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 > st
    22411 
    22412 > st
    22413 
    22414 > st
    22415 
    22416 > st
    22417 
    22418 > st
    22419 
    22420 > aw
    22421 
    22422 > isolde sim start sel
    22423 
    22424 > select up
    22425 
    22426 3 atoms, 2 bonds, 1 residue, 1 model selected 
    22427 
    22428 > delete sel
    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 > select up
    22469 
    22470 215 atoms, 216 bonds, 12 residues, 1 model selected 
    22471 
    22472 > select clear
    22473 
    22474 > st
    22475 
    22476 > st
    22477 
    22478 > st
    22479 
    22480 > st
    22481 
    22482 > st
    22483 
    22484 > st
    22485 
    22486 > st
    22487 
    22488 > select clear
    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 > st
    22529 
    22530 > st
    22531 
    22532 > st
    22533 
    22534 > st
    22535 
    22536 > st
    22537 
    22538 > st
    22539 
    22540 > st
    22541 
    22542 > st
    22543 
    22544 > st
    22545 
    22546 > st
    22547 
    22548 > st
    22549 
    22550 > st
    22551 
    22552 > st
    22553 
    22554 > st
    22555 
    22556 > st
    22557 
    22558 > st
    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 > st
    22579 
    22580 > st
    22581 
    22582 > st
    22583 
    22584 > st
    22585 
    22586 > st
    22587 
    22588 > st
    22589 
    22590 > st
    22591 
    22592 > st
    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 > select clear
    22665 
    22666 > st
    22667 
    22668 > st
    22669 
    22670 > st
    22671 
    22672 > st
    22673 
    22674 > st
    22675 
    22676 > st
    22677 
    22678 > st
    22679 
    22680 > st
    22681 
    22682 > st
    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 > st
    22705 
    22706 > st
    22707 
    22708 > st
    22709 
    22710 > st
    22711 
    22712 > st
    22713 
    22714 > st
    22715 
    22716 > st
    22717 
    22718 > st
    22719 
    22720 > st
    22721 
    22722 > st
    22723 
    22724 > select clear
    22725 
    22726 > st
    22727 
    22728 > st
    22729 
    22730 > st
    22731 
    22732 > st
    22733 
    22734 > st
    22735 
    22736 > select clear
    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 > aw
    22835 
    22836 > isolde sim start sel
    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 > select clear
    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 > select clear
    22921 
    22922 > st
    22923 
    22924 > st
    22925 
    22926 > st
    22927 
    22928 > st
    22929 
    22930 > st
    22931 
    22932 > aw
    22933 
    22934 > isolde sim start sel
    22935 
    22936 > staw
    22937 
    22938 Unknown command: staw 
    22939 
    22940 > aw
    22941 
    22942 > isolde sim start sel
    22943 
    22944 > st
    22945 
    22946 > st
    22947 
    22948 > aw
    22949 
    22950 > isolde sim start sel
    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 > select clear
    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 > st
    23071 
    23072 > st
    23073 
    23074 > st
    23075 
    23076 > st
    23077 
    23078 > st
    23079 
    23080 > st
    23081 
    23082 > st
    23083 
    23084 > st
    23085 
    23086 > st
    23087 
    23088 > awsf
    23089 
    23090 > awsf
    23091 
    23092 > select clear
    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 > select clear
    23113 
    23114 > st
    23115 
    23116 > st
    23117 
    23118 > st
    23119 
    23120 > st
    23121 
    23122 > st
    23123 
    23124 > st
    23125 
    23126 > st
    23127 
    23128 > st
    23129 
    23130 > aw
    23131 
    23132 > isolde sim start sel
    23133 
    23134 > st
    23135 
    23136 > st
    23137 
    23138 > st
    23139 
    23140 > st
    23141 
    23142 > st
    23143 
    23144 > aw
    23145 
    23146 > isolde sim start sel
    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 > select clear
    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 > select clear
    23241 
    23242 > st
    23243 
    23244 > st
    23245 
    23246 > aw
    23247 
    23248 > isolde sim start sel
    23249 
    23250 > st
    23251 
    23252 > st
    23253 
    23254 > st
    23255 
    23256 > st
    23257 
    23258 > st
    23259 
    23260 > st
    23261 
    23262 > aw
    23263 
    23264 > isolde sim start sel
    23265 
    23266 > st
    23267 
    23268 > st
    23269 
    23270 > st
    23271 
    23272 > st
    23273 
    23274 > aw
    23275 
    23276 > isolde sim start sel
    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 > st
    23315 
    23316 > st
    23317 
    23318 > st
    23319 
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    23368 > select clear
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    23378 > isolde sim start sel
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    23522 > select clear
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    23566 > select clear
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    23658 > awsf
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    23689 
    23690 > save working.cxs
    23691 
    23692 Taking snapshot of stepper: Model 1a 
    23693 opened ChimeraX session 
    23694 
    23695 > isolde start
    23696 
    23697 > set selectionWidth 4
    23698 
    23699 Done loading forcefield 
    23700 
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    23789 > awsf
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    23791 > awsf
    23792 
    23793 > select clear
    23794 
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    23801 > isolde sim start sel
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    23813 > awsf
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    23815 > awsf
    23816 
    23817 > select clear
    23818 
    23819 > st
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    23853 > select clear
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    23867 > aw
    23868 
    23869 No existing atoms found within the given distance cutoff of the target
    23870 position. You may repeat with a larger cutoff or explicitly specify the
    23871 B-factor and chain ID, but keep in mind that placing waters outside of
    23872 H-bonding distance to the model is generally inadvisable. 
    23873 
    23874 > st
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    23880 > isolde sim start sel
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    23893 
    23894 > select clear
    23895 
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    23936 > select clear
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    23946 > awsf
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    23948 > awsf
    23949 
    23950 > select clear
    23951 
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    23960 > isolde sim start sel
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    24026 > isolde sim start sel
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    24034 > select clear
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    24078 > st
    24079 
    24080 > select clear
    24081 
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    24086 > st
    24087 
    24088 > select clear
    24089 
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    24094 > aw
    24095 
    24096 > isolde sim start sel
    24097 
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    24106 > isolde sim start sel
    24107 
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    24120 > aw
    24121 
    24122 > isolde sim start sel
    24123 
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    24127 
    24128 > select clear
    24129 
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    24135 
    24136 > isolde sim start sel
    24137 
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    24166 > st
    24167 
    24168 > select clear
    24169 
    24170 > st
    24171 
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    24173 
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    24175 
    24176 > st
    24177 
    24178 > st
    24179 
    24180 > select clear
    24181 
    24182 > st
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    24226 > aw
    24227 
    24228 > isolde sim start sel
    24229 
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    24233 
    24234 > aw
    24235 
    24236 > isolde sim start sel
    24237 
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    24239 
    24240 > aw
    24241 
    24242 > isolde sim start sel
    24243 
    24244 > st
    24245 
    24246 > st
    24247 
    24248 > select clear
    24249 
    24250 > st
    24251 
    24252 > st
    24253 
    24254 > st
    24255 
    24256 > awsf
    24257 
    24258 > awsf
    24259 
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    24270 > aw
    24271 
    24272 > isolde sim start sel
    24273 
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    24299 
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    24377 
    24378 > isolde sim start sel
    24379 
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    24399 
    24400 > st
    24401 
    24402 > st
    24403 
    24404 > select clear
    24405 
    24406 > st
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    24445 
    24446 > st
    24447 
    24448 > st
    24449 
    24450 > select clear
    24451 
    24452 > st
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    24460 > st
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    24492 > aw
    24493 
    24494 > isolde sim start sel
    24495 
    24496 > st
    24497 
    24498 > aw
    24499 
    24500 > isolde sim start sel
    24501 
    24502 > st
    24503 
    24504 > st
    24505 
    24506 > st
    24507 
    24508 > select clear
    24509 
    24510 > aw
    24511 
    24512 > isolde sim start sel
    24513 
    24514 > st
    24515 
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    24528 > aw
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    24530 > isolde sim start sel
    24531 
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    24535 
    24536 > aw
    24537 
    24538 > isolde sim start sel
    24539 
    24540 > st
    24541 
    24542 > st
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    24545 
    24546 > isolde sim start sel
    24547 
    24548 > st
    24549 
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    24551 
    24552 > select clear
    24553 
    24554 > select clear
    24555 
    24556 > st
    24557 
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    24559 
    24560 > st
    24561 
    24562 > st
    24563 
    24564 > select clear
    24565 
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    24653 
    24654 > isolde sim start sel
    24655 
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    24672 > isolde sim start sel
    24673 
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    24679 
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    24685 
    24686 > isolde sim start sel
    24687 
    24688 > aw
    24689 
    24690 > isolde sim start sel
    24691 
    24692 > st
    24693 
    24694 > st
    24695 
    24696 > select clear
    24697 
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    24699 
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    24707 
    24708 > isolde sim start sel
    24709 
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    24730 > isolde sim start sel
    24731 
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    24815 
    24816 > select clear
    24817 
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    24821 
    24822 > aw
    24823 
    24824 > isolde sim start sel
    24825 
    24826 > st
    24827 
    24828 > select clear
    24829 
    24830 > st
    24831 
    24832 > st
    24833 
    24834 > select clear
    24835 
    24836 > select clear
    24837 
    24838 > aw
    24839 
    24840 > isolde sim start sel
    24841 
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    24848 > aw
    24849 
    24850 > isolde sim start sel
    24851 
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    24863 
    24864 > isolde sim start sel
    24865 
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    24873 
    24874 > isolde sim start sel
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    24905 
    24906 > select clear
    24907 
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    24927 
    24928 > select clear
    24929 
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    24951 
    24952 > select clear
    24953 
    24954 > st
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    24964 > aw
    24965 
    24966 > isolde sim start sel
    24967 
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    24969 
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    24971 
    24972 > aw
    24973 
    24974 > isolde sim start sel
    24975 
    24976 > aw
    24977 
    24978 > isolde sim start sel
    24979 
    24980 > select up
    24981 
    24982 3 atoms, 2 bonds, 1 residue, 1 model selected 
    24983 
    24984 > delete sel
    24985 
    24986 > st
    24987 
    24988 > st
    24989 
    24990 > st
    24991 
    24992 > st
    24993 
    24994 > awsf
    24995 
    24996 > awsf
    24997 
    24998 > st
    24999 
    25000 > st
    25001 
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    25003 
    25004 > st
    25005 
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    25008 > st
    25009 
    25010 > st
    25011 
    25012 > st
    25013 
    25014 > aw
    25015 
    25016 > isolde sim start sel
    25017 
    25018 > st
    25019 
    25020 > st
    25021 
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    25023 
    25024 > st
    25025 
    25026 > st
    25027 
    25028 > select clear
    25029 
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    25035 
    25036 > select clear
    25037 
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    25065 
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    25067 
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    25069 
    25070 > st
    25071 
    25072 > st
    25073 
    25074 > select clear
    25075 
    25076 > st
    25077 
    25078 > st
    25079 
    25080 > st
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    25082 > st
    25083 
    25084 > st
    25085 
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    25087 
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    25089 
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    25098 > st
    25099 
    25100 > st
    25101 
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    25103 
    25104 > st
    25105 
    25106 > st
    25107 
    25108 > st
    25109 
    25110 > st
    25111 
    25112 > st
    25113 
    25114 > st
    25115 
    25116 > aw
    25117 
    25118 No existing atoms found within the given distance cutoff of the target
    25119 position. You may repeat with a larger cutoff or explicitly specify the
    25120 B-factor and chain ID, but keep in mind that placing waters outside of
    25121 H-bonding distance to the model is generally inadvisable. 
    25122 
    25123 > awst
    25124 
    25125 Unknown command: awst 
    25126 
    25127 > st
    25128 
    25129 > st
    25130 
    25131 > st
    25132 
    25133 > awsf
    25134 
    25135 No existing atoms found within the given distance cutoff of the target
    25136 position. You may repeat with a larger cutoff or explicitly specify the
    25137 B-factor and chain ID, but keep in mind that placing waters outside of
    25138 H-bonding distance to the model is generally inadvisable. 
    25139 
    25140 > awsf
    25141 
    25142 No existing atoms found within the given distance cutoff of the target
    25143 position. You may repeat with a larger cutoff or explicitly specify the
    25144 B-factor and chain ID, but keep in mind that placing waters outside of
    25145 H-bonding distance to the model is generally inadvisable. 
    25146 
    25147 > awsf
    25148 
    25149 > awsf
    25150 
    25151 > st
    25152 
    25153 > st
    25154 
    25155 > select clear
    25156 
    25157 > st
    25158 
    25159 > awsf
    25160 
    25161 > awsf
    25162 
    25163 > st
    25164 
    25165 > st
    25166 
    25167 > select clear
    25168 
    25169 > st
    25170 
    25171 > st
    25172 
    25173 > select clear
    25174 
    25175 > st
    25176 
    25177 > aw
    25178 
    25179 > isolde sim start sel
    25180 
    25181 > aw
    25182 
    25183 > isolde sim start sel
    25184 
    25185 > aw
    25186 
    25187 > isolde sim start sel
    25188 
    25189 > st
    25190 
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    25192 
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    25194 
    25195 > st
    25196 
    25197 > st
    25198 
    25199 > st
    25200 
    25201 > st
    25202 
    25203 > select clear
    25204 
    25205 > st
    25206 
    25207 > st
    25208 
    25209 > st
    25210 
    25211 > aw
    25212 
    25213 > isolde sim start sel
    25214 
    25215 > st
    25216 
    25217 > aw
    25218 
    25219 > isolde sim start sel
    25220 
    25221 > aw
    25222 
    25223 > isolde sim start sel
    25224 
    25225 > select clear
    25226 
    25227 > st
    25228 
    25229 > st
    25230 
    25231 > st
    25232 
    25233 > st
    25234 
    25235 > st
    25236 
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    25240 
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    25244 
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    25246 
    25247 > st
    25248 
    25249 > st
    25250 
    25251 > st
    25252 
    25253 > st
    25254 
    25255 > st
    25256 
    25257 > st
    25258 
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    25260 
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    25262 
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    25264 
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    25266 
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    25268 
    25269 > st
    25270 
    25271 > st
    25272 
    25273 > st
    25274 
    25275 > aw
    25276 
    25277 > isolde sim start sel
    25278 
    25279 > st
    25280 
    25281 > select clear
    25282 
    25283 > st
    25284 
    25285 > st
    25286 
    25287 > aw
    25288 
    25289 > isolde sim start sel
    25290 
    25291 > select clear
    25292 
    25293 > st
    25294 
    25295 > st
    25296 
    25297 > st
    25298 
    25299 > select clear
    25300 
    25301 > st
    25302 
    25303 > st
    25304 
    25305 > st
    25306 
    25307 > st
    25308 
    25309 > st
    25310 
    25311 > st
    25312 
    25313 > st
    25314 
    25315 > st
    25316 
    25317 > st
    25318 
    25319 > st
    25320 
    25321 > st
    25322 
    25323 > st
    25324 
    25325 > st
    25326 
    25327 > st
    25328 
    25329 > select clear
    25330 
    25331 > st
    25332 
    25333 > st
    25334 
    25335 > st
    25336 
    25337 > st
    25338 
    25339 > st
    25340 
    25341 > st
    25342 
    25343 > st
    25344 
    25345 > select clear
    25346 
    25347 > st
    25348 
    25349 > st
    25350 
    25351 > st
    25352 
    25353 > st
    25354 
    25355 > st
    25356 
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    25358 
    25359 > st
    25360 
    25361 > st
    25362 
    25363 > st
    25364 
    25365 > st
    25366 
    25367 > st
    25368 
    25369 > aw
    25370 
    25371 > isolde sim start sel
    25372 
    25373 > st
    25374 
    25375 > st
    25376 
    25377 > st
    25378 
    25379 > st
    25380 
    25381 > st
    25382 
    25383 > st
    25384 
    25385 > st
    25386 
    25387 > st
    25388 
    25389 > st
    25390 
    25391 > st
    25392 
    25393 > st
    25394 
    25395 > st
    25396 
    25397 > st
    25398 
    25399 > st
    25400 
    25401 > st
    25402 
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    25404 
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    25406 
    25407 > st
    25408 
    25409 > st
    25410 
    25411 > st
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    25414 
    25415 > st
    25416 
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    25418 
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    25420 
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    25422 
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    25424 
    25425 > st
    25426 
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    25428 
    25429 > st
    25430 
    25431 > st
    25432 
    25433 > st
    25434 
    25435 > st
    25436 
    25437 > st
    25438 
    25439 > st
    25440 
    25441 > st
    25442 
    25443 > st
    25444 
    25445 > st
    25446 
    25447 > st
    25448 
    25449 > st
    25450 
    25451 > st
    25452 
    25453 > st
    25454 
    25455 > st
    25456 
    25457 > st
    25458 
    25459 > st
    25460 
    25461 > st
    25462 
    25463 > st
    25464 
    25465 > st
    25466 
    25467 > st
    25468 
    25469 > st
    25470 
    25471 > st
    25472 
    25473 > select clear
    25474 
    25475 > st
    25476 
    25477 > st
    25478 
    25479 > st
    25480 
    25481 > st
    25482 
    25483 > st
    25484 
    25485 > aw
    25486 
    25487 > isolde sim start sel
    25488 
    25489 > st
    25490 
    25491 > st
    25492 
    25493 > st
    25494 
    25495 > st
    25496 
    25497 > st
    25498 
    25499 > aw
    25500 
    25501 > isolde sim start sel
    25502 
    25503 > st
    25504 
    25505 > st
    25506 
    25507 > st
    25508 
    25509 > st
    25510 
    25511 > st
    25512 
    25513 > st
    25514 
    25515 > select clear
    25516 
    25517 > st
    25518 
    25519 > st
    25520 
    25521 > st
    25522 
    25523 > select clear
    25524 
    25525 > st
    25526 
    25527 > st
    25528 
    25529 > st
    25530 
    25531 > select up
    25532 
    25533 14 atoms, 14 bonds, 1 residue, 1 model selected 
    25534 
    25535 > select up
    25536 
    25537 364 atoms, 368 bonds, 29 residues, 1 model selected 
    25538 
    25539 > select clear
    25540 
    25541 > select clear
    25542 
    25543 > st
    25544 
    25545 > st
    25546 
    25547 > st
    25548 
    25549 > st
    25550 
    25551 > st
    25552 
    25553 > st
    25554 
    25555 > st
    25556 
    25557 > st
    25558 
    25559 > st
    25560 
    25561 > st
    25562 
    25563 > select clear
    25564 
    25565 > st
    25566 
    25567 > st
    25568 
    25569 > aw
    25570 
    25571 > isolde sim start sel
    25572 
    25573 > st
    25574 
    25575 > st
    25576 
    25577 > st
    25578 
    25579 > st
    25580 
    25581 > st
    25582 
    25583 > save working.cxs
    25584 
    25585 Taking snapshot of stepper: Model 1a 
    25586 
    25587 > view /ap:30
    25588 
    25589 > st
    25590 
    25591 > st
    25592 
    25593 > st
    25594 
    25595 > st
    25596 
    25597 > st
    25598 
    25599 > st
    25600 
    25601 > select clear
    25602 
    25603 > st
    25604 
    25605 > st
    25606 
    25607 > st
    25608 
    25609 > st
    25610 
    25611 > st
    25612 
    25613 > st
    25614 
    25615 > st
    25616 
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    25618 
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    25620 
    25621 > st
    25622 
    25623 > st
    25624 
    25625 > st
    25626 
    25627 > st
    25628 
    25629 > st
    25630 
    25631 > st
    25632 
    25633 > select clear
    25634 
    25635 > st
    25636 
    25637 > st
    25638 
    25639 > st
    25640 
    25641 > st
    25642 
    25643 > st
    25644 
    25645 > st
    25646 
    25647 > st
    25648 
    25649 > st
    25650 
    25651 > st
    25652 
    25653 > select clear
    25654 
    25655 > st
    25656 
    25657 > st
    25658 
    25659 > st
    25660 
    25661 > st
    25662 
    25663 > st
    25664 
    25665 > st
    25666 
    25667 > st
    25668 
    25669 > st
    25670 
    25671 > st
    25672 
    25673 > st
    25674 
    25675 > st
    25676 
    25677 > st
    25678 
    25679 > st
    25680 
    25681 > st
    25682 
    25683 > st
    25684 
    25685 > st
    25686 
    25687 > st
    25688 
    25689 > st
    25690 
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    25692 
    25693 > st
    25694 
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    25696 
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    25698 
    25699 > st
    25700 
    25701 > st
    25702 
    25703 > st
    25704 
    25705 > st
    25706 
    25707 > st
    25708 
    25709 > st
    25710 
    25711 > st
    25712 
    25713 > st
    25714 
    25715 > select clear
    25716 
    25717 > st
    25718 
    25719 > st
    25720 
    25721 > st
    25722 
    25723 > st
    25724 
    25725 > select clear
    25726 
    25727 > st
    25728 
    25729 > st
    25730 
    25731 > st
    25732 
    25733 > st
    25734 
    25735 > st
    25736 
    25737 > st
    25738 
    25739 > st
    25740 
    25741 > st
    25742 
    25743 > st
    25744 
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    25759 > select clear
    25760 
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    25770 
    25771 > select clear
    25772 
    25773 > st
    25774 
    25775 > aw
    25776 
    25777 > isolde sim start sel
    25778 
    25779 > select clear
    25780 
    25781 > st
    25782 
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    25787 > st
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    25794 
    25795 > select clear
    25796 
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    25839 > aw
    25840 
    25841 > isolde sim start sel
    25842 
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    25915 > select clear
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    25943 > select clear
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    26000 
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    26004 
    26005 > st
    26006 
    26007 > aw
    26008 
    26009 > isolde sim start sel
    26010 
    26011 > st
    26012 
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    26028 
    26029 > select clear
    26030 
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    26064 
    26065 > select clear
    26066 
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    26069 > st
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    26071 > st
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    26075 > st
    26076 
    26077 > select clear
    26078 
    26079 > st
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    26094 
    26095 > aw
    26096 
    26097 > isolde sim start sel
    26098 
    26099 > select up
    26100 
    26101 3 atoms, 2 bonds, 1 residue, 1 model selected 
    26102 
    26103 > delete sel
    26104 
    26105 > st
    26106 
    26107 > view /ap:30
    26108 
    26109 > isolde add ligand MQ8
    26110 
    26111 > isolde ignore ~sel
    26112 
    26113 ISOLDE: currently ignoring 5721 residues in model 8.2 
    26114 
    26115 > color sel purple
    26116 
    26117 > color sel byhetero
    26118 
    26119 > select /a*:30
    26120 
    26121 320 atoms, 320 bonds, 16 residues, 1 model selected 
    26122 
    26123 > select up
    26124 
    26125 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26126 
    26127 > isolde ~ignore sel
    26128 
    26129 ISOLDE: currently ignoring 5721 residues in model 8.2 
    26130 
    26131 > select up
    26132 
    26133 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26134 
    26135 > isolde ignore sel
    26136 
    26137 ISOLDE: currently ignoring 5721 residues in model 8.2 
    26138 
    26139 > select up
    26140 
    26141 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26142 
    26143 > select clear
    26144 
    26145 > isolde ~ignore
    26146 
    26147 > select up
    26148 
    26149 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26150 
    26151 > isolde ignore sel
    26152 
    26153 ISOLDE: currently ignoring 1 residues in model 8.2 
    26154 
    26155 > select up
    26156 
    26157 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26158 
    26159 > select clear
    26160 
    26161 > select clear
    26162 
    26163 > select up
    26164 
    26165 270 atoms, 272 bonds, 3 residues, 1 model selected 
    26166 
    26167 > clipper isolate sel contextDistance 0
    26168 
    26169 > clipper isolate sel contextDistance 0 maskRadius 7
    26170 
    26171 > clipper isolate sel contextDistance 0 maskRadius 5
    26172 
    26173 > clipper isolate sel contextDistance 0 maskRadius 6
    26174 
    26175 > select sel&~H
    26176 
    26177 117 atoms, 272 bonds, 3 residues, 2 models selected 
    26178 
    26179 > save alt_mq8.pdb #8 selectedOnly true
    26180 
    26181 > select up
    26182 
    26183 125 atoms, 126 bonds, 1 residue, 1 model selected 
    26184 
    26185 > delete sel
    26186 
    26187 > isolde ~ignore
    26188 
    26189 > select :CDL
    26190 
    26191 1280 atoms, 1275 bonds, 5 residues, 1 model selected 
    26192 
    26193 > select clear
    26194 
    26195 > select /a*,b*
    26196 
    26197 37197 atoms, 37702 bonds, 1867 residues, 1 model selected 
    26198 
    26199 > select /a*,b*&protein
    26200 
    26201 25462 atoms, 25870 bonds, 1614 residues, 1 model selected 
    26202 
    26203 > select :CDL
    26204 
    26205 1280 atoms, 1275 bonds, 5 residues, 1 model selected 
    26206 
    26207 > open
    26208 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/alt_mq8.pdb
    26209 
    26210 Summary of feedback from opening
    26211 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/alt_mq8.pdb 
    26212 --- 
    26213 warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
    26214 TRP A 5 1 4 
    26215 Start residue of secondary structure not found: HELIX 2 2 PRO A 10 PHE A 36 1
    26216 27 
    26217 Start residue of secondary structure not found: HELIX 3 3 ALA A 40 TYR A 46 1
    26218 7 
    26219 Start residue of secondary structure not found: HELIX 4 4 HIS A 2 TRP A 5 1 4 
    26220 Start residue of secondary structure not found: HELIX 5 5 PRO A 10 GLN A 35 1
    26221 26 
    26222 248 messages similar to the above omitted 
    26223 Cannot find LINK/SSBOND residue CYS (95 ) 
    26224 Cannot find LINK/SSBOND residue CYS (98 ) 
    26225 Cannot find LINK/SSBOND residue CYS (146 ) 
    26226 Cannot find LINK/SSBOND residue CYS (149 ) 
    26227 Cannot find LINK/SSBOND residue CYS (216 ) 
    26228 25 messages similar to the above omitted 
    26229  
    26230 
    26231 > view #1
    26232 
    26233 > select #1
    26234 
    26235 117 atoms, 119 bonds, 3 residues, 1 model selected 
    26236 
    26237 > close #1
    26238 
    26239 > st
    26240 
    26241 > st
    26242 
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    26244 
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    26253 > select clear
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    26323 > select clear
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    26329 > select clear
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    26353 > select clear
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    26375 > select clear
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    26419 > select clear
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    26437 > select clear
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    26459 > select clear
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    26479 > select clear
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    26500 
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    26509 > select clear
    26510 
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    26545 > select clear
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    26563 > select clear
    26564 
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    26571 > st
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    26581 > select clear
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    26645 > select clear
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    26689 > select clear
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    26805 > select clear
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    26810 
    26811 > st
    26812 
    26813 > st
    26814 
    26815 > st
    26816 
    26817 > aw
    26818 
    26819 > isolde sim start sel
    26820 
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    26822 
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    26824 
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    26828 
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    26833 > select clear
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    26853 > select clear
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    26878 
    26879 > select clear
    26880 
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    26894 
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    26896 
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    26898 
    26899 > st
    26900 
    26901 > st
    26902 
    26903 > st
    26904 
    26905 > st
    26906 
    26907 > st
    26908 
    26909 > st
    26910 
    26911 > st
    26912 
    26913 > st
    26914 
    26915 > st
    26916 
    26917 > st
    26918 
    26919 > st
    26920 
    26921 > st
    26922 
    26923 > st
    26924 
    26925 > st
    26926 
    26927 > st
    26928 
    26929 > st
    26930 
    26931 > st
    26932 
    26933 > st
    26934 
    26935 > st
    26936 
    26937 > st
    26938 
    26939 > st
    26940 
    26941 > st
    26942 
    26943 > st
    26944 
    26945 > st
    26946 
    26947 > st
    26948 
    26949 > st
    26950 
    26951 > st
    26952 
    26953 > st
    26954 
    26955 > st
    26956 
    26957 > st
    26958 
    26959 > st
    26960 
    26961 > st
    26962 
    26963 > st
    26964 
    26965 > st
    26966 
    26967 > st
    26968 
    26969 > st
    26970 
    26971 > st
    26972 
    26973 > st
    26974 
    26975 > st
    26976 
    26977 > st
    26978 
    26979 > st
    26980 
    26981 > st
    26982 
    26983 > st
    26984 
    26985 > st
    26986 
    26987 > st
    26988 
    26989 > st
    26990 
    26991 > st
    26992 
    26993 > st
    26994 
    26995 > st
    26996 
    26997 > st
    26998 
    26999 > st
    27000 
    27001 > st
    27002 
    27003 > st
    27004 
    27005 > st
    27006 
    27007 > st
    27008 
    27009 > delete sel
    27010 
    27011 > st
    27012 
    27013 > st
    27014 
    27015 > st
    27016 
    27017 > st
    27018 
    27019 > select clear
    27020 
    27021 > st
    27022 
    27023 > st
    27024 
    27025 > st
    27026 
    27027 > st
    27028 
    27029 > st
    27030 
    27031 > st
    27032 
    27033 > st
    27034 
    27035 > st
    27036 
    27037 > st
    27038 
    27039 > st
    27040 
    27041 > st
    27042 
    27043 > st
    27044 
    27045 > st
    27046 
    27047 > st
    27048 
    27049 > st
    27050 
    27051 > st
    27052 
    27053 > st
    27054 
    27055 > st
    27056 
    27057 > st
    27058 
    27059 > st
    27060 
    27061 > st
    27062 
    27063 > st
    27064 
    27065 > st
    27066 
    27067 > st
    27068 
    27069 > save working.cxs
    27070 
    27071 Taking snapshot of stepper: Model 1a 
    27072 
    27073 > ui tool show Shell
    27074 
    27075 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    27076 UserWarning: IPython History requires SQLite, your history will not be saved 
    27077 warn("IPython History requires SQLite, your history will not be saved") 
    27078 
    27079 > save working.cxs
    27080 
    27081 Taking snapshot of stepper: Model 1a 
    27082 Restoring stepper: Model 1a 
    27083 opened ChimeraX session 
    27084 
    27085 > select clear
    27086 
    27087 > aw
    27088 
    27089 > isolde sim start sel
    27090 
    27091 > isolde jumpto
    27092 
    27093 > select clear
    27094 
    27095 > isolde jumpto
    27096 
    27097 > select clear
    27098 
    27099 > select clear
    27100 
    27101 > aw
    27102 
    27103 > isolde sim start sel
    27104 
    27105 > isolde jumpto
    27106 
    27107 > select clear
    27108 
    27109 > select /AA-AD:1
    27110 
    27111 80 atoms, 76 bonds, 4 residues, 1 model selected 
    27112 
    27113 > select clear
    27114 
    27115 Traceback (most recent call last): 
    27116 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27117 packages/chimerax/isolde/isolde.py", line 2708, in _start_sim_or_toggle_pause 
    27118 self.start_sim() 
    27119 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27120 packages/chimerax/isolde/isolde.py", line 2728, in start_sim 
    27121 self.params, self.sim_params, excluded_residues = self.ignored_residues) 
    27122 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27123 packages/chimerax/isolde/openmm/openmm_interface.py", line 580, in __init__ 
    27124 self._prepare_validation_managers(mobile_atoms) 
    27125 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27126 packages/chimerax/isolde/openmm/openmm_interface.py", line 753, in
    27127 _prepare_validation_managers 
    27128 rota_a.restrict_to_selected_residues(mobile_res) 
    27129 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27130 packages/chimerax/isolde/validation/rota_annotation.py", line 129, in
    27131 restrict_to_selected_residues 
    27132 self.update_graphics() 
    27133 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27134 packages/chimerax/isolde/validation/rota_annotation.py", line 191, in
    27135 update_graphics 
    27136 non_favored_only = self._hide_favored) 
    27137 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27138 packages/chimerax/isolde/molobject.py", line 1660, in
    27139 validate_scale_and_color_rotamers 
    27140 non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
    27141 pointer(color_out)) 
    27142 IndexError: _Map_base::at 
    27143  
    27144 IndexError: _Map_base::at 
    27145  
    27146 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27147 packages/chimerax/isolde/molobject.py", line 1660, in
    27148 validate_scale_and_color_rotamers 
    27149 non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
    27150 pointer(color_out)) 
    27151  
    27152 See log for complete Python traceback. 
    27153  
    27154 
    27155 > save working_fme.cxs
    27156 
    27157 Taking snapshot of stepper: Model 1a 
    27158 opened ChimeraX session 
    27159 
    27160 > isolde start
    27161 
    27162 > set selectionWidth 4
    27163 
    27164 Done loading forcefield 
    27165 
    27166 > select clear
    27167 
    27168 > select clear
    27169 
    27170 > st
    27171 
    27172 > isolde jumpto
    27173 
    27174 > ui tool show Shell
    27175 
    27176 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    27177 UserWarning: IPython History requires SQLite, your history will not be saved 
    27178 warn("IPython History requires SQLite, your history will not be saved") 
    27179 
    27180 > isolde jumpto
    27181 
    27182 > aw
    27183 
    27184 > isolde sim start sel
    27185 
    27186 > select up
    27187 
    27188 3 atoms, 2 bonds, 1 residue, 1 model selected 
    27189 
    27190 > delete sel
    27191 
    27192 > st
    27193 
    27194 > isolde jumpto
    27195 
    27196 > select clear
    27197 
    27198 > isolde jumpto
    27199 
    27200 > isolde jumpto
    27201 
    27202 > select clear
    27203 
    27204 > isolde jumpto
    27205 
    27206 > isolde jumpto
    27207 
    27208 > isolde jumpto
    27209 
    27210 > aw
    27211 
    27212 > isolde sim start sel
    27213 
    27214 > isolde jumpto
    27215 
    27216 > select clear
    27217 
    27218 > isolde jumpto
    27219 
    27220 > select clear
    27221 
    27222 > select clear
    27223 
    27224 > isolde jumpto
    27225 
    27226 > select clear
    27227 
    27228 > aw
    27229 
    27230 > isolde sim start sel
    27231 
    27232 > isolde jumpto
    27233 
    27234 > select clear
    27235 
    27236 > select clear
    27237 
    27238 > isolde jumpto
    27239 
    27240 > select clear
    27241 
    27242 > isolde jumpto
    27243 
    27244 > awsf
    27245 
    27246 > select clear
    27247 
    27248 > isolde jumpto
    27249 
    27250 > isolde jumpto
    27251 
    27252 > isolde jumpto
    27253 
    27254 > select clear
    27255 
    27256 > isolde jumpto
    27257 
    27258 > select clear
    27259 
    27260 > isolde jumpto
    27261 
    27262 > isolde jumpto
    27263 
    27264 > select clear
    27265 
    27266 > aw
    27267 
    27268 > isolde sim start sel
    27269 
    27270 > isolde jumpto
    27271 
    27272 > isolde jumpto
    27273 
    27274 > isolde jumpto
    27275 
    27276 > isolde jumpto
    27277 
    27278 > isolde jumpto
    27279 
    27280 > isolde jumpto
    27281 
    27282 > isolde jumpto
    27283 
    27284 > isolde jumpto
    27285 
    27286 > isolde jumpto
    27287 
    27288 > isolde jumpto
    27289 
    27290 > isolde jumpto
    27291 
    27292 > isolde jumpto
    27293 
    27294 > isolde jumpto
    27295 
    27296 > isolde jumpto
    27297 
    27298 > isolde jumpto
    27299 
    27300 > isolde jumpto
    27301 
    27302 > isolde jumpto
    27303 
    27304 > isolde jumpto
    27305 
    27306 > isolde jumpto
    27307 
    27308 > isolde jumpto
    27309 
    27310 > isolde jumpto
    27311 
    27312 > isolde jumpto
    27313 
    27314 > isolde jumpto
    27315 
    27316 > isolde jumpto
    27317 
    27318 > isolde jumpto
    27319 
    27320 > isolde jumpto
    27321 
    27322 > isolde jumpto
    27323 
    27324 > isolde jumpto
    27325 
    27326 > isolde jumpto
    27327 
    27328 > isolde jumpto
    27329 
    27330 > isolde jumpto
    27331 
    27332 > select clear
    27333 
    27334 > isolde jumpto
    27335 
    27336 > isolde jumpto
    27337 
    27338 > isolde jumpto
    27339 
    27340 > isolde jumpto
    27341 
    27342 Traceback (most recent call last): 
    27343 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27344 packages/chimerax/isolde/isolde.py", line 2708, in _start_sim_or_toggle_pause 
    27345 self.start_sim() 
    27346 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27347 packages/chimerax/isolde/isolde.py", line 2725, in start_sim 
    27348 main_sel = self._last_main_sel = self._get_main_sim_selection() 
    27349 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27350 packages/chimerax/isolde/isolde.py", line 2908, in _get_main_sim_selection 
    27351 raise TypeError('You must select at least one atom from the current ' 
    27352 TypeError: You must select at least one atom from the current working model
    27353 prior to starting a simulation! 
    27354  
    27355 TypeError: You must select at least one atom from the current working model
    27356 prior to starting a simulation! 
    27357  
    27358 File "/home/tic20/.local/share/ChimeraX/1.1/site-
    27359 packages/chimerax/isolde/isolde.py", line 2908, in _get_main_sim_selection 
    27360 raise TypeError('You must select at least one atom from the current ' 
    27361  
    27362 See log for complete Python traceback. 
    27363  
    27364 
    27365 > isolde jumpto
    27366 
    27367 > select clear
    27368 
    27369 > aw
    27370 
    27371 > isolde sim start sel
    27372 
    27373 > isolde jumpto
    27374 
    27375 > isolde jumpto
    27376 
    27377 > select clear
    27378 
    27379 > isolde jumpto
    27380 
    27381 > select clear
    27382 
    27383 > isolde jumpto
    27384 
    27385 > isolde jumpto
    27386 
    27387 > isolde jumpto
    27388 
    27389 > isolde jumpto
    27390 
    27391 > select clear
    27392 
    27393 > isolde jumpto
    27394 
    27395 > isolde jumpto
    27396 
    27397 > isolde jumpto
    27398 
    27399 > isolde jumpto
    27400 
    27401 > save working_fme.cxs
    27402 
    27403 Taking snapshot of stepper: Model 1a 
    27404 
    27405 > select /A*,a*:1
    27406 
    27407 800 atoms, 760 bonds, 40 residues, 1 model selected 
    27408 
    27409 > select clear
    27410 
    27411 > save working_fme.cxs
    27412 
    27413 Taking snapshot of stepper: Model 1a 
    27414 opened ChimeraX session 
    27415 
    27416 > isolde start
    27417 
    27418 > set selectionWidth 4
    27419 
    27420 Done loading forcefield 
    27421 
    27422 > select clear
    27423 
    27424 > ui tool show Shell
    27425 
    27426 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    27427 UserWarning: IPython History requires SQLite, your history will not be saved 
    27428 warn("IPython History requires SQLite, your history will not be saved") 
    27429 
    27430 > select ~protein&~:HOH
    27431 
    27432 34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected 
    27433 
    27434 > select clear
    27435 
    27436 > aw
    27437 
    27438 > isolde sim start sel
    27439 
    27440 > select clear
    27441 
    27442 > select clear
    27443 
    27444 > aw
    27445 
    27446 > isolde sim start sel
    27447 
    27448 > delete sel
    27449 
    27450 > select clear
    27451 
    27452 > select clear
    27453 
    27454 > select clear
    27455 
    27456 > select clear
    27457 
    27458 > select clear
    27459 
    27460 > select clear
    27461 
    27462 > select clear
    27463 
    27464 > select clear
    27465 
    27466 > select clear
    27467 
    27468 > select clear
    27469 
    27470 > select clear
    27471 
    27472 > select clear
    27473 
    27474 > select clear
    27475 
    27476 > select clear
    27477 
    27478 > select clear
    27479 
    27480 > select clear
    27481 
    27482 > select clear
    27483 
    27484 > select clear
    27485 
    27486 > select clear
    27487 
    27488 > select clear
    27489 
    27490 > select clear
    27491 
    27492 > select clear
    27493 
    27494 > select clear
    27495 
    27496 > select clear
    27497 
    27498 > select clear
    27499 
    27500 > select clear
    27501 
    27502 > select clear
    27503 
    27504 > select clear
    27505 
    27506 > select clear
    27507 
    27508 > select clear
    27509 
    27510 > select clear
    27511 
    27512 > select clear
    27513 
    27514 > select clear
    27515 
    27516 > select clear
    27517 
    27518 > select clear
    27519 
    27520 > select clear
    27521 
    27522 > select clear
    27523 
    27524 > select clear
    27525 
    27526 > select clear
    27527 
    27528 > select clear
    27529 
    27530 > select up
    27531 
    27532 138 atoms, 139 bonds, 1 residue, 1 model selected 
    27533 
    27534 > show sel
    27535 
    27536 > awsf
    27537 
    27538 > awsf
    27539 
    27540 > aw
    27541 
    27542 > isolde sim start sel
    27543 
    27544 > select clear
    27545 
    27546 > select clear
    27547 
    27548 > select clear
    27549 
    27550 > select clear
    27551 
    27552 > select clear
    27553 
    27554 > select clear
    27555 
    27556 > select clear
    27557 
    27558 > select clear
    27559 
    27560 > select clear
    27561 
    27562 > select clear
    27563 
    27564 > select clear
    27565 
    27566 > select clear
    27567 
    27568 > select clear
    27569 
    27570 > select clear
    27571 
    27572 > select clear
    27573 
    27574 > select clear
    27575 
    27576 > select clear
    27577 
    27578 > select clear
    27579 
    27580 > select clear
    27581 
    27582 > select clear
    27583 
    27584 > select clear
    27585 
    27586 > select clear
    27587 
    27588 > select clear
    27589 
    27590 > select clear
    27591 
    27592 > select up
    27593 
    27594 140 atoms, 148 bonds, 1 residue, 1 model selected 
    27595 
    27596 > select clear
    27597 
    27598 > select clear
    27599 
    27600 > select clear
    27601 
    27602 > select clear
    27603 
    27604 > select clear
    27605 
    27606 > select clear
    27607 
    27608 > select ~protein&~:HOH
    27609 
    27610 34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 22 models selected 
    27611 
    27612 > clipper isolate sel contextDistance 0
    27613 
    27614 > hide #!8.1 models
    27615 
    27616 > ~cartoon
    27617 
    27618 > cartoon
    27619 
    27620 > show #!8.1 models
    27621 
    27622 > save working.cxs
    27623 
    27624 Taking snapshot of stepper: Model 1a 
    27625 
    27626 > isolde add ligand MQ9
    27627 
    27628 > ui mousemode right "translate selected atoms"
    27629 
    27630 > select up
    27631 
    27632 138 atoms, 139 bonds, 1 residue, 1 model selected 
    27633 
    27634 > isolde ignore ~sel
    27635 
    27636 ISOLDE: currently ignoring 5734 residues in model 8.2 
    27637 
    27638 > isolde ~ignore
    27639 
    27640 > select up
    27641 
    27642 138 atoms, 139 bonds, 1 residue, 1 model selected 
    27643 
    27644 > select clear
    27645 
    27646 > select up
    27647 
    27648 138 atoms, 139 bonds, 1 residue, 1 model selected 
    27649 
    27650 > delete sel
    27651 
    27652 > select clear
    27653 
    27654 > select clear
    27655 
    27656 > select clear
    27657 
    27658 > select clear
    27659 
    27660 > select clear
    27661 
    27662 > select clear
    27663 
    27664 > awsf
    27665 
    27666 > awsf
    27667 
    27668 > select clear
    27669 
    27670 > select clear
    27671 
    27672 > select clear
    27673 
    27674 > select up
    27675 
    27676 256 atoms, 255 bonds, 1 residue, 1 model selected 
    27677 
    27678 > select clear
    27679 
    27680 > select up
    27681 
    27682 256 atoms, 255 bonds, 1 residue, 1 model selected 
    27683 
    27684 > select clear
    27685 
    27686 > select clear
    27687 
    27688 > aw
    27689 
    27690 > isolde sim start sel
    27691 
    27692 > aw
    27693 
    27694 > isolde sim start sel
    27695 
    27696 > aw
    27697 
    27698 > isolde sim start sel
    27699 
    27700 > select clear
    27701 
    27702 > aw
    27703 
    27704 > isolde sim start sel
    27705 
    27706 > select clear
    27707 
    27708 > select clear
    27709 
    27710 > select clear
    27711 
    27712 > clipper set contourSensitivity 0.25
    27713 
    27714 > aw
    27715 
    27716 > isolde sim start sel
    27717 
    27718 > aw
    27719 
    27720 > isolde sim start sel
    27721 
    27722 > aw
    27723 
    27724 > isolde sim start sel
    27725 
    27726 > select clear
    27727 
    27728 > select clear
    27729 
    27730 > aw
    27731 
    27732 > isolde sim start sel
    27733 
    27734 > aw
    27735 
    27736 > isolde sim start sel
    27737 
    27738 > awsf
    27739 
    27740 > awsf
    27741 
    27742 > aw
    27743 
    27744 > isolde sim start sel
    27745 
    27746 > select clear
    27747 
    27748 > aw
    27749 
    27750 > isolde sim start sel
    27751 
    27752 > select clear
    27753 
    27754 > aw
    27755 
    27756 > isolde sim start sel
    27757 
    27758 > select clear
    27759 
    27760 > aw
    27761 
    27762 > isolde sim start sel
    27763 
    27764 > select clear
    27765 
    27766 > isolde add ligand LMT
    27767 
    27768 > ui mousemode right "translate selected atoms"
    27769 
    27770 > awsf
    27771 
    27772 > awsf
    27773 
    27774 > awsf
    27775 
    27776 > select clear
    27777 
    27778 > select up
    27779 
    27780 6 atoms, 4 bonds, 2 residues, 1 model selected 
    27781 
    27782 > delete sel
    27783 
    27784 > select clear
    27785 
    27786 > save working.cxs
    27787 
    27788 Taking snapshot of stepper: Model 1a 
    27789 
    27790 > select clear
    27791 
    27792 > save working.cxs
    27793 
    27794 Taking snapshot of stepper: Model 1a 
    27795 
    27796 > save working.cxs
    27797 
    27798 Taking snapshot of stepper: Model 1a 
    27799 
    27800 > open ../jsg.pdb
    27801 
    27802 Summary of feedback from opening ../jsg.pdb 
    27803 --- 
    27804 warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 43
    27805 GLY A 51 1 9 
    27806 Start residue of secondary structure not found: HELIX 2 2 PRO A 71 ALA A 76 1
    27807 6 
    27808 Start residue of secondary structure not found: HELIX 3 3 SER A 94 VAL A 102 1
    27809 9 
    27810 Start residue of secondary structure not found: HELIX 4 4 ARG A 114 PHE A 125
    27811 1 12 
    27812 Start residue of secondary structure not found: HELIX 5 5 ARG A 144 LEU A 152
    27813 1 9 
    27814 60 messages similar to the above omitted 
    27815  
    27816 
    27817 > select #1
    27818 
    27819 200 atoms, 206 bonds, 1 residue, 1 model selected 
    27820 
    27821 > close #1
    27822 
    27823 > open ../jsg.pdb
    27824 
    27825 Summary of feedback from opening ../jsg.pdb 
    27826 --- 
    27827 warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 43
    27828 GLY A 51 1 9 
    27829 Start residue of secondary structure not found: HELIX 2 2 PRO A 71 ALA A 76 1
    27830 6 
    27831 Start residue of secondary structure not found: HELIX 3 3 SER A 94 VAL A 102 1
    27832 9 
    27833 Start residue of secondary structure not found: HELIX 4 4 ARG A 114 PHE A 125
    27834 1 12 
    27835 Start residue of secondary structure not found: HELIX 5 5 ARG A 144 LEU A 152
    27836 1 9 
    27837 60 messages similar to the above omitted 
    27838  
    27839 
    27840 > select #1
    27841 
    27842 200 atoms, 206 bonds, 1 residue, 1 model selected 
    27843 
    27844 > ui mousemode right "translate selected atoms"
    27845 
    27846 > close #1
    27847 
    27848 > select clear
    27849 
    27850 > select clear
    27851 
    27852 > select clear
    27853 
    27854 > isolde add ligand GAL
    27855 
    27856 Deleted the following atoms from residue GAL L837: O1, HO1 
    27857 
    27858 > show sel
    27859 
    27860 > ui mousemode right "translate selected atoms"
    27861 
    27862 > delete sel
    27863 
    27864 > isolde add ligand GLC
    27865 
    27866 Deleted the following atoms from residue GLC L837: HO1, O1 
    27867 
    27868 > show sel
    27869 
    27870 > delete sel
    27871 
    27872 > isolde add ligand NAG
    27873 
    27874 Deleted the following atoms from residue NAG L837: O1, HO1 
    27875 
    27876 > show sel
    27877 
    27878 > delete sel
    27879 
    27880 > select clear
    27881 
    27882 > aw
    27883 
    27884 > isolde sim start sel
    27885 
    27886 > select up
    27887 
    27888 133 atoms, 132 bonds, 1 residue, 1 model selected 
    27889 
    27890 > select clear
    27891 
    27892 > select up
    27893 
    27894 141 atoms, 141 bonds, 1 residue, 1 model selected 
    27895 
    27896 > select up
    27897 
    27898 141 atoms, 141 bonds, 1 residue, 1 model selected 
    27899 
    27900 > awsf
    27901 
    27902 > awsf
    27903 
    27904 > ui mousemode right "mark point"
    27905 
    27906 > marker #1 position 206,174.5,206.2 color yellow radius 1
    27907 
    27908 > marker #1 position 208.1,175.1,203.3 color yellow radius 1
    27909 
    27910 > marker #1 position 210.5,177.7,202.2 color yellow radius 1
    27911 
    27912 > marker #1 position 209.7,176.4,199 color yellow radius 1
    27913 
    27914 > marker #1 position 213.2,175.9,196.8 color yellow radius 1
    27915 
    27916 > delete sel
    27917 
    27918 > marker #1 position 211.3,175.1,196.4 color yellow radius 1
    27919 
    27920 > marker #1 position 214.6,172.1,194.3 color yellow radius 1
    27921 
    27922 > delete sel
    27923 
    27924 > marker #1 position 213.4,173.4,193.2 color yellow radius 1
    27925 
    27926 > marker #1 position 216.9,174.5,192.6 color yellow radius 1
    27927 
    27928 > delete sel
    27929 
    27930 > marker #1 position 215.5,174.8,190.6 color yellow radius 1
    27931 
    27932 > marker #1 position 214.8,175.9,188.4 color yellow radius 1
    27933 
    27934 > view /aj:12
    27935 
    27936 > marker #1 position 198.9,164,186.4 color yellow radius 1
    27937 
    27938 > marker #1 position 199.1,162.2,189.3 color yellow radius 1
    27939 
    27940 > marker #1 position 197.6,159.5,191.3 color yellow radius 1
    27941 
    27942 > marker #1 position 197.1,156.2,191.5 color yellow radius 1
    27943 
    27944 > marker #1 position 196.1,153.9,193.2 color yellow radius 1
    27945 
    27946 > marker #1 position 195,153.8,196.9 color yellow radius 1
    27947 
    27948 > marker #1 position 195.7,152.3,200.4 color yellow radius 1
    27949 
    27950 > marker #1 position 195.6,150.6,201.3 color yellow radius 1
    27951 
    27952 > marker #1 position 193.5,148.1,198.7 color yellow radius 1
    27953 
    27954 > marker #1 position 194.5,149.2,200.1 color yellow radius 1
    27955 
    27956 > marker #1 position 193.2,148,196.4 color yellow radius 1
    27957 
    27958 > marker #1 position 197.7,166.8,183.9 color yellow radius 1
    27959 
    27960 > select /a*:12
    27961 
    27962 384 atoms, 368 bonds, 16 residues, 1 model selected 
    27963 
    27964 > open
    27965 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/class4b_r_2.35A_postprocess_masked.mrc
    27966 
    27967 Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400, pixel
    27968 0.999, shown at level 0.0164, step 2, values float32 
    27969 
    27970 > volume #8.1.1.1 level 0.03142
    27971 
    27972 > volume #8.1.1.1 level 0.02833
    27973 
    27974 > volume zone #2 nearAtoms #1 range 5
    27975 
    27976 > volume #2 step 1
    27977 
    27978 > volume #2 level 0.03435
    27979 
    27980 > volume #2 level 0.02539
    27981 
    27982 > volume zone #2 nearAtoms #1 range 4
    27983 
    27984 > volume #2 level 0.0224
    27985 
    27986 > save unknown_density_tubes.mrc #2
    27987 
    27988 > usage volume zone
    27989 
    27990 volume zone volumes nearAtoms an atoms specifier [range a number]
    27991 [bondPointSpacing a number] [minimalBounds true or false] [newMap true or
    27992 false] [invert true or false] [subregion map region] [step map step] [modelId
    27993 modelId] 
    27994 — Zero map values beyond a distance range from atoms 
    27995 modelId: a model id 
    27996 
    27997 > volume zone #2 nearAtoms #1 range 4 minimalBounds true
    27998 
    27999 > select #2
    28000 
    28001 4 models selected 
    28002 
    28003 > volume sel showOutlineBox true
    28004 
    28005 > save unknown_density_tubes.mrc #2
    28006 
    28007 > open unknown_density_tubes.mrc
    28008 
    28009 Opened unknown_density_tubes.mrc, grid size 32,39,32, pixel 0.999,0.999,0.999,
    28010 shown at level 0.0972, step 1, values float32 
    28011 
    28012 > hide #!2 models
    28013 
    28014 > volume #3 level 0.05529
    28015 
    28016 > volume #3 level 0.05219
    28017 
    28018 > volume #3 level 0.02932
    28019 
    28020 > volume #3 level 0.04173
    28021 
    28022 > close #3
    28023 
    28024 > show #!2 models
    28025 
    28026 > save unknown_density_tubes.ccp4 #2
    28027 
    28028 No known data format for file suffix '.ccp4' 
    28029 
    28030 > save unknown_density_tubes.map #2
    28031 
    28032 No known data format for file suffix '.map' 
    28033 
    28034 > surface unzone #2
    28035 
    28036 > volume zone #2 nearAtoms #1 range 4
    28037 
    28038 > surface unzone #2
    28039 
    28040 > volume zone #2 nearAtoms #1 range 4 minimalBounds true newMap true
    28041 
    28042 > hide #!3 models
    28043 
    28044 > show #!3 models
    28045 
    28046 > surface unzone #3
    28047 
    28048 > save unknown_density_tubes.mrc #3
    28049 
    28050 > open unknown_density_tubes.mrc
    28051 
    28052 Opened unknown_density_tubes.mrc, grid size 32,39,32, pixel 0.999,0.999,0.999,
    28053 shown at level 0.0254, step 1, values float32 
    28054 
    28055 > hide #!3 models
    28056 
    28057 > close #1#2-4
    28058 
    28059 > select clear
    28060 
    28061 > select clear
    28062 
    28063 > aw
    28064 
    28065 > isolde sim start sel
    28066 
    28067 > select up
    28068 
    28069 3 atoms, 2 bonds, 1 residue, 1 model selected 
    28070 
    28071 > delete sel
    28072 
    28073 > select clear
    28074 
    28075 > aw
    28076 
    28077 > isolde sim start sel
    28078 
    28079 > select up
    28080 
    28081 3 atoms, 2 bonds, 1 residue, 1 model selected 
    28082 
    28083 > delete sel
    28084 
    28085 > aw
    28086 
    28087 > isolde sim start sel
    28088 
    28089 > select clear
    28090 
    28091 > select up
    28092 
    28093 81 atoms, 82 bonds, 1 residue, 1 model selected 
    28094 
    28095 > delete sel
    28096 
    28097 > select clear
    28098 
    28099 > select clear
    28100 
    28101 > select clear
    28102 
    28103 > select clear
    28104 
    28105 > save working.cxs
    28106 
    28107 Taking snapshot of stepper: Model 1a 
    28108 Restoring stepper: Model 1a 
    28109 opened ChimeraX session 
    28110 
    28111 > volume unzone
    28112 
    28113 Missing or invalid "volumes" argument: empty atom specifier 
    28114 
    28115 > volume unzone #8
    28116 
    28117 > close #8.1
    28118 
    28119 > open
    28120 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/class4b_r_2.35A_postprocess_masked.mrc
    28121 
    28122 Opened class4b_r_2.35A_postprocess_masked.mrc, grid size 400,400,400, pixel
    28123 0.999, shown at level 0.0164, step 2, values float32 
    28124 
    28125 > volume gaussian #1 bfactor 50
    28126 
    28127 > clipper associate #1,2 toModel #8
    28128 
    28129 > clipper set contourSensitivity 0.25
    28130 
    28131 > select ~protein&~:HOH
    28132 
    28133 34491 atoms, 35465 bonds, 14 pseudobonds, 320 residues, 21 models selected 
    28134 
    28135 > select clear
    28136 
    28137 > select clear
    28138 
    28139 > save working.cxs
    28140 
    28141 Taking snapshot of stepper: Model 1a 
    28142 
    28143 > save working.cxs
    28144 
    28145 Taking snapshot of stepper: Model 1a 
    28146 
    28147 > select clear
    28148 
    28149 > select up
    28150 
    28151 124 atoms, 122 bonds, 2 residues, 1 model selected 
    28152 
    28153 > delete sel
    28154 
    28155 > isolde add ligand CDL
    28156 
    28157 place_ligand() was called with use_md_template=True, but no suitable template
    28158 was found. This command has been ignored. 
    28159 
    28160 > select up
    28161 
    28162 256 atoms, 255 bonds, 1 residue, 1 model selected 
    28163 
    28164 > ui mousemode right "translate selected atoms"
    28165 
    28166 > select up
    28167 
    28168 256 atoms, 255 bonds, 1 residue, 1 model selected 
    28169 
    28170 > isolde ignore ~sel
    28171 
    28172 ISOLDE: currently ignoring 5754 residues in model 8.2 
    28173 
    28174 > isolde ~ignore
    28175 
    28176 > select up
    28177 
    28178 256 atoms, 255 bonds, 1 residue, 1 model selected 
    28179 
    28180 > select clear
    28181 
    28182 > select up
    28183 
    28184 256 atoms, 255 bonds, 1 residue, 1 model selected 
    28185 
    28186 > select clear
    28187 
    28188 > isolde ~ignore
    28189 
    28190 > select clear
    28191 
    28192 > select clear
    28193 
    28194 > select clear
    28195 
    28196 > select up
    28197 
    28198 49 atoms, 50 bonds, 2 residues, 1 model selected 
    28199 
    28200 > select clear
    28201 
    28202 > save working.cxs
    28203 
    28204 Taking snapshot of stepper: Model 1a 
    28205 
    28206 > select #1
    28207 
    28208 Nothing selected 
    28209 
    28210 > select #8
    28211 
    28212 114704 atoms, 116622 bonds, 15 pseudobonds, 5755 residues, 23 models selected 
    28213 
    28214 > select clear
    28215 
    28216 > volume zone #8.1.1.1 nearAtoms #8 range 2.5 newMap true
    28217 
    28218 > volume subtract #8.1.1.1 #1
    28219 
    28220 > close #1
    28221 
    28222 > show #!8.1.1.1 models
    28223 
    28224 > isolde add ligand LMT
    28225 
    28226 > ui mousemode right "translate selected atoms"
    28227 
    28228 > isolde ignore ~sel
    28229 
    28230 ISOLDE: currently ignoring 5755 residues in model 8.2 
    28231 
    28232 > isolde ~ignore
    28233 
    28234 > hide #!2 models
    28235 
    28236 > ui mousemode right "mark point"
    28237 
    28238 > marker #1 position 243.7,161,187.6 color yellow radius 1
    28239 
    28240 > ui mousemode right "resize markers"
    28241 
    28242 > marker change #1:24 radius 3.127
    28243 
    28244 > show #!2 models
    28245 
    28246 > hide #!2 models
    28247 
    28248 > isolde add ligand LMT
    28249 
    28250 > ui mousemode right "translate selected atoms"
    28251 
    28252 > select up
    28253 
    28254 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28255 
    28256 > select up
    28257 
    28258 50 atoms, 49 bonds, 4 residues, 1 model selected 
    28259 
    28260 > isolde ignore sel
    28261 
    28262 ISOLDE: currently ignoring 4 residues in model 8.2 
    28263 
    28264 > isolde ~ignore
    28265 
    28266 > select clear
    28267 
    28268 > select up
    28269 
    28270 81 atoms, 82 bonds, 1 residue, 1 model selected 
    28271 
    28272 > delete sel
    28273 
    28274 > ui mousemode right "mark point"
    28275 
    28276 > marker #1 position 204.4,140.7,186.9 color yellow radius 3.127
    28277 
    28278 > color sel red
    28279 
    28280 > select clear
    28281 
    28282 > show #!2 models
    28283 
    28284 > hide #!2 models
    28285 
    28286 > show #!2 models
    28287 
    28288 > hide #1 models
    28289 
    28290 > sequence chain /C
    28291 
    28292 Chains must have same sequence 
    28293 
    28294 > sequence chain #8/C
    28295 
    28296 Chains must have same sequence 
    28297 
    28298 > select #8/C
    28299 
    28300 5225 atoms, 5244 bonds, 4 pseudobonds, 395 residues, 2 models selected 
    28301 
    28302 > hide #!2 models
    28303 
    28304 > select clear
    28305 
    28306 > select clear
    28307 
    28308 > delete sel
    28309 
    28310 > save working.cxs
    28311 
    28312 Taking snapshot of stepper: Model 1a 
    28313 
    28314 > select up
    28315 
    28316 216 atoms, 217 bonds, 12 residues, 1 model selected 
    28317 
    28318 > select clear
    28319 
    28320 > select clear
    28321 
    28322 > save working.cxs
    28323 
    28324 Taking snapshot of stepper: Model 1a 
    28325 
    28326 > save model1a_fully_rebuilt.cif #8
    28327 
    28328 Not saving entity_poly_seq for non-authoritative sequences 
    28329 
    28330 > save working.cxs
    28331 
    28332 Taking snapshot of stepper: Model 1a 
    28333 opened ChimeraX session 
    28334 
    28335 > select #1/A*:BCL
    28336 
    28337 Nothing selected 
    28338 
    28339 > select #8/A*:BCL
    28340 
    28341 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    28342 
    28343 > select clear
    28344 
    28345 > isolde start
    28346 
    28347 > set selectionWidth 4
    28348 
    28349 Done loading forcefield 
    28350 
    28351 > select #8/A*:BCL
    28352 
    28353 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    28354 
    28355 > select clear
    28356 
    28357 > awsf
    28358 
    28359 > awsf
    28360 
    28361 > awsf
    28362 
    28363 > awsf
    28364 
    28365 > open
    28366 > /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/model1a_fully_rebuilt.cif
    28367 
    28368 Summary of feedback from opening
    28369 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1a/model1a_fully_rebuilt.cif 
    28370 --- 
    28371 warnings | Unknown polymer entity '1' near line 610 
    28372 Unknown polymer entity '2' near line 2941 
    28373 Unknown polymer entity '3' near line 6564 
    28374 Unknown polymer entity '4' near line 29734 
    28375 Unknown polymer entity '5' near line 30743 
    28376 5 messages similar to the above omitted 
    28377 Unable to fetch template for 'LMX': might have incorrect bonds 
    28378 Unknown polymer entity '11' near line 71410 
    28379 Unknown polymer entity '12' near line 78114 
    28380 Unknown polymer entity '13' near line 89914 
    28381 Unknown polymer entity '14' near line 95896 
    28382 Atom C1 is not in the residue template for GPC /AA:201 
    28383 Atom C1 is not in the residue template for GPC /AB:201 
    28384 Atom C1 is not in the residue template for GPC /AC:201 
    28385 Atom C1 is not in the residue template for GPC /AD:201 
    28386 Atom C1 is not in the residue template for GPC /AE:201 
    28387 19 messages similar to the above omitted 
    28388 Atom H is not in the residue template for GLY /BQ:5 
    28389 Atom H is not in the residue template for GLY /BR:5 
    28390 Atom H is not in the residue template for GLY /BS:5 
    28391 Atom H is not in the residue template for GLY /BT:5 
    28392 Atom H is not in the residue template for GLY /C:13 
    28393 Atom O2 is not in the residue template for GUX /C:1001 
    28394 Atom H6 is not in the residue template for P5S /H1:1001 
    28395 Atom H11 is not in the residue template for BPH /L:606 
    28396 Atom H11 is not in the residue template for BPH /M:605 
    28397 Atom C1 is not in the residue template for RCC /M:701 
    28398 Atom O2 is not in the residue template for GUX /M:1001 
    28399 Atom HN2 is not in the residue template for ARG /ak:71 
    28400 Atom C1 is not in the residue template for GPC /ba:100 
    28401 Atom C1 is not in the residue template for GPC /bb:100 
    28402 Atom C26 is not in the residue template for PEX /bb:203 
    28403 Atom C26 is not in the residue template for PEX /bb:204 
    28404 Atom C1 is not in the residue template for GPC /bc:100 
    28405 Atom C1 is not in the residue template for GPC /bd:100 
    28406 Atom C26 is not in the residue template for PEX /bd:211 
    28407 Atom C26 is not in the residue template for PEX /bd:209 
    28408 Atom C1 is not in the residue template for GPC /be:100 
    28409 Atom C26 is not in the residue template for PEX /be:205 
    28410 Atom C1 is not in the residue template for GPC /bf:100 
    28411 Atom C26 is not in the residue template for PEX /bf:212 
    28412 Atom C1 is not in the residue template for GPC /bg:100 
    28413 Atom C1 is not in the residue template for GPC /bh:100 
    28414 Atom C26 is not in the residue template for PEX /bh:209 
    28415 Atom C26 is not in the residue template for PEX /bh:207 
    28416 Atom C1 is not in the residue template for GPC /bi:100 
    28417 Atom C1 is not in the residue template for GPC /bj:100 
    28418 Atom C26 is not in the residue template for PEX /bj:210 
    28419 Atom C26 is not in the residue template for PEX /bj:208 
    28420 Atom C1 is not in the residue template for GPC /bk:100 
    28421 Atom C1 is not in the residue template for GPC /bl:100 
    28422 Atom C26 is not in the residue template for PEX /bl:204 
    28423 Atom C26 is not in the residue template for PEX /bl:206 
    28424 Atom C1 is not in the residue template for GPC /bm:100 
    28425 Atom C1 is not in the residue template for GPC /bn:100 
    28426 Atom C26 is not in the residue template for PEX /bn:209 
    28427 Atom C26 is not in the residue template for PEX /bn:207 
    28428 Atom C1 is not in the residue template for GPC /bo:100 
    28429 Atom C26 is not in the residue template for PEX /bp:206 
    28430 Atom C1 is not in the residue template for GPC /bp:100 
    28431 Atom C26 is not in the residue template for PEX /bp:204 
    28432 Atom O2 is not in the residue template for GUX /M:1001 
    28433 Atom O2 is not in the residue template for GUX /C:1001 
    28434 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 
    28435  
    28436 Chain information for model1a_fully_rebuilt.cif #3 
    28437 --- 
    28438 Chain | Description 
    28439 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ? 
    28440 AC AD | ? 
    28441 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 bl
    28442 bm bo bp | ? 
    28443 BB BD BE BI BQ BR BS BT BV BW bn | ? 
    28444 C | ? 
    28445 C1 | ? 
    28446 H1 | ? 
    28447 H2 | ? 
    28448 L | ? 
    28449 M | ? 
    28450 aa ab ad ae af ag ah ai aj al am ao | ? 
    28451 ac | ? 
    28452 ak an | ? 
    28453 ap | ? 
    28454  
    28455 
    28456 > hide #1*protein
    28457 
    28458 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    28459 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    28460 
    28461 > hide #1&protein
    28462 
    28463 > hide #3&protein
    28464 
    28465 > close #1#2
    28466 
    28467 > matchmaker #3/AC to #8/AB
    28468 
    28469 Parameters 
    28470 --- 
    28471 Chain pairing | bb 
    28472 Alignment algorithm | Needleman-Wunsch 
    28473 Similarity matrix | BLOSUM-62 
    28474 SS fraction | 0.3 
    28475 Gap open (HH/SS/other) | 18/18/6 
    28476 Gap extend | 1 
    28477 SS matrix |  |  | H | S | O 
    28478 ---|---|---|--- 
    28479 H | 6 | -9 | -6 
    28480 S |  | 6 | -6 
    28481 O |  |  | 4 
    28482 Iteration cutoff | 2 
    28483  
    28484 Matchmaker Model 1a, chain AB (#8.2) with model1a_fully_rebuilt.cif, chain AC
    28485 (#3), sequence alignment score = 261.6 
    28486 RMSD between 48 pruned atom pairs is 0.331 angstroms; (across all 48 pairs:
    28487 0.331) 
    28488  
    28489 
    28490 > color #3 tan
    28491 
    28492 > color byhetero
    28493 
    28494 > hide #!3 models
    28495 
    28496 > awsf
    28497 
    28498 > awsf
    28499 
    28500 > select clear
    28501 
    28502 > show #!3 models
    28503 
    28504 > matchmaker #3/AG to #8/AF
    28505 
    28506 Parameters 
    28507 --- 
    28508 Chain pairing | bb 
    28509 Alignment algorithm | Needleman-Wunsch 
    28510 Similarity matrix | BLOSUM-62 
    28511 SS fraction | 0.3 
    28512 Gap open (HH/SS/other) | 18/18/6 
    28513 Gap extend | 1 
    28514 SS matrix |  |  | H | S | O 
    28515 ---|---|---|--- 
    28516 H | 6 | -9 | -6 
    28517 S |  | 6 | -6 
    28518 O |  |  | 4 
    28519 Iteration cutoff | 2 
    28520  
    28521 Matchmaker Model 1a, chain AF (#8.2) with model1a_fully_rebuilt.cif, chain AG
    28522 (#3), sequence alignment score = 262.1 
    28523 RMSD between 49 pruned atom pairs is 0.317 angstroms; (across all 49 pairs:
    28524 0.317) 
    28525  
    28526 
    28527 > hide #!3 models
    28528 
    28529 > select clear
    28530 
    28531 > aw
    28532 
    28533 > isolde sim start sel
    28534 
    28535 > awsf
    28536 
    28537 > awsf
    28538 
    28539 > awsf
    28540 
    28541 > awsf
    28542 
    28543 > show #!3 models
    28544 
    28545 > matchmaker #3/AM to #1/AL
    28546 
    28547 No 'to' model specified 
    28548 
    28549 > hide #!3 models
    28550 
    28551 > awsf
    28552 
    28553 > awsf
    28554 
    28555 > awsf
    28556 
    28557 > awsf
    28558 
    28559 > show #!3 models
    28560 
    28561 > matchmaker #3/AP to #1/AO
    28562 
    28563 No 'to' model specified 
    28564 
    28565 > matchmaker #3/AP to #8/AO
    28566 
    28567 Parameters 
    28568 --- 
    28569 Chain pairing | bb 
    28570 Alignment algorithm | Needleman-Wunsch 
    28571 Similarity matrix | BLOSUM-62 
    28572 SS fraction | 0.3 
    28573 Gap open (HH/SS/other) | 18/18/6 
    28574 Gap extend | 1 
    28575 SS matrix |  |  | H | S | O 
    28576 ---|---|---|--- 
    28577 H | 6 | -9 | -6 
    28578 S |  | 6 | -6 
    28579 O |  |  | 4 
    28580 Iteration cutoff | 2 
    28581  
    28582 Matchmaker Model 1a, chain AO (#8.2) with model1a_fully_rebuilt.cif, chain AP
    28583 (#3), sequence alignment score = 271.3 
    28584 RMSD between 49 pruned atom pairs is 0.357 angstroms; (across all 49 pairs:
    28585 0.357) 
    28586  
    28587 
    28588 > hide #!3 models
    28589 
    28590 > awsf
    28591 
    28592 > awsf
    28593 
    28594 > awsf
    28595 
    28596 > select clear
    28597 
    28598 > show #!3 models
    28599 
    28600 > hide #!3 models
    28601 
    28602 > awsf
    28603 
    28604 > awsf
    28605 
    28606 > select clear
    28607 
    28608 > awsf
    28609 
    28610 > awsf
    28611 
    28612 > show #!3 models
    28613 
    28614 > hide #!3 models
    28615 
    28616 > awsf
    28617 
    28618 > awsf
    28619 
    28620 > awsf
    28621 
    28622 > awsf
    28623 
    28624 > select clear
    28625 
    28626 > save working.cxs
    28627 
    28628 Taking snapshot of stepper: Model 1a 
    28629 
    28630 > select #8/A*:BCL
    28631 
    28632 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    28633 
    28634 > select clear
    28635 
    28636 > select #8/A*:BCL
    28637 
    28638 6720 atoms, 7104 bonds, 48 residues, 1 model selected 
    28639 
    28640 > save working.cxs
    28641 
    28642 Taking snapshot of stepper: Model 1a 
    28643 opened ChimeraX session 
    28644 
    28645 > isolde start
    28646 
    28647 > set selectionWidth 4
    28648 
    28649 Done loading forcefield 
    28650 
    28651 > view /M:609
    28652 
    28653 No objects specified. 
    28654 
    28655 > view /M:608
    28656 
    28657 > select clear
    28658 
    28659 > select clear
    28660 
    28661 > select clear
    28662 
    28663 > close #1
    28664 
    28665 > select up
    28666 
    28667 138 atoms, 139 bonds, 1 residue, 1 model selected 
    28668 
    28669 > isolde replace ligand sel MQ8
    28670 
    28671 Deleted the following atoms from residue MQ9 M608: H48, C47, H512, C49, H501,
    28672 C50, H471, H503, H511, C48, H513, H502, C51, H472 
    28673 
    28674 124 atoms were automatically renamed to match the template: O1->O4, C1->C4,
    28675 C2->C5, C6->C3, C7->C11, C5->C2, C8->C12, C9->C13, H8->H121, C10->C14,
    28676 C11->C15, C12->C16, C13->C17, C14->C18, H13->H171, C15->C19, C16->C20,
    28677 C17->C21, C18->C22, C19->C23, H18->H221, C20->C24, C21->C25, C22->C26,
    28678 C23->C27, C24->C28, H23->H271, C25->C29, C26->C30, C27->C31, C28->C32,
    28679 C29->C33, H28->H321, C30->C34, C31->C35, C32->C36, C33->C37, C34->C38,
    28680 H33->H371, C35->C39, C36->C40, C37->C41, C38->C42, C39->C43, H38->H421,
    28681 C40->C45, C41->C44, C42->C46, C43->C47, C44->C48, H43->H471, C45->C49,
    28682 C46->C50, C5M->C2M, C4->C1, C3->C10, C3A->C9, C3B->C8, C3C->C7, C3D->C6,
    28683 O4->O1, H3A->H91, H3B->H81, H3C->H71, H3D->H61, H111->H151, H112->H152,
    28684 H121->H161, H122->H162, H161->H201, H162->H202, H171->H211, H172->H212,
    28685 H211->H251, H212->H252, H221->H261, H222->H262, H261->H301, H262->H302,
    28686 H271->H311, H272->H312, H311->H351, H312->H352, H321->H361, H322->H362,
    28687 H361->H401, H362->H402, H371->H411, H372->H412, H411->H441, H412->H442,
    28688 H421->H461, H422->H462, H71->H111, H72->H112, H461->H501, H462->H502,
    28689 H101->H141, H102->H142, H103->H143, H151->H191, H152->H192, H153->H193,
    28690 H201->H241, H202->H242, H203->H243, H251->H291, H252->H292, H253->H293,
    28691 H301->H341, H302->H342, H303->H343, H351->H391, H352->H392, H353->H393,
    28692 H401->H451, H402->H452, H403->H453, H451->H491, H452->H492, H453->H493,
    28693 H5M1->H2M1, H5M2->H2M2, H5M3->H2M3 
    28694 
    28695 > show sel
    28696 
    28697 > select :CDL
    28698 
    28699 1536 atoms, 1530 bonds, 6 residues, 1 model selected 
    28700 
    28701 > select clear
    28702 
    28703 > save working.cxs
    28704 
    28705 Taking snapshot of stepper: Model 1a 
    28706 
    28707 > view /M:608
    28708 
    28709 > select up
    28710 
    28711 125 atoms, 126 bonds, 1 residue, 1 model selected 
    28712 
    28713 > save working.cxs
    28714 
    28715 Taking snapshot of stepper: Model 1a 
    28716 
    28717 > view /M:701
    28718 
    28719 > select /M:701
    28720 
    28721 100 atoms, 99 bonds, 1 residue, 1 model selected 
    28722 
    28723 > movie record
    28724 
    28725 > movie stop
    28726 
    28727 > movie encode RCC.mp4
    28728 
    28729 Movie saved to RCC.mp4 
    28730  
    28731 
    28732 > windowsize size
    28733 
    28734 Expected an integer >= 1 or a keyword 
    28735 
    28736 > windowsize
    28737 
    28738 window size 1136 934 
    28739 
    28740 > windowsize
    28741 
    28742 window size 1136 934 
    28743 
    28744 > show sel
    28745 
    28746 > select clear
    28747 
    28748 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    28749 bonded heavy atom. 
    28750 
    28751 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
    28752 bonded heavy atom. 
    28753 
    28754 > isolde replace ligand sel CRT
    28755 
    28756 Timed out trying to match residue RCC to template CRT. Match may not be ideal. 
    28757 
    28758 Deleted the following atoms from residue RCC M701: H27B, C27, O45, H24B, H43C,
    28759 C24, O42, H38A, H23A, C39, H28B, C29, C26, O44, H38C, H27A, H24A, C23, H43B,
    28760 C38, H28A, C28, HC25, C25, C43, H38B, H23B, C40, HC29, H43A 
    28761 
    28762 68 atoms were automatically renamed to match the template: O32->O1, C41->C1M,
    28763 C2->C4, C3->C5, C4->C6, C5->C7, HC3->H5, HC4->H6, C30->C2, C31->C3, C33->C8,
    28764 C6->C9, C7->C10, C8->C11, C9->C12, HC6->H9, HC7->H10, HC8->H11, C10->C14,
    28765 C11->C15, C12->C16, C13->C17, C34->C13, HC10->H14, HC11->H15, HC12->H16,
    28766 C35->C18, C14->C19, C15->C20, C16->C21, C17->C22, C18->C23, HC14->H19,
    28767 HC15->H20, HC16->H21, HC17->H22, C36->C24, C19->C25, C20->C26, C21->C27,
    28768 C22->C28, HC19->H25, HC20->H26, HC21->H27, C37->C29, HC2A->H41, HC2B->H42,
    28769 H30A->H21A, H30B->H22A, H30C->H23, H31B->H32A, H31C->H33, H33A->H81,
    28770 H33B->H82, H33C->H83, HC34->H131, H35A->H181, H35B->H182, H35C->H183,
    28771 H36A->H241, H36B->H242, H36C->H243, H37A->H291, H37B->H292, H37C->H293,
    28772 H41A->H1M1, H41B->H1M2, H41C->H1M3 
    28773 
    28774 > select up
    28775 
    28776 153 atoms, 152 bonds, 2 residues, 1 model selected 
    28777 
    28778 > isolde ignore sel
    28779 
    28780 ISOLDE: currently ignoring 2 residues in model 8.2 
    28781 
    28782 > isolde ~ignore
    28783 
    28784 > save working.cxs
    28785 
    28786 Taking snapshot of stepper: Model 1a 
    28787 
    28788 > select up
    28789 
    28790 3 atoms, 2 bonds, 1 residue, 1 model selected 
    28791 
    28792 > delete sel
    28793 
    28794 > save working.cxs
    28795 
    28796 Taking snapshot of stepper: Model 1a 
    28797 
    28798 > view /ah:11
    28799 
    28800 > select /ag:12
    28801 
    28802 24 atoms, 23 bonds, 1 residue, 1 model selected 
    28803 
    28804 > select /ah,ag:12
    28805 
    28806 48 atoms, 46 bonds, 2 residues, 1 model selected 
    28807 
    28808 > view /M:36
    28809 
    28810 > ui tool show Shell
    28811 
    28812 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    28813 UserWarning: IPython History requires SQLite, your history will not be saved 
    28814 warn("IPython History requires SQLite, your history will not be saved") 
    28815 
    28816 > save model_1a_working.cif #1
    28817 
    28818 no structures to save 
    28819 
    28820 > save working.cxs
    28821 
    28822 Taking snapshot of stepper: Model 1a 
    28823 opened ChimeraX session 
    28824 
    28825 > ui tool show Shell
    28826 
    28827 /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
    28828 UserWarning: IPython History requires SQLite, your history will not be saved 
    28829 warn("IPython History requires SQLite, your history will not be saved") 
    28830 
    28831 > select /M:MAN
    28832 
    28833 20 atoms, 20 bonds, 1 residue, 1 model selected 
    28834 
    28835 > view sel
    28836 
    28837 > select up
    28838 
    28839 49 atoms, 50 bonds, 2 residues, 1 model selected 
    28840 
    28841 > hide #!8.1 models
    28842 
    28843 > set bgColor black
    28844 
    28845 > hide :HOH
    28846 
    28847 > select up
    28848 
    28849 59 atoms, 60 bonds, 3 residues, 1 model selected 
    28850 
    28851 > hide protein&~sel
    28852 
    28853 > select /M:1000@O5
    28854 
    28855 1 atom, 1 residue, 1 model selected 
    28856 
    28857 > select up
    28858 
    28859 3 atoms, 1 bond, 2 residues, 1 model selected 
    28860 
    28861 > select up
    28862 
    28863 49 atoms, 50 bonds, 2 residues, 1 model selected 
    28864 
    28865 > save duplicated_sugars.jpg
    28866 
     8
     9[deleted (large) log]
    2886710
    2886811