Opened 4 years ago
Closed 4 years ago
#5096 closed defect (can't reproduce)
Bad sequence association
| Reported by: | Elaine Meng | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108221453 (2021-08-22 14:53:54 UTC)
Description
tried command "close session" after running modeller
Log:
> open /Users/meng/Desktop/startup.cxc
> alias reset view orient; view initial
> alias start tool show $1
> alias whereprefs info path user unversioned config
> alias captut open help:user/tutorials/binding-sites.html#cap-example
> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available
> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available
> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html
> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html
executed startup.cxc
UCSF ChimeraX version: 1.3.dev202108221453 (2021-08-22)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1www format mmcif fromDatabase pdb
1www title:
NGF In complex with domain 5 of the TRKA receptor [more info...]
Chain information for 1www #1
---
Chain | Description | UniProt
V W | protein (nerve growth factor) | NGF_HUMAN
X Y | protein (TRKA receptor) | NTRK1_HUMAN
> sequence chain /V
Alignment identifier is 1/V
> refine 1/V:1:10-16 adjacent 0
Unknown command: modeller refine 1/V:1:10-16 adjacent 0
> modeller loops 1/V:1:10-16 adjacentFlexible 0
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1629753190510231442370
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753190510231442370
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service1629753190510231442370 finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence
alignment score = 613.5
RMSD between 104 pruned atom pairs is 0.107 angstroms; (across all 108 pairs:
0.600)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence
alignment score = 606.3
RMSD between 104 pruned atom pairs is 0.162 angstroms; (across all 108 pairs:
1.596)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence
alignment score = 606.3
RMSD between 103 pruned atom pairs is 0.170 angstroms; (across all 108 pairs:
1.861)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence
alignment score = 613.5
RMSD between 105 pruned atom pairs is 0.182 angstroms; (across all 108 pairs:
1.354)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence
alignment score = 606.3
RMSD between 104 pruned atom pairs is 0.209 angstroms; (across all 108 pairs:
1.346)
Chain information for chain_V
---
Chain | Description
2.1/? 2.2/? 2.3/? 2.4/? 2.5/? | No description available
> close #2
> modeller loops 1/V:1:all adjacentFlexible 4 numModels 3
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1629753282567-324821795
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753282567-324821795
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service1629753282567-324821795 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 422, in <module>
main()
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main
VersionMap[cf["version"]](cf)
File "/usr/local/opal-local/bin/modeller9v8.py", line 39, in v3_run
execfile(fn)
File "ModellerModelling.py", line 90, in <module>
a.make()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py",
line 37, in make
automodel.make(self, exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 143, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 679, in _check_select_atoms
atmsel = self.select_atoms()
File "ModellerModelling.py", line 40, in select_atoms
self.residue_range(112, 120)
File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 330,
in residue_range
end = self.residues[end]._num
File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 259,
in __getitem__
(self.offset, self.length, self.suffix))
File "/usr/lib64/python2.7/site-packages/modeller/util/modutil.py", line 12,
in handle_seq_indx
raise IndexError("list index out of range")
IndexError: list index out of range
Modeller run output
MODELLER 9.22, 2019/06/19, r11413
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2019 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64
Date and time of compilation : 2019/06/19 14:00:54
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/08/23 14:14:42
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269985 263.657
0.257
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285077 278.396
0.272
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300477 293.435
0.287
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331277 323.513
0.316
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392877 383.669
0.375
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 516077 503.981
0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516105 504.009 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516133 504.036 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516161 504.063 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516189 504.091 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 517861 505.724 0.494
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518337 506.188 0.494
Read the alignment from file : alignment.ali
Total number of alignment positions: 431
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 1www_1 419 4 1www_1
2 chain_V 120 1 chain_V
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./1www_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645762 630.627
0.616
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 645762 630.627 0.616
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645933 630.794
0.616
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 646783 631.624
0.617
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 648041 632.853
0.618
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 649945 634.712
0.620
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 649945 634.712 0.620
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 650035 634.800
0.620
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 652891 637.589
0.623
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 652891 637.589 0.623
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 653026 637.721
0.623
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657310 641.904
0.627
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 657310 641.904 0.627
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657508 642.098
0.627
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 663934 648.373
0.633
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 663934 648.373 0.633
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 664231 648.663
0.633
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 673853 658.060
0.643
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 673853 658.060 0.643
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 674303 658.499
0.643
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610
0.657
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610
0.657
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689428 673.270
0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 711086 694.420
0.678
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 711086 694.420 0.678
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712094 695.404
0.679
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 744598 727.146
0.710
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 744598 727.146 0.710
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 746110 728.623
0.712
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 794866 776.236
0.758
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 794092 775.480
0.757
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
\----------------------------------------------
END OF TABLE
check_a_344_> << END OF COMMAND
openf___224_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 933344 911.469
0.890
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 934944 913.031
0.892
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 938924 916.918
0.895
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 940924 918.871
0.897
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 943924 921.801
0.900
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 948424 926.195
0.904
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 953996 931.637
0.910
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 956796 934.371
0.912
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 960996 938.473
0.916
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 967296 944.625
0.922
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 970068 947.332
0.925
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 971468 948.699
0.926
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 990151 966.944 0.944
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1084623 1059.202 1.034
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1098815 1073.062 1.048
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 120 945 966 0 0 404
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1139343 1112.640 1.087
patch_______> segment topology patched using RTF: 1 ; SER ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 120 945 966 1305 1556 404
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1183839 1156.093 1.129
patch_______> segment topology patched using RTF: 120 ; ALA ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 120 946 967 1307 1558 405
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 120 946 967 1307 1558 405
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193491 1165.519 1.138
patch_______> segment topology patched using RTF: 15 80 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 968 1309 1561 405
patch_______> segment topology patched using RTF: 58 108 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 969 1311 1564 405
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193739 1165.761 1.138
patch_______> segment topology patched using RTF: 68 110 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 970 1313 1567 405
patch_s_522_> Number of disulfides patched in MODEL: 3
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 857 89
openf___224_> Open chain_V.ini
wrpdb___568_> Residues, atoms, selected atoms: 120 946 946
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300788 1270.301
1.241
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1308980 1278.301
1.248
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1325364 1294.301
1.264
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1358132 1326.301
1.295
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1390900 1358.301
1.326
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1456436 1422.301
1.389
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1489204 1454.301
1.420
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1521972 1486.301
1.451
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1587508 1550.301
1.514
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 970 1313 1480 402
Total number of restraints before, now : 0 4165
make_re_422_> Number of previous, current restraints : 0 4165
make_re_423_> Number of previous, current selected restraints: 0 4165
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656187 1617.370
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4165 4283
make_re_423_> Number of previous, current selected restraints: 4165 4283
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/omega.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/omega.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 122
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 4283 4402
make_re_423_> Number of previous, current selected restraints: 4283 4280
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4402 4508
make_re_423_> Number of previous, current selected restraints: 4280 4386
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi2.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1721739 1681.386
1.642
make_re_422_> Number of previous, current restraints : 4508 4574
make_re_423_> Number of previous, current selected restraints: 4386 4452
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386
1.642
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi3.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4574 4602
make_re_423_> Number of previous, current selected restraints: 4452 4480
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386
1.642
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4602 4619
make_re_423_> Number of previous, current selected restraints: 4480 4497
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1994151 1947.413
1.902
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2125223 2075.413
2.027
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2190759 2139.413
2.089
make_re_422_> Number of previous, current restraints : 4619 5995
make_re_423_> Number of previous, current selected restraints: 4497 5873
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5995 7622
make_re_423_> Number of previous, current selected restraints: 5873 7500
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2321831 2267.413
2.214
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2583975 2523.413
2.464
make_re_422_> Number of previous, current restraints : 7622 9530
make_re_423_> Number of previous, current selected restraints: 7500 9408
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 9530 10276
make_re_423_> Number of previous, current selected restraints: 9408 10154
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
rmdupl__427_> 710 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10276 9444
openf___224_> Open chain_V.rsr
openf___224_> Open chain_V.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2246420 2193.770
2.142
rdcsr2__307_> Number of restraints read : 9444
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 9444 9444
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> modeller loops 1/V:1:internal adjacent 4 num 3
Missing or invalid "targets" argument: Sequence position is not a comma-
separated list of integer positions or position ranges
> modeller loops 1/V:1:non adjacentFlexible 4 numModels 3
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16297533412211397169005
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16297533412211397169005
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16297533412211397169005 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 422, in <module>
main()
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main
VersionMap[cf["version"]](cf)
File "/usr/local/opal-local/bin/modeller9v8.py", line 39, in v3_run
execfile(fn)
File "ModellerModelling.py", line 88, in <module>
a.make()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py",
line 37, in make
automodel.make(self, exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 143, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 679, in _check_select_atoms
atmsel = self.select_atoms()
File "ModellerModelling.py", line 39, in select_atoms
self.residue_range(112, 120)
File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 330,
in residue_range
end = self.residues[end]._num
File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 259,
in __getitem__
(self.offset, self.length, self.suffix))
File "/usr/lib64/python2.7/site-packages/modeller/util/modutil.py", line 12,
in handle_seq_indx
raise IndexError("list index out of range")
IndexError: list index out of range
Modeller run output
MODELLER 9.22, 2019/06/19, r11413
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2019 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64
Date and time of compilation : 2019/06/19 14:00:54
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/08/23 14:15:41
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269985 263.657
0.257
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285077 278.396
0.272
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300477 293.435
0.287
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331277 323.513
0.316
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392877 383.669
0.375
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 516077 503.981
0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516105 504.009 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516133 504.036 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516161 504.063 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516189 504.091 0.492
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 517861 505.724 0.494
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518337 506.188 0.494
Read the alignment from file : alignment.ali
Total number of alignment positions: 431
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 1www_1 419 4 1www_1
2 chain_V 120 1 chain_V
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./1www_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645762 630.627
0.616
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 645762 630.627 0.616
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645933 630.794
0.616
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 646783 631.624
0.617
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 648041 632.853
0.618
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 649945 634.712
0.620
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 649945 634.712 0.620
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 650035 634.800
0.620
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 652891 637.589
0.623
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 652891 637.589 0.623
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 653026 637.721
0.623
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657310 641.904
0.627
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 657310 641.904 0.627
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657508 642.098
0.627
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 663934 648.373
0.633
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 663934 648.373 0.633
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 664231 648.663
0.633
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 673853 658.060
0.643
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 673853 658.060 0.643
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 674303 658.499
0.643
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610
0.657
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610
0.657
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689428 673.270
0.657
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 711086 694.420
0.678
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 711086 694.420 0.678
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712094 695.404
0.679
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 744598 727.146
0.710
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 744598 727.146 0.710
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 746110 728.623
0.712
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 794866 776.236
0.758
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 794092 775.480
0.757
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
\----------------------------------------------
END OF TABLE
check_a_344_> << END OF COMMAND
openf___224_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 933344 911.469
0.890
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 934944 913.031
0.892
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 938924 916.918
0.895
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 940924 918.871
0.897
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 943924 921.801
0.900
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 948424 926.195
0.904
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 953996 931.637
0.910
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 956796 934.371
0.912
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 960996 938.473
0.916
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 967296 944.625
0.922
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 970068 947.332
0.925
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 971468 948.699
0.926
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 990151 966.944 0.944
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1084623 1059.202 1.034
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1098815 1073.062 1.048
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 120 945 966 0 0 404
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1139343 1112.640 1.087
patch_______> segment topology patched using RTF: 1 ; SER ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 120 945 966 1305 1556 404
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1183839 1156.093 1.129
patch_______> segment topology patched using RTF: 120 ; ALA ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 120 946 967 1307 1558 405
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 120 946 967 1307 1558 405
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193491 1165.519 1.138
patch_______> segment topology patched using RTF: 15 80 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 968 1309 1561 405
patch_______> segment topology patched using RTF: 58 108 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 969 1311 1564 405
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193739 1165.761 1.138
patch_______> segment topology patched using RTF: 68 110 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 120 946 970 1313 1567 405
patch_s_522_> Number of disulfides patched in MODEL: 3
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 857 89
openf___224_> Open chain_V.ini
wrpdb___568_> Residues, atoms, selected atoms: 120 946 946
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300788 1270.301
1.241
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1308980 1278.301
1.248
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1325364 1294.301
1.264
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1358132 1326.301
1.295
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1390900 1358.301
1.326
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1456436 1422.301
1.389
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1489204 1454.301
1.420
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1521972 1486.301
1.451
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1587508 1550.301
1.514
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 970 1313 1480 402
Total number of restraints before, now : 0 4165
make_re_422_> Number of previous, current restraints : 0 4165
make_re_423_> Number of previous, current selected restraints: 0 4165
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656187 1617.370
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4165 4283
make_re_423_> Number of previous, current selected restraints: 4165 4283
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/omega.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/omega.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 122
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 4283 4402
make_re_423_> Number of previous, current selected restraints: 4283 4280
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4402 4508
make_re_423_> Number of previous, current selected restraints: 4280 4386
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386
1.579
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi2.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1721739 1681.386
1.642
make_re_422_> Number of previous, current restraints : 4508 4574
make_re_423_> Number of previous, current selected restraints: 4386 4452
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386
1.642
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi3.mdt
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4574 4602
make_re_423_> Number of previous, current selected restraints: 4452 4480
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386
1.642
openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL9v22}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: 1www_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4602 4619
make_re_423_> Number of previous, current selected restraints: 4480 4497
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1994151 1947.413
1.902
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2125223 2075.413
2.027
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2190759 2139.413
2.089
make_re_422_> Number of previous, current restraints : 4619 5995
make_re_423_> Number of previous, current selected restraints: 4497 5873
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5995 7622
make_re_423_> Number of previous, current selected restraints: 5873 7500
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2321831 2267.413
2.214
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2583975 2523.413
2.464
make_re_422_> Number of previous, current restraints : 7622 9530
make_re_423_> Number of previous, current selected restraints: 7500 9408
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 9530 10276
make_re_423_> Number of previous, current selected restraints: 9408 10154
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 10276 10276
make_re_423_> Number of previous, current selected restraints: 10154 10154
rmdupl__427_> 710 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 10276 9444
openf___224_> Open chain_V.rsr
openf___224_> Open chain_V.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2246420 2193.770
2.142
rdcsr2__307_> Number of restraints read : 9444
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 9444 9444
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> close
> open 2mnr
2mnr title:
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
structure of mandelate racemase At 2.5 angstroms resolution: identification of
the active site and possible catalytic residues [more info...]
Chain information for 2mnr #1
---
Chain | Description | UniProt
A | mandelate racemase | MANR_PSEPU
Non-standard residues in 2mnr #1
---
MN — manganese (II) ion
SO4 — sulfate ion
2mnr mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close
> open 1muc
1muc title:
Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more
info...]
Chain information for 1muc #1
---
Chain | Description | UniProt
A B | muconate lactonizing enzyme | CATB_PSEPU
Non-standard residues in 1muc #1
---
MN — manganese (II) ion
1muc mmCIF Assemblies
---
1| author_and_software_defined_assembly
> delete /A
> sequence chain /B
Alignment identifier is 1/B
> select clear
> close
> open 1gcn
1gcn title:
X-ray analysis of glucagon and its relationship to receptor binding [more
info...]
Chain information for 1gcn #1
---
Chain | Description | UniProt
A | glucagon | GLUC_PIG
> delete :16-20
> sequence chain /A
Alignment identifier is 1/A
> modeller loops 1/A:1:all adjacentFlexible 4 numModels 3
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1629753992889-221087584
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753992889-221087584
stdout.txt = standard output
stderr.txt = standard error
> ui tool show Log
Modeller job ID appModeller9v8Service1629753992889-221087584 finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 132.1
RMSD between 18 pruned atom pairs is 0.171 angstroms; (across all 24 pairs:
4.125)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 132.1
RMSD between 18 pruned atom pairs is 0.145 angstroms; (across all 24 pairs:
4.516)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 132.1
RMSD between 19 pruned atom pairs is 0.424 angstroms; (across all 24 pairs:
3.854)
Chain information for chain_A
---
Chain | Description
2.1/? 2.2/? 2.3/? | No description available
> close #2
> modeller loops 1/A:1:all adjacentFlexible 1 numModels 3
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16297540519661264090585
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16297540519661264090585
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16297540519661264090585 finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 133.9
RMSD between 24 pruned atom pairs is 0.141 angstroms; (across all 24 pairs:
0.141)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 123.1
RMSD between 23 pruned atom pairs is 0.037 angstroms; (across all 24 pairs:
1.448)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence
alignment score = 123.1
RMSD between 23 pruned atom pairs is 0.081 angstroms; (across all 24 pairs:
1.456)
Chain information for chain_A
---
Chain | Description
2.1/? 2.2/? 2.3/? | No description available
> close session
Traceback (most recent call last):
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)
KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x7ffe98811670>
Error processing trigger "modified":
KeyError:
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 427.140.8.0.0
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 6:21
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
charset-normalizer: 2.0.4
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.28.1
ChimeraX-AtomicLibrary: 4.1.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.4
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202108221453
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.4
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.1
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0
ChimeraX-MDcrds: 2.5
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.1
ChimeraX-ModelPanel: 1.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.11.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.0.1
cycler: 0.10.0
Cython: 0.29.23
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 2.11.3
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.1
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.6.2
numexpr: 2.7.3
numpy: 1.21.0
numpydoc: 1.1.0
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.20
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.9.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.2.1
qtconsole: 5.1.0
QtPy: 1.10.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
setuptools: 57.0.0
sfftk-rw: 0.7.0.post1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.0.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Bad sequence association |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
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Can't reproduce. The error is possibly the result of bad state due to previous errors. Hopefully fixing those will make this go away.