![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8945 closed defect (can't reproduce)
Unsupported scale factor (0.000000) detected on Display0
| 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.dev202302280423 (2023-02-28 04:23:03 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 0x000000010b01a600 (most recent call first):
File "/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.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" : 460000,
"procLaunch" : "2023-05-03 23:30:01.6996 +0300",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"procStartAbsTime" : 454720028498358,
"coalitionID" : 62889,
"osVersion" : {
"train" : "macOS 12.6",
"build" : "21G115",
"releaseType" : "User"
},
"captureTime" : "2023-05-04 11:50:27.1754 +0300",
"incident" : "F1D16A6C-FACA-4ED7-B015-355535795F9A",
"bug_type" : "309",
"pid" : 68684,
"procExitAbsTime" : 469602173896655,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2AB0F2FE-1C6A-5935-909A-AC9779E4A2A1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D2307553-8BC8-E7BE-DF5F-47E41435EDDA",
"wakeTime" : 12957,
"bridgeVersion" : {"build":"19P6067","train":"6.6"},
"sleepWakeUUID" : "6BADE49B-B0C3-47E8-948E-15EE51DC2BE1",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487564776\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff3f000-7ffffff40000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487564776\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff3f000-7ffffff40000 [ 4K] r-x\/r-x SM=ALI ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202302280423 (2023-02-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Lucia/Downloads/AF-Q5JIZ5-F1-model_v4.pdb
AF-Q5JIZ5-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for subtilisin-like serine protease (Q5JIZ5)
[more info...]
Chain information for AF-Q5JIZ5-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | subtilisin-like serine protease | TKSP_THEKO 1-663
> open /Users/Lucia/Downloads/AF-B0FXD9-F1-model_v4.pdb
AF-B0FXD9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for APRX (B0FXD9) [more info...]
Chain information for AF-B0FXD9-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | APRX | B0FXD9_PSEFL 1-477
> open /Users/Lucia/Downloads/AF-B0FXE0-F1-model_v4.pdb
AF-B0FXE0-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for APRX (B0FXE0) [more info...]
Chain information for AF-B0FXE0-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | APRX | B0FXE0_PSEFL 1-482
> view
> ui tool show Matchmaker
> matchmaker #3 to #2
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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> hide #1 models
> undo
> hide #1 models
> undo
> hide #1 models
> ui tool show Matchmaker
> matchmaker #3 to #2
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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> ui tool show "Blast Protein"
> ui tool show Matchmaker
> matchmaker #3 to #2
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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> matchmaker #3 to #2
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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> select #1/A
5014 atoms, 5135 bonds, 663 residues, 1 model selected
> view
> select #2/A#3/A
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> cartoon hide sel
> undo
> show #1 models
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #2/A
3489 atoms, 3560 bonds, 477 residues, 1 model selected
> select #2/A#3/A
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> select #2/A#3/A
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> undo
> hide #1 models
> undo
> hide #1 models
> hide #2 models
> show #2 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> undo
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> undo
> set bgColor black
> select clear
> ui tool show "Modeller Comparative"
> ui tool show "Blast Protein"
> ui tool show "Model Loops"
No alignments chosen for modeling
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
Cannot run BLAST without some kind of sequence.
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "move picked models"
> view
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select add #2
3489 atoms, 3560 bonds, 477 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3489 atoms, 3560 bonds, 477 residues, 1 model selected
> select add #3
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> select sequence #@
Nothing selected
> select sequence #2
Nothing selected
> show sequence
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sequence #2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> view
> select
> #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479
685 atoms, 685 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select #2/A:360-395
242 atoms, 246 bonds, 36 residues, 1 model selected
> select #2/A:360-395
242 atoms, 246 bonds, 36 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select
> #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472
709 atoms, 708 bonds, 87 residues, 1 model selected
> select #2/A:360-395
242 atoms, 246 bonds, 36 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select #2/A:360-395
242 atoms, 246 bonds, 36 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479
685 atoms, 685 bonds, 88 residues, 1 model selected
> select #3/A:10-11
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:1-11
82 atoms, 81 bonds, 11 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-17
119 atoms, 118 bonds, 17 residues, 1 model selected
> select #3/A:1-11
82 atoms, 81 bonds, 11 residues, 1 model selected
> select #3/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:1-11
82 atoms, 81 bonds, 11 residues, 1 model selected
> select #2/A:16-17
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:1-17
119 atoms, 118 bonds, 17 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472
709 atoms, 708 bonds, 87 residues, 1 model selected
> select
> #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479
685 atoms, 685 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select
> #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474
676 atoms, 675 bonds, 88 residues, 1 model selected
> select
> #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467
680 atoms, 679 bonds, 84 residues, 1 model selected
> select
> #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472
709 atoms, 708 bonds, 87 residues, 1 model selected
> select
> #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479
685 atoms, 685 bonds, 88 residues, 1 model selected
> view
> select #2/A:473
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:456-473
121 atoms, 122 bonds, 18 residues, 1 model selected
> select #2/A:457
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:457-477
146 atoms, 147 bonds, 21 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-20
142 atoms, 142 bonds, 20 residues, 1 model selected
> select #2/A:476-477
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:464-477
93 atoms, 92 bonds, 14 residues, 1 model selected
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right "move picked models"
> undo
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.69000,0.08000
> key pos 0.68000,0.08000
> key pos 0.67000,0.08000
> key pos 0.66000,0.08000
> key pos 0.65000,0.08000
> key pos 0.64000,0.08000
> key pos 0.65000,0.08000
> key pos 0.66000,0.08000
> key pos 0.67000,0.08000
> key pos 0.68000,0.08000
> key pos 0.69000,0.08000
> key pos 0.70000,0.08000
> key pos 0.71000,0.08000
> key pos 0.70000,0.08000
> key pos 0.69000,0.08000
> key pos 0.68000,0.08000
> key pos 0.67000,0.08000
> key pos 0.66000,0.08000
> key pos 0.64000,0.08000
> key pos 0.63000,0.08000
> key pos 0.62000,0.08000
> key pos 0.61000,0.08000
> key pos 0.60000,0.08000
> key pos 0.59000,0.08000
> key pos 0.58000,0.08000
> key pos 0.57000,0.08000
> key pos 0.56000,0.08000
> key pos 0.55000,0.08000
> key pos 0.54000,0.08000
> key pos 0.53000,0.08000
> key pos 0.52000,0.08000
> key pos 0.51000,0.08000
> key pos 0.50000,0.08000
> key pos 0.49000,0.08000
> key pos 0.48000,0.08000
> key pos 0.47000,0.08000
> key pos 0.46000,0.08000
> ui mousemode right "move picked models"
> ui mousemode right "color key"
> key delete
> ui mousemode right "move picked models"
> ui tool show "Color Actions"
> color sel orange
> color sel byelement
> color sel byhetero
> select #2/A:464-477
93 atoms, 92 bonds, 14 residues, 1 model selected
> select add #2/A#3/A
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> select add #2/A#3/A
7039 atoms, 7182 bonds, 959 residues, 2 models selected
> select sequence #2
Nothing selected
> ui windowfill toggle
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> sequence chain #3/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
> show #1 models
> ui tool show Matchmaker
> matchmaker #1,3 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
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: AF-B0FXD9-F1-model_v4.pdb
#2/A, AF-B0FXE0-F1-model_v4.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> matchmaker #1,3 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: AF-B0FXD9-F1-model_v4.pdb
#2/A, AF-B0FXE0-F1-model_v4.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> hide #2 models
> show #2 models
> hide #3 models
> view
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-13
100 atoms, 101 bonds, 13 residues, 1 model selected
> select #2/A:302
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:302-304
23 atoms, 22 bonds, 3 residues, 1 model selected
> hide #1 models
> show #3 models
> select #2/A:2-10
68 atoms, 67 bonds, 9 residues, 1 model selected
> select #2/A:1-10
76 atoms, 75 bonds, 10 residues, 1 model selected
> select #3/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:11-37
200 atoms, 203 bonds, 27 residues, 1 model selected
> select #3/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:2-11
74 atoms, 73 bonds, 10 residues, 1 model selected
> select #2/A:149-150
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/A:149-150
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-10
76 atoms, 75 bonds, 10 residues, 1 model selected
> select #2/A:197
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:187-197
83 atoms, 86 bonds, 11 residues, 1 model selected
> select #2/A:11-148,152-477 #3/A:11-148,157-482
6803 atoms, 6942 bonds, 928 residues, 2 models selected
> select #2/A:62-63
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/A:62-63
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:65-69
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #2/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:11-14
25 atoms, 24 bonds, 4 residues, 1 model selected
> select #2/A:11-148,152-477 #3/A:11-148,157-482
6803 atoms, 6942 bonds, 928 residues, 2 models selected
> select #2/A:12-13
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/A:12-16
30 atoms, 29 bonds, 5 residues, 1 model selected
> select #2/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:6-7
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:2-10
68 atoms, 67 bonds, 9 residues, 1 model selected
> mattch #2 to #3
Unknown command: mattch #2 to #3
> matchmaker #2 to #3
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 AF-B0FXE0-F1-model_v4.pdb, chain A (#3) with
AF-B0FXD9-F1-model_v4.pdb, chain A (#2), sequence alignment score = 2178.6
RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs:
0.851)
> view matrix models
> #2,1,-2.0327e-17,-2.0611e-19,-0.0091452,2.0327e-17,1,1.4021e-17,0.0038494,2.0611e-19,-1.4021e-17,1,0.00027844
> select add #2/A:11 #3/A:11
80 atoms, 77 bonds, 11 residues, 2 models selected
> select #2/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:11-13
16 atoms, 15 bonds, 3 residues, 1 model selected
> select #2/A:10-11
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:10-12
18 atoms, 17 bonds, 3 residues, 1 model selected
> unselect
Unknown command: unselect
> select up
112 atoms, 111 bonds, 16 residues, 1 model selected
> select up
3489 atoms, 3560 bonds, 477 residues, 1 model selected
> select down
112 atoms, 111 bonds, 16 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #3/A:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #3 models
> show #3 models
> select #3/A:8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:3-8
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
112 atoms, 111 bonds, 16 residues, 1 model selected
> select #2/A:5-6
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:2-6
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #2/A:4 #3/A:4
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2/A:4 #3/A:4
14 atoms, 12 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 4] region AF-B0FXD9-F1-model_v4.pdb, chain
A..AF-B0FXE0-F1-model_v4.pdb, chain A [4] RMSD: 5.181
> select #3/A:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/A:24 #3/A:24
19 atoms, 16 bonds, 3 residues, 2 models selected
> select #2/A:2-6
39 atoms, 38 bonds, 5 residues, 1 model selected
> deselct
Unknown command: deselct
> select #1/A:38-39
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:36-39
38 atoms, 38 bonds, 4 residues, 1 model selected
> view
> color #3 #e1d261ff
> color #3 #345ee1ff
> color #2 #ec67ccff
> color #2 #ec97dbff
> save /Users/Lucia/Downloads/B0FXE0_B0FXD9.gif width 1262 height 1136
> supersample 3
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> undo
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> undo
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color #2 #4c65ecff
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> sym #1 copies true
AF-Q5JIZ5-F1-model_v4.pdb mmCIF Assemblies
---
> save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink).jpg width 1262 height
> 1136 supersample 3
> sym #2 copies true
AF-B0FXD9-F1-model_v4.pdb mmCIF Assemblies
---
> close #2
> undo
> open /Users/Lucia/Downloads/AF-B0FXD9-F1-model_v4.pdb
AF-B0FXD9-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for APRX (B0FXD9) [more info...]
Chain information for AF-B0FXD9-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | APRX | B0FXD9_PSEFL 1-477
Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 2: AF-B0FXD9-F1-model_v4.pdb
#2/A, AF-B0FXE0-F1-model_v4.pdb #3/A
Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 3: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 4: AF-B0FXD9-F1-model_v4.pdb
#2/A, AF-B0FXE0-F1-model_v4.pdb #3/A
> hide #!1 models
> zoom 1.1
> turn 180
Expected an axis vector or a keyword
> zoom 1.1
> turn 180
Expected an axis vector or a keyword
> save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink)_2.jpg width 1262
> height 1136 supersample 3
> surf/a
Unknown command: surf/a
> lighiting gentle
Unknown command: lighiting gentle
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color #2 #e961ebff
> color #3 #8d86ebff
> color #3 #3568ebff
> color #3 #3567ebff
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> rainbow paleete PuBu-5
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> rainbow paleete PuBu-5 to #2
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> hide #2 models
> rainbow paleete PuBu-5
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> show #2 models
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 12053 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select #3/A:149-150
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:149-156
68 atoms, 69 bonds, 8 residues, 1 model selected
> select #2/A:149
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:149-151
16 atoms, 15 bonds, 3 residues, 1 model selected
> select #2/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:7-10
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:149-150
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/A:149-150
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:7-10
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:150
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:7-10
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:149-150
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/A:149-151
16 atoms, 15 bonds, 3 residues, 1 model selected
> select #2/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:7-10
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:7-10,133-148
138 atoms, 140 bonds, 20 residues, 1 model selected
> select #2/A:11-148,152-477 #3/A:11-148,157-482
6803 atoms, 6942 bonds, 928 residues, 2 models selected
> undo
> select #2/A:133
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:133-147
105 atoms, 108 bonds, 15 residues, 1 model selected
> select #2/A:133
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:133-139
47 atoms, 47 bonds, 7 residues, 1 model selected
> select add #2/A:137 #3/A:137
56 atoms, 55 bonds, 8 residues, 3 models selected
> select #2/A:7-8
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:7-10
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:7-10,149-151
45 atoms, 43 bonds, 7 residues, 1 model selected
> color (#!2 & sel) red
> save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink)_2_selecttion(red).jpg
> width 1262 height 1136 supersample 3
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!1 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
> ui tool show Matchmaker
> matchmaker #!1 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
> matchmaker #!1 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
> ui tool show Matchmaker
> matchmaker #!1 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
> matchmaker #!1 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 AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with
AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
> select #2/A:454
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:454 #1/A:465
19 atoms, 18 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 2] region AF-B0FXD9-F1-model_v4.pdb, chain
A..AF-Q5JIZ5-F1-model_v4.pdb, chain A [549] RMSD: 0.637
> select #2/A:455
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:455-458
24 atoms, 24 bonds, 4 residues, 1 model selected
> select #2/A:454
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:454 #1/A:465
19 atoms, 18 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 2] region AF-B0FXD9-F1-model_v4.pdb, chain
A..AF-Q5JIZ5-F1-model_v4.pdb, chain A [549] RMSD: 0.637
> select #2/A:455-456
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/A:455-458
24 atoms, 24 bonds, 4 residues, 1 model selected
> select #1/A:466
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:466-469
19 atoms, 18 bonds, 4 residues, 1 model selected
> select #2/A:419
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:419-424
37 atoms, 36 bonds, 6 residues, 1 model selected
> select #2/A:453
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:453-455
25 atoms, 25 bonds, 3 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!2-3 to #1 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 AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1) with
AF-B0FXD9-F1-model_v4.pdb, chain A (#2), sequence alignment score = 108.6
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXD9-F1-model_v4.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs:
28.210)
Matchmaker AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1) with
AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 100
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: AF-Q5JIZ5-F1-model_v4.pdb
#1/A, AF-B0FXE0-F1-model_v4.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 7 pruned atom pairs is 1.061 angstroms; (across all 398 pairs:
29.294)
> show #!3 models
> hide #!2 models
> select #3/A:29-30
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:256
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:256-264
74 atoms, 74 bonds, 9 residues, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.dev202302280423 (2023-02-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 34 days 55 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501P-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.0
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: 3.0.1
ChimeraX-AddCharge: 1.5.8
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.8
ChimeraX-AtomicLibrary: 10.0.5
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: 1.2.1
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.dev202302280423
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: 1.1
ChimeraX-DistMonitor: 1.3.3
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-ExperimentalCommands: 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: 2.0.11
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: 1.5.8
ChimeraX-ModelPanel: 1.3.6
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-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.6.13
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: 1.0
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: 1.10.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
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: 1.27.3
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: 0.1.2
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.0.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.4
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.2.0
jupyterlab-widgets: 3.0.5
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
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
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: 3.0.0
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
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: 6.4.2
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.2
python-dateutil: 2.8.2
pytz: 2022.7.1
pyzmq: 25.0.0
qtconsole: 5.4.0
QtPy: 2.3.0
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
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: 1.0.2
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.14
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.5
zipp: 3.15.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unsupported scale factor (0.000000) detected on Display0 |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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*Probably* the same as #8226. The user does have two displays.