![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#14945 closed defect (can't reproduce)
Crash in Chromium backend
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000200dff2c0 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 66000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 2711,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2024-04-10 09:42:09.9783 +0200",
"incident" : "5D67DAC0-73D5-4DFD-8B2F-58D890CF7E88",
"pid" : 57555,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-09 10:55:04.6136 +0200",
"procStartAbsTime" : 847860747723,
"procExitAbsTime" : 1584127583586,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5CDF073F-E15D-55D8-83EB-4BF634E94595","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FD94E8AF-28E3-E9E7-AEBF-8A0243BFDD15",
"throttleTimeout" : 2147483647,
"wakeTime" : 11,
"sleepWakeUUID" : "229103D8-07A6-41D4-901D-A5FB77A19CA1",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140722675728360\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc8d194000-7ffc97c60000 [170.8M] r-x\/r-x SM=COW ...t_id=50f9c711",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140722675728360\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc8d194000-7ffc97c60000 [170.8M] r-x\/r-x SM=COW ...t_id=50f9c711",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/mayin/Desktop/Murphy lab/CODH_ACS/3git.pdb"
3git.pdb title:
Crystal structure of A truncated acetyl-coa synthase [more info...]
Chain information for 3git.pdb #1
---
Chain | Description | UniProt
A B C D E F | carbon monoxide dehydrogenase/acetyl-coa synthase subunit α |
DCMA_MOOTH 311-729
Non-standard residues in 3git.pdb #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
H2S — hydrosulfuric acid (hydrogen sulfide)
SF4 — iron/sulfur cluster
SO4 — sulfate ion
ZN — zinc ion
> show cartoons
> hide atoms
> lighting soft
> ui tool show "Model Panel"
> ui tool show "Unit Cell"
> unitcell #1
> unitcell #1 cells 2,1,1
> unitcell delete #1
> unitcell #1 cells 2,1,1
> select #2.8
20147 atoms, 20350 bonds, 48 pseudobonds, 2765 residues, 2 models selected
> select #2.8/c
3348 atoms, 3388 bonds, 8 pseudobonds, 454 residues, 2 models selected
> cofr sel
> open
> /Users/mayin/Desktop/CODHACS_20221216_processing/CODHACS_CoFeSP_model_building/jobs_from_terminal/CODHACS2/Semi-
> extended_ACS_J1646/RealSpaceRefine_772_J1646_fullCODH_12_ADP/CODHACS_semi_extended_real_space_refined_772.pdb
Chain information for CODHACS_semi_extended_real_space_refined_772.pdb #3
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> mmaker #3/d to #2.8/c
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 3git.pdb #8, chain C (#2.8) with
CODHACS_semi_extended_real_space_refined_772.pdb, chain D (#3), sequence
alignment score = 1335.7
RMSD between 361 pruned atom pairs is 1.199 angstroms; (across all 413 pairs:
1.500)
> ~select
Nothing selected
> hide #!1 models
> hide #!2 models
> dssp
> show #!2 models
> mmaker #3/d:290-473 to #2.8/c
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 3git.pdb #8, chain C (#2.8) with
CODHACS_semi_extended_real_space_refined_772.pdb, chain D (#3), sequence
alignment score = 539.6
RMSD between 168 pruned atom pairs is 0.772 angstroms; (across all 177 pairs:
1.366)
> hide #!3 models
> show #!3 models
> mmaker #3/d:473-end to #2.8/c
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 3git.pdb #8, chain C (#2.8) with
CODHACS_semi_extended_real_space_refined_772.pdb, chain D (#3), sequence
alignment score = 795.3
RMSD between 228 pruned atom pairs is 0.840 angstroms; (across all 235 pairs:
0.929)
> hide #3 & ~#3/d:290-end target abc
> mmaker #3/d:290-473 to #2.8/c
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 3git.pdb #8, chain C (#2.8) with
CODHACS_semi_extended_real_space_refined_772.pdb, chain D (#3), sequence
alignment score = 539.6
RMSD between 168 pruned atom pairs is 0.772 angstroms; (across all 177 pairs:
1.366)
> unitcell #1 cells 2,2,2
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> select sel :> 100 & ~sel
709495 atoms, 716184 bonds, 1689 pseudobonds, 97341 residues, 86 models
selected
> ~select
Nothing selected
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> select sel :> 150 & ~sel
554273 atoms, 559351 bonds, 1317 pseudobonds, 76152 residues, 65 models
selected
> hide sel target abc
> ~select
Nothing selected
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> select sel :> 70 & ~sel
811080 atoms, 818723 bonds, 1938 pseudobonds, 111410 residues, 91 models
selected
> hide sel target abc
> ~select
Nothing selected
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> cofr sel
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!2 models
> show #!1 models
> select add #1
20147 atoms, 20350 bonds, 48 pseudobonds, 2765 residues, 2 models selected
> view #3 clip false
> cofr sel
> ~select
Nothing selected
> show #!2 models
> hide #!1 models
> show #!3 models
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> cofr sel
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open "/Users/mayin/Desktop/Murphy lab/CODH_ACS/6ytt.pdb"
6ytt.pdb title:
Co-dehydrogenase/acetyl-coa synthase (codh/acs) from clostridium
autoethanogenum At 3.0-A resolution [more info...]
Chain information for 6ytt.pdb #4
---
Chain | Description | UniProt
A | Co dehydrogenase/acetyl-coa synthase complex, β subunit | U5RWA4_9CLOT
1-708
B C | carbon-monoxide dehydrogenase (acceptor),carbon-monoxide dehydrogenase
(acceptor) | U5RTE2_9CLOT 1-400
D | Co dehydrogenase/acetyl-coa synthase complex, β subunit | U5RWA4_9CLOT
1-708
Non-standard residues in 6ytt.pdb #4
---
F — fluoride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
NI — nickel (II) ion
PE4 — 2-{2-[2-(2-{2-[2-(2-ethoxy-
ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol (polyethylene glycol
PEG4000)
SF4 — iron/sulfur cluster
XCC — Fe(4)-Ni(1)-S(4) cluster (C cluster)
> hide #!3 models
> select add #4
20389 atoms, 20720 bonds, 25 pseudobonds, 2711 residues, 3 models selected
> cofr sel
> select subtract #4
Nothing selected
> unitcell #4 cells 2,2,2
> color #5.2 #ec8b7cff
> color #5.6 #b1b8ecff
> select add #5.6
20389 atoms, 20720 bonds, 25 pseudobonds, 2711 residues, 3 models selected
> cofr sel
> select subtract #5.6
Nothing selected
> select add #5.6
20389 atoms, 20720 bonds, 25 pseudobonds, 2711 residues, 3 models selected
> select sel :> 70 & ~sel
2109769 atoms, 2137756 bonds, 3667 pseudobonds, 284354 residues, 285 models
selected
> hide sel target abc
> open "/Users/mayin/Desktop/Murphy lab/CODH_ACS/Manuscript/REFMAC.pdb"
REFMAC.pdb title:
\--- [more info...]
Chain information for REFMAC.pdb #6
---
Chain | Description
A D | No description available
B | No description available
C | No description available
Non-standard residues in REFMAC.pdb #6
---
ACO — (ACO)
CA — (CA)
EDO — (EDO)
GOL — (GOL)
NA — (NA)
NI — (NI)
PE4 — (PE4)
PEG — (PEG)
SF4 — (SF4)
XCC — (XCC)
> mmaker #6/d to #5.6/a:290-473
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 6ytt.pdb #6, chain A (#5.6) with REFMAC.pdb, chain D (#6), sequence
alignment score = 834.8
RMSD between 174 pruned atom pairs is 0.764 angstroms; (across all 184 pairs:
1.159)
> select #5.13/B:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> cofr sel
> ~select
Nothing selected
> mmaker #6/d to #5.2/d:290-473
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 6ytt.pdb #2, chain D (#5.2) with REFMAC.pdb, chain D (#6), sequence
alignment score = 826.9
RMSD between 171 pruned atom pairs is 0.713 angstroms; (across all 181 pairs:
1.083)
> hide #!4 models
> hide #!5 models
> cofr sel
> ~select
Nothing selected
> show #!5 models
> hide #!6 models
> mmaker #3/d to #5.2/d:290-473
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 6ytt.pdb #2, chain D (#5.2) with
CODHACS_semi_extended_real_space_refined_772.pdb, chain D (#3), sequence
alignment score = 874.9
RMSD between 172 pruned atom pairs is 0.705 angstroms; (across all 181 pairs:
1.080)
> show #!3 models
> hide #!5 models
> select add #3
17018 atoms, 17243 bonds, 106 pseudobonds, 2261 residues, 2 models selected
> show sel cartoons
> select subtract #3
Nothing selected
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!3 models
> unitcell #4 cells 1,1,2
> unitcell #4 cells 2,2,2
> open "/Users/mayin/Desktop/Murphy
> lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/3GIT_chainA_alignedTo_J1308.pdb"
3GIT_chainA_alignedTo_J1308.pdb title:
Crystal structure of A truncated acetyl-coa synthase [more info...]
Chain information for 3GIT_chainA_alignedTo_J1308.pdb #7
---
Chain | Description | UniProt
A B C D | carbon monoxide dehydrogenase/acetyl-coa synthase subunit α |
DCMA_MOOTH 311-729
Non-standard residues in 3GIT_chainA_alignedTo_J1308.pdb #7
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
H2S — hydrosulfuric acid (hydrogen sulfide)
SF4 — iron/sulfur cluster
SO4 — sulfate ion
ZN — zinc ion
> open "/Users/mayin/Desktop/Murphy
> lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/acetylCoA_alignedTo_J1308.pdb"
Summary of feedback from opening /Users/mayin/Desktop/Murphy
lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/acetylCoA_alignedTo_J1308.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 3
VAL A 26 1 24
Start residue of secondary structure not found: HELIX 2 2 PRO A 45 THR A 51 1
7
Start residue of secondary structure not found: HELIX 3 3 VAL A 58 GLU A 62 1
5
Start residue of secondary structure not found: HELIX 4 4 GLY A 63 LEU A 65 1
3
Start residue of secondary structure not found: HELIX 5 5 ASP A 66 SER A 70 1
5
224 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (523 )
Cannot find LINK/SSBOND residue CYS (333 )
Cannot find LINK/SSBOND residue CYS (481 )
Cannot find LINK/SSBOND residue SF4 (708 )
Cannot find LINK/SSBOND residue CYS (295 )
47 messages similar to the above omitted
acetylCoA_alignedTo_J1308.pdb title:
\--- [more info...]
Non-standard residues in acetylCoA_alignedTo_J1308.pdb #8
---
ACO — (ACO)
> hide #!6 models
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> view clip false
> hide #7 & ~#7/a target abc
> select #7/A:740@S
1 atom, 1 residue, 1 model selected
> style sel ball
Changed 1 atom style
> select #7/A:408
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #7
13439 atoms, 13578 bonds, 32 pseudobonds, 1841 residues, 2 models selected
> select subtract #7
Nothing selected
> open "/Users/mayin/Desktop/Murphy
> lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/acetylCoABound_alignedTo_J1308.pdb"
acetylCoABound_alignedTo_J1308.pdb title:
\--- [more info...]
Chain information for acetylCoABound_alignedTo_J1308.pdb #9
---
Chain | Description
A D | No description available
B | No description available
C | No description available
Non-standard residues in acetylCoABound_alignedTo_J1308.pdb #9
---
ACO — (ACO)
CA — (CA)
EDO — (EDO)
GOL — (GOL)
NA — (NA)
NI — (NI)
PE4 — (PE4)
PEG — (PEG)
SF4 — (SF4)
XCC — (XCC)
> hide #!7 models
> hide #8 models
> open "/Users/mayin/Desktop/Murphy
> lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/6YTT_chainA_alignedTo_J1308.pdb"
6YTT_chainA_alignedTo_J1308.pdb title:
Co-dehydrogenase/acetyl-coa synthase (codh/acs) from clostridium
autoethanogenum At 3.0-A resolution [more info...]
Chain information for 6YTT_chainA_alignedTo_J1308.pdb #10
---
Chain | Description | UniProt
A | Co dehydrogenase/acetyl-coa synthase complex, β subunit | U5RWA4_9CLOT
1-708
B C | carbon-monoxide dehydrogenase (acceptor),carbon-monoxide dehydrogenase
(acceptor) | U5RTE2_9CLOT 1-400
D | Co dehydrogenase/acetyl-coa synthase complex, β subunit | U5RWA4_9CLOT
1-708
Non-standard residues in 6YTT_chainA_alignedTo_J1308.pdb #10
---
F — fluoride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
NI — nickel (II) ion
PE4 — 2-{2-[2-(2-{2-[2-(2-ethoxy-
ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol (polyethylene glycol
PEG4000)
SF4 — iron/sulfur cluster
XCC — Fe(4)-Ni(1)-S(4) cluster (C cluster)
> show #8 models
> hide #!9 models
> open "/Users/mayin/Desktop/Murphy
> lab/CODH_ACS/Manuscript/Useful_summary/Structures_alignedTo_J1308_ACScentral/semiextended_alignedTo_J1308.pdb"
Chain information for semiextended_alignedTo_J1308.pdb #11
---
Chain | Description
A | No description available
B C | No description available
D | No description available
> hide #!10 models
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes sel restrict #11 interModel false ignoreHiddenModels true reveal
> true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> ui tool show Clashes
> clashes sel restrict #11 ignoreHiddenModels true reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
23 clashes
atom1 atom2 overlap distance
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 P3B (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 NH2 1.854 1.886
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.631 1.769
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O7A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 NH2 1.407 1.253
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 1.291 2.009
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.195 2.175
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.160 2.360
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.146 2.224
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.134 2.266
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 1.106 2.654
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLU 596 OE1 1.105 1.955
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C5A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.083 2.287
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.078 2.442
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C4A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 0.899 2.471
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N4P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 NH1 0.868 2.412
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C3P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 NH1 0.837 2.683
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ASN 322 CB 0.783 2.737
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLU 596 OE1 0.779 2.251
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N3A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 0.758 2.642
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLY 608 CA 0.750 3.010
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O7A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 CZ 0.706 2.324
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 O 0.678 2.162
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CD 0.645 3.115
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 0.622 2.868
23 clashes
> show #!9 models
> hide #12 models
> hide #!9 models
> select subtract #8
Nothing selected
> select #11/d#8
5445 atoms, 5533 bonds, 41 pseudobonds, 711 residues, 4 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
semiextended_alignedTo_J1308.pdb #11/D ILE 707 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue ACO (net charge -4) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmph1q3sz93/ante.in.mol2 -fi
mol2 -o
/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmph1q3sz93/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(ACO) ``
(ACO) `Welcome to antechamber 20.0: molecular input file processor.`
(ACO) ``
(ACO) `Info: Finished reading file
(/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmph1q3sz93/ante.in.mol2);
atoms read (85), bonds read (87).`
(ACO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ACO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ACO) ``
(ACO) ``
(ACO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ACO) `Info: Total number of electrons: 422; net charge: -4`
(ACO) ``
(ACO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(ACO) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(ACO) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =144
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 238
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.075135 seconds
| QMMM: Dspev diag routine = 0.055825 seconds
| QMMM: Dspevd diag routine = 0.042277 seconds
| QMMM: Dspevx diag routine = 0.195198 seconds
| QMMM: Dsyev diag routine = 0.060438 seconds
| QMMM: Dsyevd diag routine = 0.044720 seconds
| QMMM: Dsyevr diag routine = 0.049573 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.030363 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 221.0810 303.5410 202.9490
QMMM: 2 2 C 220.6050 304.7230 202.5280
QMMM: 3 3 N 220.5650 305.2180 201.2880
QMMM: 4 4 C 221.0910 304.3570 200.3890
QMMM: 5 5 C 221.6090 303.1020 200.6680
QMMM: 6 6 C 221.5920 302.6860 202.0220
QMMM: 7 7 N 222.0510 301.5060 202.4340
QMMM: 8 8 N 222.0580 302.4920 199.4950
QMMM: 9 9 C 221.8120 303.3670 198.5440
QMMM: 10 10 N 221.1780 304.5070 199.0190
QMMM: 11 11 C 220.8910 305.7180 198.2030
QMMM: 12 12 C 219.7300 306.6700 198.5250
QMMM: 13 13 O 218.6820 306.5450 197.5900
QMMM: 14 14 C 220.3710 308.0800 198.4730
QMMM: 15 15 O 220.5150 308.8080 197.2410
QMMM: 16 16 P 221.5520 310.0990 197.2780
QMMM: 17 17 O 222.0930 310.4080 198.6540
QMMM: 18 18 O 222.7140 309.7960 196.3310
QMMM: 19 19 O 220.6720 311.2370 196.7920
QMMM: 20 20 C 221.7850 307.7820 198.9230
QMMM: 21 21 O 222.0710 306.4800 198.3450
QMMM: 22 22 C 221.9810 307.8100 200.4230
QMMM: 23 23 O 221.1260 308.8270 201.0160
QMMM: 24 24 P 221.6620 309.6670 202.2740
QMMM: 25 25 O 221.4470 308.8620 203.5100
QMMM: 26 26 O 223.0560 310.1350 201.9800
QMMM: 27 27 O 220.5990 310.8900 202.2890
QMMM: 28 28 P 219.5960 311.6410 203.3170
QMMM: 29 29 O 219.9090 311.1950 204.7060
QMMM: 30 30 O 219.6580 313.1120 203.0540
QMMM: 31 31 O 218.1240 311.1130 202.8900
QMMM: 32 32 C 216.4460 309.2690 202.8600
QMMM: 33 33 C 217.8990 309.6860 202.5600
QMMM: 34 34 C 215.7020 309.1860 201.5160
QMMM: 35 35 C 215.7460 310.3670 203.6790
QMMM: 36 36 C 216.2660 307.9090 203.5950
QMMM: 37 37 O 216.3370 306.8920 202.5850
QMMM: 38 38 C 217.1590 307.4790 204.7700
QMMM: 39 39 O 217.1390 306.2860 205.1140
QMMM: 40 40 N 217.9020 308.4080 205.3930
QMMM: 41 41 C 218.8440 308.1460 206.4880
QMMM: 42 42 C 220.0270 309.1450 206.5360
QMMM: 43 43 C 220.8010 309.1980 207.8460
QMMM: 44 44 O 221.0760 310.2860 208.3600
QMMM: 45 45 N 221.1260 308.0370 208.4430
QMMM: 46 46 C 222.0080 307.8930 209.6020
QMMM: 47 47 C 221.5080 308.5350 210.8900
QMMM: 48 48 S 222.4460 308.0020 212.3810
QMMM: 49 49 C 223.6810 306.6650 212.6010
QMMM: 50 50 O 224.1640 306.0790 211.6560
QMMM: 51 51 C 224.0020 306.2910 214.0390
QMMM: 52 52 H 220.1980 305.3620 203.2980
QMMM: 53 53 H 222.0140 301.2640 203.4140
QMMM: 54 54 H 222.4360 300.8530 201.7670
QMMM: 55 55 H 222.0750 303.2150 197.5070
QMMM: 56 56 H 220.8040 305.4140 197.1600
QMMM: 57 57 H 219.3560 306.4710 199.5290
QMMM: 58 58 H 217.9740 307.1520 197.8190
QMMM: 59 59 H 219.8880 308.7200 199.2120
QMMM: 60 60 H 222.4540 308.5150 198.4720
QMMM: 61 61 H 221.7250 306.8360 200.8390
QMMM: 62 62 H 223.0230 308.0370 200.6480
QMMM: 63 63 H 218.1030 309.5290 201.5010
QMMM: 64 64 H 218.5780 309.0700 203.1500
QMMM: 65 65 H 216.1610 308.4180 200.8930
QMMM: 66 66 H 214.6570 308.9330 201.6950
QMMM: 67 67 H 215.7610 310.1490 201.0080
QMMM: 68 68 H 214.7610 310.0180 203.9880
QMMM: 69 69 H 215.6380 311.2630 203.0680
QMMM: 70 70 H 216.3430 310.5980 204.5610
QMMM: 71 71 H 215.2420 307.8970 203.9690
QMMM: 72 72 H 216.5710 306.0540 202.9900
QMMM: 73 73 H 217.8050 309.3640 205.0830
QMMM: 74 74 H 218.3020 308.2070 207.4320
QMMM: 75 75 H 219.2410 307.1370 206.3760
QMMM: 76 76 H 219.6300 310.1420 206.3420
QMMM: 77 77 H 220.7230 308.8910 205.7360
QMMM: 78 78 H 220.7270 307.1920 208.0580
QMMM: 79 79 H 222.1450 306.8280 209.7890
QMMM: 80 80 H 222.9770 308.3270 209.3540
QMMM: 81 81 H 221.5970 309.6170 210.7940
QMMM: 82 82 H 220.4570 308.2790 211.0260
QMMM: 83 83 H 224.7430 305.4910 214.0500
QMMM: 84 84 H 223.0940 305.9520 214.5370
QMMM: 85 85 H 224.3990 307.1620 214.5610
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2586E+07 DeltaE = -0.1466E+03 DeltaP = 0.9773E+00
QMMM: Smallest DeltaE = 0.6473E-07 DeltaP = 0.4039E-04 Step = 105
Failure running ANTECHAMBER for residue ACO Check reply log for details
> ~select
Nothing selected
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue ACO (net charge -4) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmptav42asw/ante.in.mol2 -fi
mol2 -o
/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmptav42asw/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(ACO) ``
(ACO) `Welcome to antechamber 20.0: molecular input file processor.`
(ACO) ``
(ACO) `Info: Finished reading file
(/var/folders/5t/kbx948_s5gg2sppp35y68r5w0000gq/T/tmptav42asw/ante.in.mol2);
atoms read (85), bonds read (87).`
(ACO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ACO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ACO) ``
(ACO) ``
(ACO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ACO) `Info: Total number of electrons: 422; net charge: -4`
(ACO) ``
(ACO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(ACO) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(ACO) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =144
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 238
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.072425 seconds
| QMMM: Dspev diag routine = 0.055914 seconds
| QMMM: Dspevd diag routine = 0.041653 seconds
| QMMM: Dspevx diag routine = 0.194984 seconds
| QMMM: Dsyev diag routine = 0.060147 seconds
| QMMM: Dsyevd diag routine = 0.044156 seconds
| QMMM: Dsyevr diag routine = 0.049788 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.030042 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 221.0810 303.5410 202.9490
QMMM: 2 2 C 220.6050 304.7230 202.5280
QMMM: 3 3 N 220.5650 305.2180 201.2880
QMMM: 4 4 C 221.0910 304.3570 200.3890
QMMM: 5 5 C 221.6090 303.1020 200.6680
QMMM: 6 6 C 221.5920 302.6860 202.0220
QMMM: 7 7 N 222.0510 301.5060 202.4340
QMMM: 8 8 N 222.0580 302.4920 199.4950
QMMM: 9 9 C 221.8120 303.3670 198.5440
QMMM: 10 10 N 221.1780 304.5070 199.0190
QMMM: 11 11 C 220.8910 305.7180 198.2030
QMMM: 12 12 C 219.7300 306.6700 198.5250
QMMM: 13 13 O 218.6820 306.5450 197.5900
QMMM: 14 14 C 220.3710 308.0800 198.4730
QMMM: 15 15 O 220.5150 308.8080 197.2410
QMMM: 16 16 P 221.5520 310.0990 197.2780
QMMM: 17 17 O 222.0930 310.4080 198.6540
QMMM: 18 18 O 222.7140 309.7960 196.3310
QMMM: 19 19 O 220.6720 311.2370 196.7920
QMMM: 20 20 C 221.7850 307.7820 198.9230
QMMM: 21 21 O 222.0710 306.4800 198.3450
QMMM: 22 22 C 221.9810 307.8100 200.4230
QMMM: 23 23 O 221.1260 308.8270 201.0160
QMMM: 24 24 P 221.6620 309.6670 202.2740
QMMM: 25 25 O 221.4470 308.8620 203.5100
QMMM: 26 26 O 223.0560 310.1350 201.9800
QMMM: 27 27 O 220.5990 310.8900 202.2890
QMMM: 28 28 P 219.5960 311.6410 203.3170
QMMM: 29 29 O 219.9090 311.1950 204.7060
QMMM: 30 30 O 219.6580 313.1120 203.0540
QMMM: 31 31 O 218.1240 311.1130 202.8900
QMMM: 32 32 C 216.4460 309.2690 202.8600
QMMM: 33 33 C 217.8990 309.6860 202.5600
QMMM: 34 34 C 215.7020 309.1860 201.5160
QMMM: 35 35 C 215.7460 310.3670 203.6790
QMMM: 36 36 C 216.2660 307.9090 203.5950
QMMM: 37 37 O 216.3370 306.8920 202.5850
QMMM: 38 38 C 217.1590 307.4790 204.7700
QMMM: 39 39 O 217.1390 306.2860 205.1140
QMMM: 40 40 N 217.9020 308.4080 205.3930
QMMM: 41 41 C 218.8440 308.1460 206.4880
QMMM: 42 42 C 220.0270 309.1450 206.5360
QMMM: 43 43 C 220.8010 309.1980 207.8460
QMMM: 44 44 O 221.0760 310.2860 208.3600
QMMM: 45 45 N 221.1260 308.0370 208.4430
QMMM: 46 46 C 222.0080 307.8930 209.6020
QMMM: 47 47 C 221.5080 308.5350 210.8900
QMMM: 48 48 S 222.4460 308.0020 212.3810
QMMM: 49 49 C 223.6810 306.6650 212.6010
QMMM: 50 50 O 224.1640 306.0790 211.6560
QMMM: 51 51 C 224.0020 306.2910 214.0390
QMMM: 52 52 H 220.1980 305.3620 203.2980
QMMM: 53 53 H 222.0140 301.2640 203.4140
QMMM: 54 54 H 222.4360 300.8530 201.7670
QMMM: 55 55 H 222.0750 303.2150 197.5070
QMMM: 56 56 H 220.8040 305.4140 197.1600
QMMM: 57 57 H 219.3560 306.4710 199.5290
QMMM: 58 58 H 217.9740 307.1520 197.8190
QMMM: 59 59 H 219.8880 308.7200 199.2120
QMMM: 60 60 H 222.4540 308.5150 198.4720
QMMM: 61 61 H 221.7250 306.8360 200.8390
QMMM: 62 62 H 223.0230 308.0370 200.6480
QMMM: 63 63 H 218.1030 309.5290 201.5010
QMMM: 64 64 H 218.5780 309.0700 203.1500
QMMM: 65 65 H 216.1610 308.4180 200.8930
QMMM: 66 66 H 214.6570 308.9330 201.6950
QMMM: 67 67 H 215.7610 310.1490 201.0080
QMMM: 68 68 H 214.7610 310.0180 203.9880
QMMM: 69 69 H 215.6380 311.2630 203.0680
QMMM: 70 70 H 216.3430 310.5980 204.5610
QMMM: 71 71 H 215.2420 307.8970 203.9690
QMMM: 72 72 H 216.5710 306.0540 202.9900
QMMM: 73 73 H 217.8050 309.3640 205.0830
QMMM: 74 74 H 218.3020 308.2070 207.4320
QMMM: 75 75 H 219.2410 307.1370 206.3760
QMMM: 76 76 H 219.6300 310.1420 206.3420
QMMM: 77 77 H 220.7230 308.8910 205.7360
QMMM: 78 78 H 220.7270 307.1920 208.0580
QMMM: 79 79 H 222.1450 306.8280 209.7890
QMMM: 80 80 H 222.9770 308.3270 209.3540
QMMM: 81 81 H 221.5970 309.6170 210.7940
QMMM: 82 82 H 220.4570 308.2790 211.0260
QMMM: 83 83 H 224.7430 305.4910 214.0500
QMMM: 84 84 H 223.0940 305.9520 214.5370
QMMM: 85 85 H 224.3990 307.1620 214.5610
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2586E+07 DeltaE = -0.1466E+03 DeltaP = 0.9773E+00
QMMM: Smallest DeltaE = 0.6473E-07 DeltaP = 0.4039E-04 Step = 105
Failure running ANTECHAMBER for residue ACO Check reply log for details
> select #11/d#8
5445 atoms, 5533 bonds, 41 pseudobonds, 711 residues, 4 models selected
> mlp sel
Map values for surface "semiextended_alignedTo_J1308.pdb_D SES surface":
minimum -27.72, mean -3.862, maximum 24.82
To also show corresponding color key, enter the above mlp command and add key
true
> ~select
Nothing selected
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> mlp sel
mlp: no amino acids specified
> close #11.2
> select #11/d#8
5445 atoms, 5533 bonds, 41 pseudobonds, 711 residues, 4 models selected
> SURFACE SEL
Unknown command: SURFACE SEL
> surface sel
> ~select
Nothing selected
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> surface sel
> select subtract #8
1 model selected
> lighting full
> hide #11.2 models
> show #11.2 models
> show #!7 models
> hide #!8 models
> hide #!11 models
> hide #11.1 models
> hide #11.2 models
> show #!8 models
> hide #8.1 models
> show #!11 models
> hide #!7 models
> show #!7 models
> lighting soft
> hide #!7 models
> show #!7 models
> dssp
> show #!10 models
> hide #!7 models
> hide #!11 models
> show #12 models
> show #!11 models
> hide #!10 models
> show #!7 models
> hide #!11 models
> hide #12 models
> show #!9 models
> hide #!8 models
> select #9/D:1005@C
1 atom, 1 residue, 1 model selected
> cofr sel
> ~select
Nothing selected
> hide #!7 models
> show #!11 models
> show #12 models
> hide #!9 models
> show #!8 models
> show #!10 models
> hide #!11 models
> select add #8
51 atoms, 53 bonds, 1 residue, 1 model selected
> ui tool show Clashes
> clashes sel restrict #10 ignoreHiddenModels true reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
46 clashes
atom1 atom2 overlap distance
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CAP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 2.141 1.499
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 P3B (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 311 NH1 2.027 1.713
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 S1P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A CYS 576 CB 2.021 1.629
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A CYS 576 CA 1.731 2.029
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CD 1.636 2.124
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 CA 1.627 2.133
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CE1 1.620 1.750
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 1.542 1.828
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C3P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 NH1 1.412 2.108
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N4P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 NH1 1.346 1.934
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CA 1.322 1.978
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 S1P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A CYS 576 CA 1.301 2.349
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N8P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CE1 1.263 2.137
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O8A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 311 NH1 1.262 1.398
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CDP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 N 1.259 2.261
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A CYS 576 CB 1.248 2.512
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CG 1.237 2.063
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 N 1.197 2.323
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CAP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CE1 1.181 2.459
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CB 1.124 2.176
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CAP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CG 1.124 2.366
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CE1 1.102 2.078
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CG 1.078 2.682
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CBP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 1.005 2.635
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CAP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CB 0.937 2.823
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CDP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 CA 0.913 2.847
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 311 NH1 0.894 1.766
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CD 0.859 2.901
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 0.852 2.788
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 C 0.826 2.664
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C5B (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A TRP 405 CH2 0.811 2.829
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 0.801 2.379
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C9P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CG 0.777 2.713
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 NH1 0.775 2.745
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N8P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 0.734 2.666
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CBP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 N 0.713 2.807
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CE1 0.706 2.934
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A CYS 576 C 0.704 2.786
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CBP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A GLY 608 CA 0.700 3.060
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 P3B (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 311 CZ 0.698 3.012
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O5A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 309 NH1 0.672 1.988
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N4P (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 595 CD 0.671 2.849
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A TRP 405 CZ3 0.638 2.882
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 P2A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 309 NH1 0.638 3.102
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 OAP (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A PHE 607 CD1 0.629 2.591
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O8A (alt loc B) 6YTT_chainA_alignedTo_J1308.pdb #10/A ARG 311 CZ 0.606 2.424
46 clashes
> ui mousemode right distance
> distance #10/A:808@NI #8/D:1005@S1P
Distance between 6YTT_chainA_alignedTo_J1308.pdb #10/A NI 808 NI and
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 S1P (alt loc B): 5.747Å
> hide #!10 models
> show #!11 models
> distance #11/D:1003@NI #8/D:1005@S1P
Distance between semiextended_alignedTo_J1308.pdb #11/D NI 1003 NI and
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 S1P (alt loc B): 6.954Å
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!10 models
> show #!7 models
> hide #!10 models
> distance #7/A:739@ZN #8/D:1005@S1P
Distance between 3GIT_chainA_alignedTo_J1308.pdb #7/A ZN 739 ZN and
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 S1P (alt loc B): 4.303Å
> hide #!7 models
> show #!10 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #!11 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!11 models
> ui tool show Clashes
> show #!11 models
> hide #!10 models
> ui tool show Clashes
> clashes sel restrict #11 ignoreHiddenModels true reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
23 clashes
atom1 atom2 overlap distance
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 P3B (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 NH2 1.854 1.886
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.631 1.769
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O7A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 NH2 1.407 1.253
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 1.291 2.009
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.195 2.175
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.160 2.360
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CZ3 1.146 2.224
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.134 2.266
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 1.106 2.654
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N1A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLU 596 OE1 1.105 1.955
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C5A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.083 2.287
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C2A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 1.078 2.442
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C4A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 0.899 2.471
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N4P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 NH1 0.868 2.412
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C3P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 NH1 0.837 2.683
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ASN 322 CB 0.783 2.737
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C6A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLU 596 OE1 0.779 2.251
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 N3A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D TRP 405 CH2 0.758 2.642
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 CEP (alt loc B) semiextended_alignedTo_J1308.pdb #11/D GLY 608 CA 0.750 3.010
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O7A (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 311 CZ 0.706 2.324
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 O9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 O 0.678 2.162
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C7P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CD 0.645 3.115
acetylCoA_alignedTo_J1308.pdb #8/D ACO 1005 C9P (alt loc B) semiextended_alignedTo_J1308.pdb #11/D ARG 595 CG 0.622 2.868
23 clashes
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!7 models
> hide #!11 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!11 models
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11F000FWD/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 1 day, 23 hours, 55 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LEN P32p-20:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in Chromium backend |
comment:2 by , 19 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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