![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 3 years ago
#6528 closed defect (can't reproduce)
Crash opening mmCIF file
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.19.0-20-amd64-x86_64-with-glibc2.28
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007f8701f76700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007f8714a5b700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007f88d383b740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 40 in open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 403 in remember_data_format
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 432 in collated_open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 181 in provider_open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 155 in _qt_safe
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> mousemode setting zoom speed 3
> mousemode setting rotate speed 0.15
> mousemode setting translate speed 2
> mousemode setting "rotate selected models" speed 0.2
> mousemode setting "translate selected models" speed 2
> mousemode setting "contour level" speed 0.2
> mousemode control wheelMode "contour level"
> mousemode middleMode pivot
> alias boyau cartoon style nucleic xsect oval width 1.6 thick 1.6
> alias model-color-IC3 color #$1/2,A-Z,0,3,a,b #ead4ae ; color #$1/4 #ffc800
> ; color #$1/5 #00007a ; color #$1/6 #e35300 ; color #$1/7 #009ddc
> alias model-color-aIF5B color #$1/$2:2-229 #c0c0c0 ; color #$1/$2:601,701
> #c0c0c0 ; color #$1/$2:14-21 #292478 ; color #$1/$2:34-45 #7f7fff ; color
> #$1/$2:79-96 #1287ba ; color #$1/$2:230-349 yellow ; color #$1/$2:350-438
> #21ab21 ; color #$1/$2:439-464 red ; color #$1/$2:465-591 blue ; color
> #$1/$2:592-598 purple
> alias name-30S-Pab name head #$1/O,T,L,S,Z,Y,P,U,H,K,X,3/2:894-1363 ; name
> h5 #$1/2:54-66,363-374 ; name h15 #$1/2:375-403 ; name h14 #$1/2:348-359
> alias model-color-IC0 color #$1 #ead4ae ; color #$1/5 #00007a ; color #$1/4
> #ffd700 ; color #$1/6 #e35300 ; color #$1/1 #a24fdc ; color #$1/7,8,9
> #488e3e
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open chimerax-webinar.cxs
opened ChimeraX session
> show #1 models
> show #2 models
> show #3 models
> hide #!6 models
> view list
Named views: GTP-zone, start-codon
> view GTP-zone
> view start-codon
> hide #3 models
> show #3 models
> hide #3 models
> show #!5 models
> show #!4 models
> hide #2 models
> hide #1 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> open /work/ramy/Chimera/PDB/1G7T.cif
1G7T.cif title:
X-ray structure of translation initiation factor IF2/EIF5B complexed with
gdpnp [more info...]
Chain information for 1G7T.cif #13
---
Chain | Description | UniProt
A | translation initiation factor IF2/EIF5B | IF2P_METTH
Non-standard residues in 1G7T.cif #13
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
> hide #!5 models
> show #1 models
> mmaker #13 to #1
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 model_emma_aIF5B-DeltaC_refine_28.pdb, chain A (#1) with 1G7T.cif,
chain A (#13), sequence alignment score = 1456.4
RMSD between 80 pruned atom pairs is 1.269 angstroms; (across all 440 pairs:
9.438)
> open /work/ramy/Chimera/PDB/5FG3.pdb
Chain information for 5FG3.pdb #14
---
Chain | Description
A | No description available
> mmaker #14 to #1
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 model_emma_aIF5B-DeltaC_refine_28.pdb, chain A (#1) with 5FG3.pdb,
chain A (#14), sequence alignment score = 1489.7
RMSD between 164 pruned atom pairs is 0.846 angstroms; (across all 451 pairs:
11.338)
> hide #1 models
Drag select of 207 atoms, 1167 residues, 8 pseudobonds, 173 bonds
> cofr sel
> select clear
> hide #!13 models
> hide #14 atoms
> graphics silhouettes false
Drag select of 598 residues
> cofr sel
> select clear
> model-color-aIF5B 14 a
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #2 models
> color #14/A:13-237 #c0c0c0
> color #14/A:26-33 #292478
> color #14/A:45-56 #7f7fff
> color #14/A:90-107 #1287ba
> color #14/A:238-358 yellow
> color #$1/$2:350-438 #21ab21 ; color #$1/$2:439-464 red ; color
> #$1/$2:465-591 blue ; color #$1/$2:592-598 purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> hide #2 models
> show #1 models
> show #2 models
> hide #1 models
> color #14 pink
> hide #2 models
> show #3 models
> hide #3 models
> color #14/A:13-237 #c0c0c0
> color #14/A:26-33 #292478
> color #14/A:45-56 #7f7fff
> color #14/A:90-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-591 blue
> color #14/A:599-610 purple
> color #14/A:13-237 #c0c0c0
> color #14/A:26-33 #292478
> color #14/A:45-56 #7f7fff
> color #14/A:90-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> show #3 models
> hide #14 models
> show #14 models
> hide #3 models
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:45-56 #7f7fff
> color #14/A:90-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> show #1 models
> show #3 models
> hide #1 models
> show #2 models
> hide #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:90-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> hide #2 models
> show #2 models
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:86-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:87-107 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> hide #2 models
> show #2 models
> hide #14 models
> show #14 models
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:87-106 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:87-105 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> hide #2 models
> ui tool show Matchmaker
> matchmaker #14 to #2 showAlignment true
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 model_emma_aIF5B-FL_refine_12.pdb, chain A (#2) with 5FG3.pdb,
chain A (#14), sequence alignment score = 1884.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
model_emma_aIF5B-FL_refine_12.pdb #2/A, 5FG3.pdb #14/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 293 pruned atom pairs is 0.962 angstroms; (across all 592 pairs:
10.575)
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!13 models
> matchmaker #!13 to #14 showAlignment true
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 5FG3.pdb, chain A (#14) with 1G7T.cif, chain A (#13), sequence
alignment score = 1791.3
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 1G7T.cif #13/A, 5FG3.pdb #14/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 260 pruned atom pairs is 1.090 angstroms; (across all 566 pairs:
10.622)
> color zone #13 near #14
color zone: No surfaces specified.
> select #13
4734 atoms, 4470 bonds, 8 pseudobonds, 899 residues, 3 models selected
> hide sel atoms
> select clear
> hide #14 models
> show #14 models
> hide #!13 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!11 models
> show #!13 models
> hide #14 models
> hide #!13 models
> show #14 models
> color #14/A:13-237 #c0c0c0
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> color #14/A:13-237 #c0c0c0
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-610 blue
> pwd
Current working directory is: /work/ramy/Documents/Creation/Congres/Webinar
> cd ../../
Current working directory is: /work/ramy/Documents/Creation
> cd Thesis
Current working directory is: /work/ramy/Documents/Creation/Thesis
> cd Images
Current working directory is: /work/ramy/Documents/Creation/Thesis/Images
> cd Introduction
Current working directory is:
/work/ramy/Documents/Creation/Thesis/Images/Introduction
> pwd
Current working directory is:
/work/ramy/Documents/Creation/Thesis/Images/Introduction
> save figure-aIF5B-5FG3.png transparentBackground true
> graphics silhouettes true
> save figure-aIF5B-5FG3-silh.png transparentBackground true
> color #14/A:13-237 #c0c0c0
> color #14/A:238-358 yellow
> color #14/A:359-445 #21ab21
> color #14/A:446-472 red
> color #14/A:473-610 blue
> save figure-aIF5B-5FG3-silh.png transparentBackground true
> graphics silhouettes false
> save figure-aIF5B-5FG3.png transparentBackground true
> select #14/A:238-610
2911 atoms, 2950 bonds, 373 residues, 1 model selected
> hide sel cartoons
> color #14/A:13-237 #c0c0c0
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> color #14/A:13-237 #c0c0c0
> color #14/A:22-29 #292478
> color #14/A:42-55 #7f7fff
> color #14/A:87-106 #1287ba
> color #14/A:238-358 yellow
> color #14/A:359-446 #21ab21
> color #14/A:447-472 red
> color #14/A:473-598 blue
> color #14/A:599-610 purple
> show #1 models
> hide #14 models
> select #2/A:132
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:132-136
44 atoms, 43 bonds, 5 residues, 1 model selected
> hide #1 models
> show #2 models
> show #14 models
> color #14/A:141-145 orange
> hide #14 models
> select #2/A:195-196
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:196-203
62 atoms, 63 bonds, 8 residues, 1 model selected
> show #14 models
> select #2/A:200
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:200-202
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #14/A:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #14/A:209-211
22 atoms, 21 bonds, 3 residues, 1 model selected
> hide #2 models
> color sel green
> select clear
> select #14 & ligand
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> graphics silhouettes true
> select #14/A:701@O2'
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 30 bonds, 1 residue, 1 model selected
> color sel #c0c0c0
> color sel byhetero
> select #14 & ions
Nothing selected
> select clear
> show #14 atoms
> hide #14 atoms
> select #14 & ligand
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save figure-aIF5B-5FG3-domain-I.png transparentBackground true
> pwd
Current working directory is:
/work/ramy/Documents/Creation/Thesis/Images/Introduction
> save figure-aIF5B-5FG3-domain-I.png transparentBackground true
> hide #14 models
> open /work/ramy/Chimera/PDB/4N3N.pdb
4N3N.pdb title:
Crystal structure of eukaryotic translation initiation factor EIF5B (517-1116)
from chaetomium thermophilum, apo form [more info...]
Chain information for 4N3N.pdb #15
---
Chain | Description | UniProt
A | eukaryotic translation initiation factor 5B-like protein, EIF5B(517-C) |
G0S8G9_CHATD
Non-standard residues in 4N3N.pdb #15
---
LAC — lactic acid
> show #!5 models
> hide #!15 models
> close #15
> open /work/ramy/Chimera/PDB/4N3S.pdb
4N3S.pdb title:
Crystal structure of eukaryotic translation initiation factor EIF5B (399-852)
from saccharomyces cerevisiae, apo form [more info...]
Chain information for 4N3S.pdb #15
---
Chain | Description | UniProt
A | eukaryotic translation initiation factor 5B | IF2P_YEAST
B | eukaryotic translation initiation factor 5B | IF2P_YEAST
Non-standard residues in 4N3S.pdb #15
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
> select #15/B
3846 atoms, 3516 bonds, 2 pseudobonds, 823 residues, 2 models selected
> delete sel
> mmaker #15 to #5
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 6WOO.cif, chain 1 (#5) with 4N3S.pdb, chain A (#15), sequence
alignment score = 1854.2
RMSD between 125 pruned atom pairs is 0.890 angstroms; (across all 441 pairs:
8.394)
> mmaker #15 to #5:1-627
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 6WOO.cif, chain 1 (#5) with 4N3S.pdb, chain A (#15), sequence
alignment score = 933.3
RMSD between 177 pruned atom pairs is 0.798 angstroms; (across all 216 pairs:
4.814)
> select #15
3868 atoms, 3520 bonds, 2 pseudobonds, 840 residues, 2 models selected
> hide sel atoms
> select clear
> mmaker #15 to #5:1-627 showAli true
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 6WOO.cif, chain 1 (#5) with 4N3S.pdb, chain A (#15), sequence
alignment score = 933.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6WOO.cif #5/1, 4N3S.pdb #15/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 177 pruned atom pairs is 0.798 angstroms; (across all 216 pairs:
4.814)
> name list
There are no user-defined specifier names.
> hide #!5 models
> show #!5 models
> hide #!15 models
> color #15/A:401-627 #c0c0c0
> color #15/A:412-419 #292478
> color #15/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-744 yellow
> color #15/A:745-835 #21ab21
> color #15/A:836-861 red
> color #15/A:862-1000 blue
> show #!15 models
> select #5:852-1000
1181 atoms, 1199 bonds, 149 residues, 1 model selected
> hide sel cartoons
> color #15/A:401-627 #c0c0c0
> color #15/A:412-420 #292478
> color #15/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-744 yellow
> color #15/A:745-835 #21ab21
> color #15/A:836-861 red
> color #15/A:862-1000 blue
> hide #!15 models
> select #5 & ligand
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!15 models
> hide #!5 models
> select #15 & ligand
18 atoms, 14 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #15
3868 atoms, 3520 bonds, 2 pseudobonds, 840 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select clear
> show #!5 models
> hide #!5,15 atoms
> select #55 & ligand
Nothing selected
> select #5 & ligand
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #c0c0c0
> color sel byhetero
> select clear
> color #15/A:401-627 #c0c0c0
> color #15/A:412-420 #292478
> color #5/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-744 yellow
> color #15/A:745-835 #21ab21
> color #15/A:836-861 red
> color #15/A:862-1000 blue
> color #15/A:401-627 #c0c0c0
> color #15/A:412-420 #292478
> color #15/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-744 yellow
> color #15/A:745-835 #21ab21
> color #15/A:836-861 red
> color #15/A:862-1000 blue
> color #5/1:431-443 #7f7fff
> hide #!15 models
> show #!15 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #2 models
> select #2
4783 atoms, 4819 bonds, 638 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/A:912@C5'
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 30 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> show #!5 models
> hide #2 models
> hide #!15 models
> show #!15 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!15 models
> show #!15 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!15 models
> save figure-eIF5B-6woo-switch-on.png transparentBackground true
> view name figure-switches
> show #!15 models
> select #5
4732 atoms, 4806 bonds, 601 residues, 1 model selected
> hide sel cartoons
> select clear
> save figure-eIF5B-4n3s-switch-off.png transparentBackground true
> hide #!15 models
> show #!15 models
> select #5
4732 atoms, 4806 bonds, 601 residues, 1 model selected
> show sel cartoons
> select clear
> view figure-switches
> color #15/A:401-627 #c0c0c0
> color #15/A:412-420 #292478
> color #15/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-746 yellow
> color #15/A:747-834 #21ab21
> color #15/A:835-861 red
> color #15/A:862-1000 blue
> color #15/A:401-627 #c0c0c0
> color #15/A:412-420 #292478
> color #15/A:431-443 #7f7fff
> color #15/A:476-495 #1287ba
> color #15/A:628-746 yellow
> color #15/A:747-834 #21ab21
> color #15/A:835-861 red
> color #15/A:862-1000 blue
> select #5/1:852-1000
1181 atoms, 1199 bonds, 149 residues, 1 model selected
> hide sel cartoons
> view
> show #1 models
> hide #1 models
> open /work/ramy/Chimera/PDB/6UZ7.cif
Summary of feedback from opening /work/ramy/Chimera/PDB/6UZ7.cif
---
note | Fetching CCD GCP from http://ligand-expo.rcsb.org/reports/G/GCP/GCP.cif
6UZ7.cif title:
K.lactis 80S ribosome with p/PE tRNA and eIF5B [more info...]
Chain information for 6UZ7.cif #16
---
Chain | Description | UniProt
1 | KLLA0F23265p | Q6CIX3_KLULA
2 | 18S ribosomal RNA |
3 | RNA (76-mer) |
5 | 25S ribosomal RNA |
7 | RNA (121-mer) |
8 | 5.8S ribosomal RNA |
A | 40S ribosomal protein S0 | RSSA_KLULA
AA | KLLA0D16027p | Q6CQM3_KLULA
AB | 60S ribosomal protein L3 | RL3_KLULA
AC | KLLA0B07139p | Q6CW41_KLULA
AD | KLLA0D06941p | Q6CRR9_KLULA
AE | KLLA0B04686p | Q6CWE7_KLULA
AF | KLLA0D03410p | Q6CS71_KLULA
AG | KLLA0E00573p | B4UN96_KLULA
AH | KLLA0F04499p | Q6CLA6_KLULA
AI | KLLA0D05643p | Q6CRX7_KLULA
AJ | KLLA0F08261p | Q6CKT4_KLULA
AK | GDPCP |
AL | 60S ribosomal protein L13 | Q875M0_KLULC
AM | KLLA0B13409p | Q6CVB1_KLULA
AN | Ribosomal protein L15 | Q6CJL7_KLULA
AO | KLLA0F04675p | Q6CL98_KLULA
AP | KLLA0A06336p | Q6CXQ6_KLULA
AQ | KLLA0A07227p | Q6CXL8_KLULA
AR | KLLA0E12453p | Q6CNH9_KLULA
AS | 60S ribosomal protein L20 |
AT | KLLA0E23651p | Q6CM20_KLULA
AU | KLLA0D05181p | Q6CRZ8_KLULA
AV | KLLA0E06997p | Q6CP75_KLULA
AW | 60S ribosomal protein L24 | RL24_KLULA
AX | 60S ribosomal protein L25 | RL25_KLULA
AY | KLLA0B05742p | Q6CW97_KLULA
AZ | KLLA0E03455p | Q6CPN9_KLULA
B | 40S ribosomal protein S1 | RS3A_KLULA
Ba | RPL28 | Q8J287_KLULC
Bb | 60S ribosomal protein L29 | Q6CQM1_KLULA
Bc | 60S ribosomal protein L30 | RL30_KLULA
Bd | KLLA0B02937p | Q6CWM6_KLULA
Be | KLLA0E06843p | Q6CP82_KLULA
Bf | KLLA0D07405p | Q6CRP7_KLULA
Bg | KLLA0C08371p | Q6CU17_KLULA
Bh | KLLA0F05247p | Q6CL71_KLULA
Bi | 60S ribosomal protein L36 | Q6CR18_KLULA
Bj | Ribosomal protein L37 | Q6CUW0_KLULA
Bk | KLLA0C18216p | Q6CSS8_KLULA
Bl | 60S ribosomal protein L39 |
Bm | Ubiquitin fusion protein | Q9Y854_KLULC
Bn | 60S ribosomal protein L41 |
Bo | 60S ribosomal protein L44 | RL44_KLULA
Bp | KLLA0E05941p | Q6CPC5_KLULA
Bq | Ribosomal protein | Q6CWR9_KLULA
Br | 60S acidic ribosomal protein P0 | Q6CW89_KLULA
C | KLLA0F09812p | Q6CKL3_KLULA
D | KLLA0D08305p | Q6CRK7_KLULA
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA
F | KLLA0D10659p | Q6CRA3_KLULA
G | 40S ribosomal protein S6 | RS6_KLULA
H | 40S ribosomal protein S7 | Q6CTD6_KLULA
I | 40S ribosomal protein S8 | Q6CMG3_KLULA
J | KLLA0E23673p | Q6CM18_KLULA
K | KLLA0B08173p | Q6CVZ5_KLULA
L | KLLA0A10483p | Q6CX80_KLULA
M | 40S ribosomal protein S12 | Q6CLU4_KLULA
N | KLLA0F18040p | Q6CJK0_KLULA
O | 40S ribosomal protein S14 | RS14_KLULA
P | KLLA0F07843p | Q6CKV4_KLULA
Q | 40S ribosomal protein S16 | RS16_KLULA
R | KLLA0B01474p | Q6CWU3_KLULA
S | KLLA0B01562p | Q6CWT9_KLULA
T | KLLA0A07194p | Q6CXM0_KLULA
U | KLLA0F25542p | Q6CIM1_KLULA
V | 40S ribosomal protein S21 | RS21_KLULA
W | 40S ribosomal protein S22 | RS22_KLULA
X | RPS23 | Q875M3_KLULC
Y | 40S ribosomal protein S24 | Q6CU44_KLULA
Z | 40S ribosomal protein S25 | Q6CW78_KLULA
a | 40S ribosomal protein S26 | Q6CS01_KLULA
b | 40S ribosomal protein S27 | Q6CNL2_KLULA
c | 40S ribosomal protein S28 | RS28_KLULA
d | 40S ribosomal protein S29 | RS29_KLULA
e | 40S ribosomal protein S30 | Q6CUH5_KLULA
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA
g | KLLA0E12277p | Q6CNI7_KLULA
Non-standard residues in 6UZ7.cif #16
---
GCP — phosphomethylphosphonic acid guanylate ester
ZN — zinc ion
Associated 6UZ7.cif chain 1 to 4N3S.pdb, chain A with 68 mismatches
Associated 6UZ7.cif chain AK to 4N3S.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 6WOO.cif #5/1, 4N3S.pdb #15/A,
6UZ7.cif #16/AK
> select #16
211187 atoms, 226519 bonds, 4562 pseudobonds, 17563 residues, 4 models
selected
> ~select #16/1
206453 atoms, 221709 bonds, 4562 pseudobonds, 16962 residues, 4 models
selected
> delete sel
Chains used in RMSD evaluation for alignment 1: 6WOO.cif #5/1, 4N3S.pdb #15/A,
6UZ7.cif #16/1
> mmaker #16 to #5
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 6WOO.cif, chain 1 (#5) with 6UZ7.cif, chain 1 (#16), sequence
alignment score = 2305.9
RMSD between 506 pruned atom pairs is 1.166 angstroms; (across all 600 pairs:
2.156)
> select #16
4734 atoms, 4810 bonds, 601 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #!5 models
> hide #!15 models
> select #16 & ligand
32 atoms, 34 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #16/A:401-627 #c0c0c0
> color #16/A:412-420 #292478
> color #16/A:431-443 #7f7fff
> color #16/A:476-495 #1287ba
> color #16/A:628-746 yellow
> color #16/A:747-834 #21ab21
> color #16/A:835-861 red
> color #16/A:862-1000 blue
> color #16/1:401-627 #c0c0c0
> color #16/1:412-420 #292478
> color #16/1:431-443 #7f7fff
> color #16/1:476-495 #1287ba
> color #16/1:628-746 yellow
> color #16/1:747-834 #21ab21
> color #16/1:835-861 red
> color #16/1:862-1000 blue
> show #!5 models
> open /work/ramy/Chimera/PDB/4V8Z.cif
===== Log before crash end =====
Log:
> mousemode setting zoom speed 3
> mousemode setting rotate speed 0.15
> mousemode setting translate speed 2
> mousemode setting "rotate selected models" speed 0.2
> mousemode setting "translate selected models" speed 2
> mousemode setting "contour level" speed 0.2
> mousemode control wheelMode "contour level"
> mousemode middleMode pivot
> alias boyau cartoon style nucleic xsect oval width 1.6 thick 1.6
> alias model-color-IC3 color #$1/2,A-Z,0,3,a,b #ead4ae ; color #$1/4 #ffc800
> ; color #$1/5 #00007a ; color #$1/6 #e35300 ; color #$1/7 #009ddc
> alias model-color-aIF5B color #$1/$2:2-229 #c0c0c0 ; color #$1/$2:601,701
> #c0c0c0 ; color #$1/$2:14-21 #292478 ; color #$1/$2:34-45 #7f7fff ; color
> #$1/$2:79-96 #1287ba ; color #$1/$2:230-349 yellow ; color #$1/$2:350-438
> #21ab21 ; color #$1/$2:439-464 red ; color #$1/$2:465-591 blue ; color
> #$1/$2:592-598 purple
> alias name-30S-Pab name head #$1/O,T,L,S,Z,Y,P,U,H,K,X,3/2:894-1363 ; name
> h5 #$1/2:54-66,363-374 ; name h15 #$1/2:375-403 ; name h14 #$1/2:348-359
> alias model-color-IC0 color #$1 #ead4ae ; color #$1/5 #00007a ; color #$1/4
> #ffd700 ; color #$1/6 #e35300 ; color #$1/1 #a24fdc ; color #$1/7,8,9
> #488e3e
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 418.211.00
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7820 Tower
OS: Debian GNU/Linux 10 buster
Architecture: 64bit ELF
Virutal Machine: none
CPU: 40 Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
Cache Size: 14080 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 12Gi 32Gi 801Mi 17Gi 48Gi
Swap: 37Gi 0B 37Gi
Graphics:
9e:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [10de:1bb1] (rev a1)
Subsystem: NVIDIA Corporation GP104GL [Quadro P4000] [10de:11a3]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening mmCIF file |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
