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Opened 22 months ago
Closed 18 months ago
#10424 closed defect (fixed)
KeyError in tasks after opening then closing session with BLAST failure
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Task Manager/Web Services | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
trying to close session
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_colored_structure.cxs
> format session
Log from Wed Jan 3 15:29:38 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_colored_structure.cxs
Log from Fri Dec 29 14:59:12 2023UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_structure.cxs
Log from Fri Dec 29 14:35:09 2023UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure2_structure.cxs
Log from Fri Dec 29 13:35:01 2023 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5fkv
Summary of feedback from opening 5fkv fetched from pdb
---
note | Fetching compressed mmCIF 5fkv from
http://files.rcsb.org/download/5fkv.cif
5fkv title:
cryo-EM structure of the E. coli replicative DNA polymerase complex bound to
DNA (DNA polymerase III alpha, beta, epsilon, τ complex) [more info...]
Chain information for 5fkv #1
---
Chain | Description | UniProt
A | DNA POLYMERASE III SUBUNIT ALPHA | DPO3A_ECOLI 1-1160
B C | DNA POLYMERASE III BETA | DPO3B_ECOLI 1-366
D | DNA POLYMERASE III EPSILON | DPO3E_ECOLI 1-243
E | DNA POLYMERASE III TAU | DPO3X_ECOLI 500-643
P | PRIMER-TEMPLATE DUPLEX DNA |
T | PRIMER-TEMPLATE DUPLEX DNA |
> open 5m1s
Summary of feedback from opening 5m1s fetched from pdb
---
note | Fetching compressed mmCIF 5m1s from
http://files.rcsb.org/download/5m1s.cif
5m1s title:
Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-
theta complex bound to DNA in the editing mode [more info...]
Chain information for 5m1s #2
---
Chain | Description | UniProt
A | DNA polymerase III subunit alpha | DPO3A_ECOLI 1-927
B C | DNA polymerase III subunit beta | DPO3B_ECOLI 1-366
D | DNA polymerase III subunit epsilon | DPO3E_ECOLI 1-243
F | DNA polymerase III subunit theta | HOLE_ECOLI 10-65
P | DNA Primer Strand |
T | DNA Template Strand |
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
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 5fkv, chain A (#1) with 5m1s, chain A (#2), sequence alignment
score = 4686.8
RMSD between 591 pruned atom pairs is 1.162 angstroms; (across all 927 pairs:
2.283)
> select
34406 atoms, 35237 bonds, 97 pseudobonds, 4247 residues, 6 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel surfaces
> transparency (#!1-2 & sel) 50
> set bgColor white
> select clear
> select #1/B#1/C
5688 atoms, 5786 bonds, 732 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/A
9020 atoms, 9199 bonds, 1 pseudobond, 1145 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/A
7274 atoms, 7427 bonds, 927 residues, 1 model selected
> select #1/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> select #1/P#1/T
1047 atoms, 1173 bonds, 61 pseudobonds, 51 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select
18651 atoms, 19079 bonds, 35 pseudobonds, 2319 residues, 5 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> open 5m1s
5m1s title:
Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-
theta complex bound to DNA in the editing mode [more info...]
Chain information for 5m1s #1
---
Chain | Description | UniProt
A | DNA polymerase III subunit alpha | DPO3A_ECOLI 1-927
B C | DNA polymerase III subunit beta | DPO3B_ECOLI 1-366
D | DNA polymerase III subunit epsilon | DPO3E_ECOLI 1-243
F | DNA polymerase III subunit theta | HOLE_ECOLI 10-65
P | DNA Primer Strand |
T | DNA Template Strand |
> open 5fkv
5fkv title:
cryo-EM structure of the E. coli replicative DNA polymerase complex bound to
DNA (DNA polymerase III alpha, beta, epsilon, τ complex) [more info...]
Chain information for 5fkv #2
---
Chain | Description | UniProt
A | DNA POLYMERASE III SUBUNIT ALPHA | DPO3A_ECOLI 1-1160
B C | DNA POLYMERASE III BETA | DPO3B_ECOLI 1-366
D | DNA POLYMERASE III EPSILON | DPO3E_ECOLI 1-243
E | DNA POLYMERASE III TAU | DPO3X_ECOLI 500-643
P | PRIMER-TEMPLATE DUPLEX DNA |
T | PRIMER-TEMPLATE DUPLEX DNA |
> select
34406 atoms, 35237 bonds, 97 pseudobonds, 4247 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> transparency (#!1-2 & sel) 30
> select clear
> select
34406 atoms, 35237 bonds, 97 pseudobonds, 4247 residues, 6 models selected
> transparency (#!1-2 & sel) 70
> select clear
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
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 5m1s, chain A (#1) with 5fkv, chain A (#2), sequence alignment
score = 4686.8
RMSD between 591 pruned atom pairs is 1.162 angstroms; (across all 927 pairs:
2.283)
> select #1/A
7274 atoms, 7427 bonds, 927 residues, 1 model selected
> delete atoms (#!1 & sel)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change
item_names = self._item_names()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>
filter_func=lambda c, ref=chain: c.structure != ref.structure)
^^^^^^^^^^^^^
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in
filter_func=lambda c, ref=chain: c.structure != ref.structure)
^^^^^^^^^^^^^
See log for complete Python traceback.
> delete bonds (#!1 & sel)
> select #1/B#1/C
5688 atoms, 5786 bonds, 732 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/D
1800 atoms, 1830 bonds, 1 pseudobond, 229 residues, 2 models selected
> select #2/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> select #1/D
1800 atoms, 1830 bonds, 1 pseudobond, 229 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/E
914 atoms, 927 bonds, 117 residues, 1 model selected
> select #2/E
914 atoms, 927 bonds, 117 residues, 1 model selected
> select #1/P
354 atoms, 398 bonds, 17 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/T
448 atoms, 500 bonds, 22 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/P#2/T
1047 atoms, 1173 bonds, 61 pseudobonds, 51 residues, 2 models selected
> color (#!2 & sel) black
> hide sel surfaces
> select clear
> select #2/B
2844 atoms, 2893 bonds, 366 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> color sel sandy brown
> color sel salmon
> color sel sandy brown
> color sel goldenrod
> color sel sandy brown
> color sel gold
> color sel sandy brown
> select #2/C
2844 atoms, 2893 bonds, 366 residues, 1 model selected
> color sel goldenrod
> color sel yellow
> color sel gold
> color sel goldenrod
> color sel gold
> select #2/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> color sel yellow green
> select #2/A
9020 atoms, 9199 bonds, 1 pseudobond, 1145 residues, 2 models selected
> color sel medium slate blue
> color sel medium purple
> color sel royal blue
> color sel cornflower blue
> select #2/E
914 atoms, 927 bonds, 117 residues, 1 model selected
> color sel dark turquoise
> color sel deep sky blue
> select #1/F
456 atoms, 464 bonds, 56 residues, 1 model selected
> color sel light gray
> color sel silver
> select
18842 atoms, 19296 bonds, 63 pseudobonds, 2320 residues, 4 models selected
> transparency (#!1-2 & sel) 50
> select clear
> ui tool show AlphaFold
Fetching compressed P03007 UniProt info from
https://www.uniprot.org/uniprot/P03007.xml
> alphafold match P03007
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P03007 from
https://alphafold.ebi.ac.uk/files/AF-P03007-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: P03007 (UniProt P03007)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P03007 | P03007 | 100.0 | 100.0
Opened 1 AlphaFold model
> ui tool show Matchmaker
> matchmaker #3/A to #2/D pairing ss
| 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 5fkv, chain D (#2) with AlphaFold P03007, chain A (#3), sequence
alignment score = 1152.3
RMSD between 139 pruned atom pairs is 0.837 angstroms; (across all 219 pairs:
34.921)
> ui tool show "Model Loops"
> select #2/D:127@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
31 atoms, 30 bonds, 4 residues, 2 models selected
> select up
1437 atoms, 1464 bonds, 183 residues, 2 models selected
> select up
1515 atoms, 1542 bonds, 193 residues, 2 models selected
> select up
1717 atoms, 1747 bonds, 219 residues, 2 models selected
> ui tool show "Model Loops"
No alignments chosen for modeling
Alignment identifier is 2/D
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Modeller Comparative"
> select add #3/A:217
1722 atoms, 1751 bonds, 220 residues, 3 models selected
> select up
1747 atoms, 1777 bonds, 223 residues, 3 models selected
> select up
3620 atoms, 3681 bonds, 462 residues, 3 models selected
> select up
20289 atoms, 20766 bonds, 2507 residues, 3 models selected
> select down
3620 atoms, 3681 bonds, 462 residues, 9 models selected
> ui tool show "Modeller Comparative"
> modeller refine 2/D:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: 5HHDD9DMI6PHVYF8
Modeller job (ID 5HHDD9DMI6PHVYF8) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 95, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:25:37
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278125 1248.169
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2288
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 243 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959050 1913.135
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959050 1913.135
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959221 1913.302
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960071 1914.132
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961329 1915.360
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963233 1917.220
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963233 1917.220
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963323 1917.308
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966179 1920.097
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966179 1920.097
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966314 1920.229
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970598 1924.412
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970598 1924.412
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970796 1924.605
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977222 1930.881
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977222 1930.881
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977519 1931.171
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987141 1940.567
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987141 1940.567
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987591 1941.007
1.896
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002041 1955.118
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002041 1955.118
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002716 1955.777
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024374 1976.928
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024374 1976.928
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025382 1977.912
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057886 2009.654
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057886 2009.654
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059398 2011.131
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108154 2058.744
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108154 2058.744
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110422 2060.959
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183556 2132.379
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183556 2132.379
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186958 2135.701
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296642 2242.814
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296642 2242.814
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466271 2408.468
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466271 2408.468
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473930 2415.947
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718135 2654.429
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> select #3/A:217
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
30 atoms, 30 bonds, 4 residues, 1 model selected
> select up
1903 atoms, 1934 bonds, 243 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> hide sel surfaces
> select clear
> select #2/D:92@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
9 atoms, 8 bonds, 2 residues, 2 models selected
> select up
1437 atoms, 1464 bonds, 183 residues, 2 models selected
> select up
1515 atoms, 1542 bonds, 193 residues, 2 models selected
> select up
1717 atoms, 1747 bonds, 219 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 2/D:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: X0MVKTLW1R9LQIC3
Modeller job (ID X0MVKTLW1R9LQIC3) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:27:27
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278101 1248.146
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2282
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 237 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959197 1913.278
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960047 1914.108
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961305 1915.337
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963299 1917.284
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966290 1920.205
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970772 1924.582
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977495 1931.147
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987567 1940.983
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002692 1955.754
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025358 1977.889
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059374 2011.107
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110398 2060.936
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186934 2135.678
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473906 2415.924
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718111 2654.405
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> ui tool show "Model Loops"
[Repeated 1 time(s)]
> select #2/D:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:189-208
17 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> modeller refine 2/D:1:190-207 numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: 3JVE6C2OB0C08T14
Modeller job (ID 3JVE6C2OB0C08T14) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:32:58
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278101 1248.146
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2282
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 237 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959197 1913.278
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960047 1914.108
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961305 1915.337
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963299 1917.284
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966290 1920.205
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970772 1924.582
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977495 1931.147
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987567 1940.983
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002692 1955.754
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025358 1977.889
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059374 2011.107
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110398 2060.936
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186934 2135.678
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473906 2415.924
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718111 2654.405
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> ui tool show Matchmaker
> select #2/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> select clear
> select #2/D:7
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 2/D:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: 2XNGYIL6N8LD21P4
Modeller job (ID 2XNGYIL6N8LD21P4) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 95, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:38:53
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278125 1248.169
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2288
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 243 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959050 1913.135
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959050 1913.135
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959221 1913.302
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960071 1914.132
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961329 1915.360
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963233 1917.220
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963233 1917.220
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963323 1917.308
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966179 1920.097
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966179 1920.097
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966314 1920.229
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970598 1924.412
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970598 1924.412
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970796 1924.605
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977222 1930.881
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977222 1930.881
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977519 1931.171
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987141 1940.567
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987141 1940.567
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987591 1941.007
1.896
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002041 1955.118
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002041 1955.118
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002716 1955.777
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024374 1976.928
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024374 1976.928
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025382 1977.912
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057886 2009.654
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057886 2009.654
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059398 2011.131
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108154 2058.744
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108154 2058.744
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110422 2060.959
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183556 2132.379
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183556 2132.379
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186958 2135.701
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296642 2242.814
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296642 2242.814
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301745 2247.798
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466271 2408.468
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466271 2408.468
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473930 2415.947
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720736 2656.969
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718135 2654.429
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> hide #2.2 models
> show #2.2 models
> select add #2.2
1717 atoms, 1747 bonds, 2 pseudobonds, 219 residues, 3 models selected
> select subtract #2.2
1717 atoms, 1747 bonds, 219 residues, 2 models selected
> select add #2.2
1717 atoms, 1747 bonds, 2 pseudobonds, 219 residues, 3 models selected
> select subtract #2.2
1717 atoms, 1747 bonds, 219 residues, 2 models selected
> select add #2.2
1717 atoms, 1747 bonds, 2 pseudobonds, 219 residues, 3 models selected
> select subtract #2.2
1717 atoms, 1747 bonds, 219 residues, 2 models selected
> select add #2.2
1717 atoms, 1747 bonds, 2 pseudobonds, 219 residues, 3 models selected
> select subtract #2.6
1 pseudobond, 2 models selected
> select add #2.6
1717 atoms, 1 pseudobond, 219 residues, 2 models selected
> hide #2.6 models
> show #2.6 models
Destroying pre-existing alignment with identifier 2/D
Alignment identifier is 2/D
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Destroying pre-existing alignment with identifier 2/D
Alignment identifier is 2/D
> toolshed show
> ui tool show "Blast Protein"
Cannot run BLAST without some kind of sequence.
> blastprotein #2/D database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1
Webservices job id: 55XC2Q2ZLKUGJV7V
> open pdb:5FKV
5fkv title:
cryo-EM structure of the E. coli replicative DNA polymerase complex bound to
DNA (DNA polymerase III alpha, beta, epsilon, τ complex) [more info...]
Chain information for 5fkv #4
---
Chain | Description | UniProt
A | DNA POLYMERASE III SUBUNIT ALPHA | DPO3A_ECOLI 1-1160
B C | DNA POLYMERASE III BETA | DPO3B_ECOLI 1-366
D | DNA POLYMERASE III EPSILON | DPO3E_ECOLI 1-243
E | DNA POLYMERASE III TAU | DPO3X_ECOLI 500-643
P | PRIMER-TEMPLATE DUPLEX DNA |
T | PRIMER-TEMPLATE DUPLEX DNA |
> matchmaker #4/D to #2/D
Parameters
---
Chain pairing | bb
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 5fkv, chain D (#2) with 5fkv, chain D (#4), sequence alignment
score = 1198.6
RMSD between 219 pruned atom pairs is 0.000 angstroms; (across all 219 pairs:
0.000)
> select #4
18386 atoms, 18832 bonds, 63 pseudobonds, 2264 residues, 3 models selected
> hide (#!4 & sel) target a
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
> ui tool show "Model Loops"
> sequence chain /D
Destroying pre-existing alignment with identifier 2/D
Alignment identifier is 2/D
Alignment identifier is 1/F
Alignment identifier is 2/A
Alignment identifier is 1
Destroying pre-existing alignment with identifier 2/D
Alignment identifier is 2/D
Alignment identifier is 2/E
Alignment identifier is 2/P
Alignment identifier is 2/T
Alignment identifier is 3/A
> sequence chain /D
Alignment identifier is 2/D
> ui tool show "Model Loops"
> modeller refine 2/D:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: SAVQLPND0JO4ZW7W
Modeller job (ID SAVQLPND0JO4ZW7W) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:49:52
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278101 1248.146
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2282
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 237 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959197 1913.278
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960047 1914.108
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961305 1915.337
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963299 1917.284
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966290 1920.205
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970772 1924.582
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977495 1931.147
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987567 1940.983
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002692 1955.754
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025358 1977.889
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059374 2011.107
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110398 2060.936
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186934 2135.678
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473906 2415.924
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718111 2654.405
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> open 1t2p
Summary of feedback from opening 1t2p fetched from pdb
---
note | Fetching compressed mmCIF 1t2p from
http://files.rcsb.org/download/1t2p.cif
1t2p title:
Crystal structure of Sortase A from Staphylococcus aureus [more info...]
Chain information for 1t2p #4
---
Chain | Description | UniProt
A B C | sortase | Q9S446_STAAU 61-206
1t2p mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> select #4/A:62-206
1155 atoms, 1177 bonds, 145 residues, 1 model selected
> select #4/B:61-206
1091 atoms, 1111 bonds, 1 pseudobond, 138 residues, 2 models selected
Alignment identifier is 4/B
> ui tool show "Model Loops"
> modeller refine 4/B:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: TMFM3A8RYATK0RJP
Modeller job (ID TMFM3A8RYATK0RJP) 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 1t2p, chain B (#4) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.040 angstroms; (across all 138 pairs:
0.040)
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 1t2p, chain B (#4) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.038 angstroms; (across all 138 pairs:
0.038)
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 1t2p, chain B (#4) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.020 angstroms; (across all 138 pairs:
0.020)
Associated chain_B chain B to chain B with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_B
---
Chain | Description
5.1/B 5.2/B 5.3/B | No description available
> select #4
3759 atoms, 3461 bonds, 1 pseudobond, 790 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #5
3480 atoms, 3546 bonds, 438 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/D:119@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
43 atoms, 43 bonds, 5 residues, 2 models selected
> select up
1437 atoms, 1464 bonds, 183 residues, 2 models selected
> select up
1515 atoms, 1542 bonds, 193 residues, 2 models selected
> select up
1717 atoms, 1747 bonds, 219 residues, 2 models selected
Destroying pre-existing alignment with identifier 2/D
Alignment identifier is 2/D
> sequence refseq ":chain D"
> ui tool show "Modeller Comparative"
> modeller comparative 2/D:1 numModels 3 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: ADKCZKPLFKOQDU13
Modeller job (ID ADKCZKPLFKOQDU13) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 72, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 03:58:04
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806
0.269
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583
0.298
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405317 395.817
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528517 516.130
0.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 774917 756.755
0.739
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1267717 1238.005
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267745 1238.032
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267773 1238.060
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267801 1238.087
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267829 1238.114
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267857 1238.142
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267885 1238.169
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267913 1238.196
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1276965 1247.036
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277933 1247.981
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2288
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 243 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1958858 1912.947
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1958858 1912.947
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959029 1913.114
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959879 1913.944
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961137 1915.173
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963041 1917.032
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963041 1917.032
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963131 1917.120
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1965987 1919.909
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1965987 1919.909
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966122 1920.041
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970406 1924.225
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970406 1924.225
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970604 1924.418
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977030 1930.693
1.885
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977030 1930.693
1.885
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977327 1930.983
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1986949 1940.380
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1986949 1940.380
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987399 1940.819
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2001849 1954.931
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2001849 1954.931
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002524 1955.590
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024182 1976.740
1.930
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024182 1976.740
1.930
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025190 1977.725
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057694 2009.467
1.962
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057694 2009.467
1.962
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059206 2010.943
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2107962 2058.557
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2107962 2058.557
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110230 2060.771
2.012
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183364 2132.191
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183364 2132.191
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186766 2135.514
2.085
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296450 2242.627
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296450 2242.627
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301553 2247.610
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301553 2247.610
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301553 2247.610
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466079 2408.280
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466079 2408.280
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473738 2415.760
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720544 2656.781
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720544 2656.781
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720544 2656.781
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720544 2656.781
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720544 2656.781
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2717943 2654.241
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> select 2/D:1
Expected an objects specifier or a keyword
> select #2/D:1
Nothing selected
> select #2/D:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> modeller refine 2/D:internal-missing numModels 3 fast false adjacentFlexible
> 1 protocol standard
> modeller loops 2/D:internal-missing numModels 3 fast false adjacentFlexible
> 1 protocol standard
Missing or invalid "targets" argument: No sequences match '2/D'
> modeller refine 2/D:10:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
> modeller loops 2/D:10:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Missing or invalid "targets" argument: Sequence index (10) larger than number
of sequences in alignment (1)
> modeller refine 2/D:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: LG6E3RQG5ER1H42F
Modeller job (ID LG6E3RQG5ER1H42F) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, 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 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 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 wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/12/29 04:00:23
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/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 ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/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 amaxalignment [B,KiB,MiB]: 1267909 1238.192
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267937 1238.220
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267965 1238.247
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1267993 1238.274
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268021 1238.302
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268049 1238.329
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268077 1238.356
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1268105 1238.384
1.209
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1277157 1247.224
1.218
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1278101 1248.146
1.219
Read the alignment from file : alignment.ali
Total number of alignment positions: 2282
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5fkv_2 2264 7 5fkv_2
2 chain_D 237 1 chain_D
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5fkv_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1959026 1913.111
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1959197 1913.278
1.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1960047 1914.108
1.869
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1961305 1915.337
1.870
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1963209 1917.196
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1963299 1917.284
1.872
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1966155 1920.073
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1966290 1920.205
1.875
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1970574 1924.389
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1970772 1924.582
1.879
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1977198 1930.857
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1977495 1931.147
1.886
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1987117 1940.544
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1987567 1940.983
1.895
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2002017 1955.095
1.909
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2002692 1955.754
1.910
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2024350 1976.904
1.931
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2025358 1977.889
1.932
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2057862 2009.631
1.963
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2059374 2011.107
1.964
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2108130 2058.721
2.010
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2110398 2060.936
2.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2183532 2132.355
2.082
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2186934 2135.678
2.086
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2296618 2242.791
2.190
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2301721 2247.774
2.195
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2466247 2408.444
2.352
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2473906 2415.924
2.359
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 2720712 2656.945
2.595
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2718111 2654.405
2.592
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 2214)
Alignment IIADN/GGAGTAGTACTAGGACGAAGGACTC/GGAGTCCTTCGTCCTAGTACTACTCC/
PDB IIADN/llelteltejtellejleellejtj/lleltjjttjltjjteltejtejtjj/
Match ****** * *
Alignment residue type 6 (G, GLY) does not match pdb
residue type 50 (l, DGUA),
for align code 5fkv_2 (atom file 5fkv_2), pdb residue number " 1", chain "P"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5fkv_2
No output models from Modeller; see log for Modeller text output.
> open /Users/krystian/Downloads/modeller.pdb
Summary of feedback from opening /Users/krystian/Downloads/modeller.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 54
HIS A 60 1 7
Start residue of secondary structure not found: HELIX 2 2 ASP A 64 PHE A 66 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA A 77 ILE A 84 1
8
Start residue of secondary structure not found: HELIX 4 4 ALA A 94 LEU A 108 1
15
Start residue of secondary structure not found: HELIX 5 5 THR A 115 THR A 117
1 3
9 messages similar to the above omitted
Chain information for modeller.pdb
---
Chain | Description
4.1/A | No description available
4.2/A | No description available
> select #4.1/A
1862 atoms, 1893 bonds, 237 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4.1/A to #2/D pairing ss
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 5fkv, chain D (#2) with modeller.pdb, chain A (#4.1), sequence
alignment score = 1179.7
RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 219 pairs:
0.158)
> matchmaker #4.2/A to #2/A pairing ss
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 5fkv, chain A (#2) with modeller.pdb, chain A (#4.2), sequence
alignment score = 5949.4
RMSD between 1145 pruned atom pairs is 0.024 angstroms; (across all 1145
pairs: 0.024)
> surface sel
> ui tool show "Color Actions"
> color sel dark sea green
> color sel yellow green
> transparency (#!4.1 & sel) 50
> select #2/D
1717 atoms, 1747 bonds, 1 pseudobond, 219 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #4.2/A
9138 atoms, 9320 bonds, 1160 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> ui tool show "Color Actions"
> color sel steel blue
> color sel cornflower blue
> transparency (#!4.2 & sel) 50
> select #2/A
9020 atoms, 9199 bonds, 1 pseudobond, 1145 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> select clear
> save /Users/krystian/Downloads/Figure2_structure.cxs
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> ui tool show "Side View"
> select #2/B
2844 atoms, 2893 bonds, 366 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> select #2/C
2844 atoms, 2893 bonds, 366 residues, 1 model selected
> color sel goldenrod
> select #2/B#2/C
5688 atoms, 5786 bonds, 732 residues, 1 model selected
> transparency (#!2 & sel) 50
> select clear
> select #2/E
914 atoms, 927 bonds, 117 residues, 1 model selected
> select #1/F
456 atoms, 464 bonds, 56 residues, 1 model selected
> color (#!1 & sel) dark gray
> transparency (#!1 & sel) 50
> select clear
> save /Users/krystian/Downloads/Figure2_structure.cxs
> select #2/E
914 atoms, 927 bonds, 117 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark turquoise
> color sel deep sky blue
> transparency (#!2 & sel) 50
> select clear
> save /Users/krystian/Downloads/Figure2_structure.cxs
> save /Users/krystian/Desktop/image10.png supersample 3
> rotate z 180
Unknown command: rotate z 180
> rotate
Unknown command: rotate
> turn z 80
> turn z -80
> turn x 180
[Repeated 1 time(s)]
> turn y 180
> save /Users/krystian/Desktop/image11.png supersample 3
> turn y 180
> save /Users/krystian/Desktop/image12.png supersample 3
> save /Users/krystian/Downloads/Figure2_structure.cxs
——— End of log from Fri Dec 29 13:35:01 2023 ———
opened ChimeraX session
BLAST job failed
> save /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_structure.cxs
> ui tool show "Side View"
> select #2/A
9020 atoms, 9199 bonds, 1 pseudobond, 1145 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #3/A
1903 atoms, 1934 bonds, 243 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4.2/A
9138 atoms, 9320 bonds, 1160 residues, 1 model selected
> select ~sel
11684 atoms, 11990 bonds, 62 pseudobonds, 1412 residues, 12 models selected
> hide sel cartoons
> surface style #1-2#4.1 dot
> select clear
> save /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_structure.cxs
——— End of log from Fri Dec 29 14:35:09 2023 ———
opened ChimeraX session
BLAST job failed
> select #4.2/A
9138 atoms, 9320 bonds, 1160 residues, 1 model selected
> select ~sel
11684 atoms, 11990 bonds, 62 pseudobonds, 1412 residues, 12 models selected
> surface style #1-2#4.1 dot
> select clear
> select #4.2/A:1-272
2109 atoms, 2151 bonds, 272 residues, 1 model selected
> color (#!4.2 & sel) orange
> select #4.2/A:273-560
2287 atoms, 2340 bonds, 288 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> select #4.2/A:431-511
622 atoms, 634 bonds, 81 residues, 1 model selected
> color sel dark sea green
> select #4.2/A:561-928
2883 atoms, 2939 bonds, 368 residues, 1 model selected
> select #4.2/A:929-1078
1187 atoms, 1203 bonds, 150 residues, 1 model selected
> color sel silver
> color sel dark gray
> select #4.2/A:1079-1160
672 atoms, 683 bonds, 82 residues, 1 model selected
> color sel goldenrod
> select clear
> turn y 90
[Repeated 2 time(s)]
> turn z 90
> turn z -90
> turn y 90
[Repeated 1 time(s)]
> turn z 90
[Repeated 2 time(s)]
> select #2/P#2/T
1047 atoms, 1173 bonds, 61 pseudobonds, 51 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1047 atom styles
> show sel cartoons
> color (#!2 & sel) dim gray
> select clear
> save /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_colored_structure.cxs
——— End of log from Fri Dec 29 14:59:12 2023 ———
opened ChimeraX session
BLAST job failed
> ui tool show "Side View"
> select #4.2/A:618@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
84 atoms, 83 bonds, 10 residues, 2 models selected
> select up
9138 atoms, 9320 bonds, 1160 residues, 2 models selected
> select down
84 atoms, 83 bonds, 10 residues, 2 models selected
> select add #2/T:12
106 atoms, 107 bonds, 11 residues, 3 models selected
> select #4.2/A:644@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
23 atoms, 22 bonds, 3 residues, 2 models selected
> select up
9138 atoms, 9320 bonds, 1160 residues, 2 models selected
> select #2/T:12
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4.2/A:650@N
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
78 atoms, 78 bonds, 9 residues, 2 models selected
> select up
9138 atoms, 9320 bonds, 1160 residues, 2 models selected
> select add #2/T:13
9160 atoms, 9344 bonds, 1161 residues, 3 models selected
> select subtract #2/T:13
9138 atoms, 9320 bonds, 1160 residues, 3 models selected
> select clear
> select #4.2/A:649@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
78 atoms, 78 bonds, 9 residues, 2 models selected
> select up
9138 atoms, 9320 bonds, 1160 residues, 2 models selected
> select ~sel
11684 atoms, 11990 bonds, 62 pseudobonds, 1412 residues, 12 models selected
> surface style #1-2#4.1 dot
> transparency (#!1-2#!4.1 & sel) 90
> select clear
> turn x 90
> select #4.2/A:561-952
3076 atoms, 3138 bonds, 392 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> select #4.2/A:1079-1160
672 atoms, 683 bonds, 82 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> select clear
> save /Users/krystian/Library/CloudStorage/OneDrive-
> Osobisty/Dokumenty/Doktorat/Publikacja/Review/Structures/Figure3A_colored_structure.cxs
——— End of log from Wed Jan 3 15:29:38 2024 ———
opened ChimeraX session
BLAST job failed
> close session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1071, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 721, in file_close_cb
run(session, 'close session')
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/close.py", line 71, in close_session
session.reset()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 5
KeyError: 5
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
See log for complete Python traceback.
> close session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1071, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 721, in file_close_cb
run(session, 'close session')
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/close.py", line 71, in close_session
session.reset()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 552, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 641, in reset_state
task.terminate()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 208, in terminate
self.session.tasks.remove(self)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 556, in remove
self.__delitem__(task.id)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
KeyError: 5
KeyError: 5
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 545, in __delitem__
task = self._tasks[key]
~~~~~~~~~~~^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63ZE/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 3 godziny i 6 minut
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Display:
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900 @ 60.00Hz
Mirror: Off
Online: Yes
Television: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 22 months ago
| Component: | Unassigned → Task Manager/Web Services |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → KeyError in tasks after opening then closing session with BLAST failure |
comment:2 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
It is no longer possible for that function to fail.
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Reported by Krystian