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Opened 8 days ago
Closed 7 days ago
#19419 closed defect (duplicate)
alignment widget not properly destroying when tool closed
| Reported by: | 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: Linux-6.14.0-36-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/wang/下载/3AFA2.pdb
3AFA2.pdb title:
The human nucleosome structure [more info...]
Chain information for 3AFA2.pdb #1
---
Chain | Description | UniProt
A E | histone H3.1 | H31_HUMAN 0-135
B F | histone H4 | H4_HUMAN 0-102
C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D | histone H2B type 1-J | H2B1J_HUMAN 0-125
H | histone H2B type 1-J | H2B1J_HUMAN 0-125
Non-standard residues in 3AFA2.pdb #1
---
CL — chloride ion
MN — manganese (II) ion
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 3 fast true
> adjacentFlexible 1 protocol standard
Webservices job id: VB4GITYBXWJUN2G5
Webservices job finished: VB4GITYBXWJUN2G5
Modeller job (ID VB4GITYBXWJUN2G5) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 97, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 700, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.81.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/11/24 00:10:10
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 775109 756.942
0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775137 756.970 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775165 756.997 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775193 757.024 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775221 757.052 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775249 757.079 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775277 757.106 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775305 757.134 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 775333 757.161 0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778361 760.118 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778745 760.493 0.743
Read the alignment from file : alignment.ali
Total number of alignment positions: 758
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 3AFA2.pdb 758 8 3AFA2.pdb_1
2 chain_A 97 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./3AFA2.pdb_1.pdb
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 309
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 347
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 371
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 392
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 421
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 457
No more warnings will be printed for truncated lines in this file.
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1007870 984.248
0.961
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1007870 984.248
0.961
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1008041 984.415
0.961
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1008891 985.245
0.962
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1010149 986.474
0.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1012053 988.333
0.965
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014909 991.122
0.968
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1014909 991.122
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014999 991.210
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1019283 995.394
0.972
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1019283 995.394
0.972
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1019418 995.525
0.972
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1025844 1001.801
0.978
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1025844 1001.801
0.978
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026042 1001.994
0.979
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1026042 1001.994
0.979
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026339 1002.284
0.979
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1035961 1011.681
0.988
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1035961 1011.681
0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1035961 1011.681
0.988
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1035961 1011.681
0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1036411 1012.120
0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1050861 1026.231
1.002
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1050861 1026.231
1.002
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1051536 1026.891
1.003
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1073194 1048.041
1.023
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1073194 1048.041
1.023
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1074202 1049.025
1.024
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1106706 1080.768
1.055
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1106706 1080.768
1.055
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1108218 1082.244
1.057
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1156974 1129.857
1.103
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1156974 1129.857
1.103
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1156974 1129.857
1.103
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1156974 1129.857
1.103
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1159242 1132.072
1.106
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1232376 1203.492
1.175
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1232376 1203.492
1.175
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1232376 1203.492
1.175
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1232376 1203.492
1.175
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1235778 1206.814
1.179
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1232385 1203.501
1.175
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]: 1371637 1339.489
1.308
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1373237 1341.052
1.310
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1377217 1344.938
1.313
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1379217 1346.892
1.315
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1382217 1349.821
1.318
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1386717 1354.216
1.322
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1392289 1359.657
1.328
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1395089 1362.392
1.330
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1399289 1366.493
1.334
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1405589 1372.646
1.340
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1408361 1375.353
1.343
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1409761 1376.720
1.344
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1424833 1391.438 1.359
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1505193 1469.915 1.435
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1516833 1481.282 1.447
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 13 1
atom names : N -C CA CD
atom indices : 1 0 2 3
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 97 801 813 0 0 320
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1550077 1513.747 1.478
patch_______> segment topology patched using RTF: 1 ; PRO ; PROP
segments residues atoms bonds angles dihedrals impropers:
1 97 801 813 1090 1262 320
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1587173 1549.974 1.514
patch_______> segment topology patched using RTF: 97 ; ARG ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 97 802 814 1092 1264 321
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 97 802 814 1092 1264 321
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: 801 1
openf___224_> Open chain_A.ini
wrpdb___568_> Residues, atoms, selected atoms: 97 802 802
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1694622 1654.904
1.616
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1702814 1662.904
1.624
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1719198 1678.904
1.640
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1751966 1710.904
1.671
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1784734 1742.904
1.702
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1850270 1806.904
1.765
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1883038 1838.904
1.796
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 814 1092 1185 318
Total number of restraints before, now : 0 3409
make_re_422_> Number of previous, current restraints : 0 3409
make_re_423_> Number of previous, current selected restraints: 0 3409
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1939314 1893.861
1.849
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3409 3504
make_re_423_> Number of previous, current selected restraints: 3409 3504
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1939330 1893.877
1.849
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 99
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 3504 3600
make_re_423_> Number of previous, current selected restraints: 3504 3501
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1939330 1893.877
1.849
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1972098 1925.877
1.881
make_re_422_> Number of previous, current restraints : 3600 3685
make_re_423_> Number of previous, current selected restraints: 3501 3586
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1972098 1925.877
1.881
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3685 3755
make_re_423_> Number of previous, current selected restraints: 3586 3656
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1972098 1925.877
1.881
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2037634 1989.877
1.943
make_re_422_> Number of previous, current restraints : 3755 3793
make_re_423_> Number of previous, current selected restraints: 3656 3694
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2037634 1989.877
1.943
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/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: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3793 3812
make_re_423_> Number of previous, current selected restraints: 3694 3713
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2268574 2215.404
2.163
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2334110 2279.404
2.226
make_re_422_> Number of previous, current restraints : 3812 4303
make_re_423_> Number of previous, current selected restraints: 3713 4204
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 4303 4606
make_re_423_> Number of previous, current selected restraints: 4204 4507
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2465182 2407.404
2.351
make_re_422_> Number of previous, current restraints : 4606 5516
make_re_423_> Number of previous, current selected restraints: 4507 5417
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2530718 2471.404
2.413
make_re_422_> Number of previous, current restraints : 5516 5905
make_re_423_> Number of previous, current selected restraints: 5417 5806
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 : 5905 5905
make_re_423_> Number of previous, current selected restraints: 5806 5806
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5905 5905
make_re_423_> Number of previous, current selected restraints: 5806 5806
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5905 5905
make_re_423_> Number of previous, current selected restraints: 5806 5806
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5905 5905
make_re_423_> Number of previous, current selected restraints: 5806 5806
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 : 5905 5905
make_re_423_> Number of previous, current selected restraints: 5806 5806
rmdupl__427_> 601 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 5905 5205
openf___224_> Open chain_A.rsr
openf___224_> Open chain_A.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1635881 1597.540
1.560
rdcsr2__307_> Number of restraints read : 5205
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 5205 5205
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> ui tool show "Model Loops"
> modeller refine 1/A:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: DIGLL0QYFFLXN412
> hide atoms
> show cartoons
Webservices job finished: DIGLL0QYFFLXN412
Modeller job (ID DIGLL0QYFFLXN412) 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 3AFA2.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 627.3
RMSD between 97 pruned atom pairs is 0.183 angstroms; (across all 97 pairs:
0.183)
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 3AFA2.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 627.3
RMSD between 97 pruned atom pairs is 0.088 angstroms; (across all 97 pairs:
0.088)
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 3AFA2.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 627.3
RMSD between 97 pruned atom pairs is 0.049 angstroms; (across all 97 pairs:
0.049)
Associated chain_A chain A to chain A with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_A
---
Chain | Description
2.1/A 2.2/A 2.3/A | No description available
> save /home/wang/A.pdb
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> ui tool show "Model Loops"
> modeller refine 1/B:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: E0M2UUAQC9NEQAPH
Webservices job finished: E0M2UUAQC9NEQAPH
Modeller job (ID E0M2UUAQC9NEQAPH) 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 3AFA2.pdb, chain B (#1) with chain_B, chain B (#), sequence
alignment score = 485.6
RMSD between 78 pruned atom pairs is 0.025 angstroms; (across all 78 pairs:
0.025)
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 3AFA2.pdb, chain B (#1) with chain_B, chain B (#), sequence
alignment score = 485.6
RMSD between 78 pruned atom pairs is 0.077 angstroms; (across all 78 pairs:
0.077)
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 3AFA2.pdb, chain B (#1) with chain_B, chain B (#), sequence
alignment score = 482.6
RMSD between 78 pruned atom pairs is 0.048 angstroms; (across all 78 pairs:
0.048)
Associated chain_B chain B to chain B with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_B
---
Chain | Description
3.1/B 3.2/B 3.3/B | No description available
> save /home/wang/B.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> ui tool show "Model Loops"
> modeller refine 1/C:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: VTCDO0ZI5DO76N4O
Webservices job finished: VTCDO0ZI5DO76N4O
Modeller job (ID VTCDO0ZI5DO76N4O) 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 3AFA2.pdb, chain C (#1) with chain_C, chain C (#), sequence
alignment score = 608.1
RMSD between 108 pruned atom pairs is 0.036 angstroms; (across all 108 pairs:
0.036)
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 3AFA2.pdb, chain C (#1) with chain_C, chain C (#), sequence
alignment score = 608.1
RMSD between 108 pruned atom pairs is 0.100 angstroms; (across all 108 pairs:
0.100)
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 3AFA2.pdb, chain C (#1) with chain_C, chain C (#), sequence
alignment score = 608.1
RMSD between 108 pruned atom pairs is 0.040 angstroms; (across all 108 pairs:
0.040)
Associated chain_C chain C to chain C with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_C
---
Chain | Description
4.1/C 4.2/C 4.3/C | No description available
> save /home/wang/C.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> ui tool show "Model Loops"
> modeller refine 1/D:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: H2YNPIYBW8WAHU6U
Webservices job finished: H2YNPIYBW8WAHU6U
Modeller job (ID H2YNPIYBW8WAHU6U) 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 3AFA2.pdb, chain D (#1) with chain_D, chain D (#), sequence
alignment score = 592.7
RMSD between 96 pruned atom pairs is 0.057 angstroms; (across all 96 pairs:
0.057)
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 3AFA2.pdb, chain D (#1) with chain_D, chain D (#), sequence
alignment score = 592.7
RMSD between 96 pruned atom pairs is 0.075 angstroms; (across all 96 pairs:
0.075)
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 3AFA2.pdb, chain D (#1) with chain_D, chain D (#), sequence
alignment score = 592.7
RMSD between 96 pruned atom pairs is 0.055 angstroms; (across all 96 pairs:
0.055)
Associated chain_D chain D to chain D with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_D
---
Chain | Description
5.1/D 5.2/D 5.3/D | No description available
> save /home/wang/D.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E
Alignment identifier is 1/E
> ui tool show "Model Loops"
> modeller refine 1/E:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: RXFCW872DZ9QL55S
Webservices job finished: RXFCW872DZ9QL55S
Modeller job (ID RXFCW872DZ9QL55S) 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 3AFA2.pdb, chain E (#1) with chain_E, chain E (#), sequence
alignment score = 629.7
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 99 pairs:
0.253)
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 3AFA2.pdb, chain E (#1) with chain_E, chain E (#), sequence
alignment score = 629.7
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 99 pairs:
0.254)
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 3AFA2.pdb, chain E (#1) with chain_E, chain E (#), sequence
alignment score = 629.7
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 99 pairs:
0.263)
Associated chain_E chain E to chain E with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_E
---
Chain | Description
6.1/E 6.2/E 6.3/E | No description available
> ui tool show "Show Sequence Viewer"
> save /home/wang/E.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/F
Alignment identifier is 1/F
> ui tool show "Model Loops"
> modeller refine 1/F:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: 2PX33GY28YAAESW9
> ui tool show "Show Sequence Viewer"
Webservices job finished: 2PX33GY28YAAESW9
Modeller job (ID 2PX33GY28YAAESW9) 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 3AFA2.pdb, chain F (#1) with chain_F, chain F (#), sequence
alignment score = 485
RMSD between 84 pruned atom pairs is 0.121 angstroms; (across all 84 pairs:
0.121)
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 3AFA2.pdb, chain F (#1) with chain_F, chain F (#), sequence
alignment score = 485
RMSD between 84 pruned atom pairs is 0.073 angstroms; (across all 84 pairs:
0.073)
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 3AFA2.pdb, chain F (#1) with chain_F, chain F (#), sequence
alignment score = 485
RMSD between 84 pruned atom pairs is 0.020 angstroms; (across all 84 pairs:
0.020)
Associated chain_F chain F to chain F with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_F
---
Chain | Description
7.1/F 7.2/F 7.3/F | No description available
> save /home/wang/F.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/G
Alignment identifier is 1/G
> ui tool show "Model Loops"
> modeller refine 1/G:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Webservices job id: D0Y9QFPVHLZKCPB3
Webservices job finished: D0Y9QFPVHLZKCPB3
Modeller job (ID D0Y9QFPVHLZKCPB3) 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 3AFA2.pdb, chain G (#1) with chain_G, chain G (#), sequence
alignment score = 612.9
RMSD between 104 pruned atom pairs is 0.088 angstroms; (across all 104 pairs:
0.088)
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 3AFA2.pdb, chain G (#1) with chain_G, chain G (#), sequence
alignment score = 612.9
RMSD between 104 pruned atom pairs is 0.125 angstroms; (across all 104 pairs:
0.125)
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 3AFA2.pdb, chain G (#1) with chain_G, chain G (#), sequence
alignment score = 612.9
RMSD between 104 pruned atom pairs is 0.070 angstroms; (across all 104 pairs:
0.070)
Associated chain_G chain G to chain G with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_G
---
Chain | Description
8.1/G 8.2/G 8.3/G | No description available
> save /home/wang/G.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> ui tool show "Model Loops"
> modeller refine 1/H:1:all-missing numModels 3 fast true adjacentFlexible 1
> protocol standard
Drag select of 72 residues
Webservices job id: BSAJ7O8V8YWRLJZH
Webservices job finished: BSAJ7O8V8YWRLJZH
Modeller job (ID BSAJ7O8V8YWRLJZH) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 97, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 700, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.81.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/11/24 00:29:06
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528737 516.345 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528765 516.372 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528793 516.399 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528821 516.427 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528849 516.454 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528877 516.481 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528905 516.509 0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 531933 519.466 0.507
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 532297 519.821 0.508
Read the alignment from file : alignment.ali
Total number of alignment positions: 758
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 3AFA2.pdb 758 8 3AFA2.pdb_1
2 chain_H 92 1 chain_H
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./3AFA2.pdb_1.pdb
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 309
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 347
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 371
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 392
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 421
Modeller will only read the first 80 characters of this line.
readlinef__W> File: ./3AFA2.pdb_1.pdb, Line: 457
No more warnings will be printed for truncated lines in this file.
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761422 743.576
0.726
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 761422 743.576 0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761593 743.743
0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 762443 744.573
0.727
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 763701 745.802
0.728
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 765605 747.661
0.730
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768461 750.450
0.733
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 768461 750.450 0.733
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768551 750.538
0.733
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 772835 754.722
0.737
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 772835 754.722 0.737
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 772970 754.854
0.737
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779396 761.129
0.743
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 779396 761.129 0.743
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779594 761.322
0.743
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 779594 761.322 0.743
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779891 761.612
0.744
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 789513 771.009
0.753
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 789513 771.009 0.753
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 789513 771.009
0.753
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 789513 771.009 0.753
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 789963 771.448
0.753
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 804413 785.560
0.767
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 804413 785.560 0.767
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 805088 786.219
0.768
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 826746 807.369
0.788
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 826746 807.369 0.788
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 827754 808.354
0.789
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 860258 840.096
0.820
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 860258 840.096 0.820
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861770 841.572
0.822
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 910526 889.186
0.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 910526 889.186 0.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 910526 889.186
0.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 910526 889.186 0.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 912794 891.400
0.871
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 985928 962.820
0.940
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 985928 962.820 0.940
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 985928 962.820
0.940
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 985928 962.820 0.940
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 989330 966.143
0.943
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 985937 962.829
0.940
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]: 1125189 1098.817
1.073
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1126789 1100.380
1.075
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1130769 1104.267
1.078
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1132769 1106.220
1.080
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1135769 1109.149
1.083
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1140269 1113.544
1.087
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1145841 1118.985
1.093
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1148641 1121.720
1.095
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1152841 1125.821
1.099
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1159141 1131.974
1.105
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1161913 1134.681
1.108
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1163313 1136.048
1.109
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1177600 1150.000 1.123
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1249924 1220.629 1.192
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1260580 1231.035 1.202
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 92 719 730 0 0 301
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1290800 1260.547 1.231
patch_______> segment topology patched using RTF: 1 ; ARG ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 92 719 730 982 1154 301
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1321736 1290.758 1.261
patch_______> segment topology patched using RTF: 92 ; ALA ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 92 720 731 984 1156 302
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 92 720 731 984 1156 302
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: 719 1
openf___224_> Open chain_H.ini
wrpdb___568_> Residues, atoms, selected atoms: 92 720 720
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1429185 1395.688
1.363
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1437377 1403.688
1.371
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1453761 1419.688
1.386
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1486529 1451.688
1.418
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1519297 1483.688
1.449
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1584833 1547.688
1.511
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1617601 1579.688
1.543
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 731 984 1083 300
Total number of restraints before, now : 0 3098
make_re_422_> Number of previous, current restraints : 0 3098
make_re_423_> Number of previous, current selected restraints: 0 3098
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1669544 1630.414
1.592
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3098 3188
make_re_423_> Number of previous, current selected restraints: 3098 3188
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1669560 1630.430
1.592
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 93
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 3188 3279
make_re_423_> Number of previous, current selected restraints: 3188 3186
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1669560 1630.430
1.592
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1702328 1662.430
1.623
make_re_422_> Number of previous, current restraints : 3279 3357
make_re_423_> Number of previous, current selected restraints: 3186 3264
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1702328 1662.430
1.623
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3357 3411
make_re_423_> Number of previous, current selected restraints: 3264 3318
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1702328 1662.430
1.623
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt
getdata_643_> Protein accepted: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3411 3437
make_re_423_> Number of previous, current selected restraints: 3318 3344
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1702328 1662.430
1.623
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/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: 3AFA2.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 3437 3451
make_re_423_> Number of previous, current selected restraints: 3344 3358
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1909652 1864.895
1.821
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1975188 1928.895
1.884
make_re_422_> Number of previous, current restraints : 3451 3953
make_re_423_> Number of previous, current selected restraints: 3358 3860
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2040724 1992.895
1.946
make_re_422_> Number of previous, current restraints : 3953 4260
make_re_423_> Number of previous, current selected restraints: 3860 4167
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2171796 2120.895
2.071
make_re_422_> Number of previous, current restraints : 4260 5113
make_re_423_> Number of previous, current selected restraints: 4167 5020
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5113 5348
make_re_423_> Number of previous, current selected restraints: 5020 5255
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 : 5348 5348
make_re_423_> Number of previous, current selected restraints: 5255 5255
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5348 5348
make_re_423_> Number of previous, current selected restraints: 5255 5255
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5348 5348
make_re_423_> Number of previous, current selected restraints: 5255 5255
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 5348 5348
make_re_423_> Number of previous, current selected restraints: 5255 5255
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 : 5348 5348
make_re_423_> Number of previous, current selected restraints: 5255 5255
rmdupl__427_> 543 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 5348 4712
openf___224_> Open chain_H.rsr
openf___224_> Open chain_H.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1527740 1491.934
1.457
rdcsr2__307_> Number of restraints read : 4712
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 4712 4712
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Destroying pre-existing alignment with identifier 1/H
Alignment identifier is 1/H
> ui tool show "Model Loops"
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 347, in _update_sequence_menus
row_info.fieldItem.widget().destroy()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/widgets.py", line 104, in destroy
self.alignment.remove_observer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 780, in remove_observer
self.observers.remove(observer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 780, in remove_observer
self.observers.remove(observer)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x75532c230710>
KeyError:
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 334, in _list_selection_cb
mb = self.seq_menu[sel_aln]
~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 264, in launch_modeller
seq_menu = self.seq_menu[aln]
~~~~~~~~~~~~~^^^^^
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x75532c230710>
KeyError:
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 264, in launch_modeller
seq_menu = self.seq_menu[aln]
~~~~~~~~~~~~~^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 264, in launch_modeller
seq_menu = self.seq_menu[aln]
~~~~~~~~~~~~~^^^^^
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x75532c230710>
KeyError:
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 264, in launch_modeller
seq_menu = self.seq_menu[aln]
~~~~~~~~~~~~~^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 580.95.05
OpenGL renderer: NVIDIA GeForce RTX 4060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 90X00003CP
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Core(TM) i5-14400F
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 4.1Gi 25Gi 112Mi 2.3Gi 26Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD107 [GeForce RTX 4060] [10de:2882] (rev a1)
Subsystem: Lenovo AD107 [GeForce RTX 4060] [17aa:2336]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 7 days ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → alignment widget not properly destroying when tool closed |
comment:2 by , 7 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #18702