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 Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Bad sequence association

comment:2 by Eric Pettersen, 4 years ago

Resolution: → can't reproduce
Status: accepted → closed

Can't reproduce. The error is possibly the result of bad state due to previous errors. Hopefully fixing those will make this go away.

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