![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9637 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| 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-13.5-arm64-arm-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 0x00000002070be080 (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" : 190000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,12",
"coalitionID" : 2723,
"osVersion" : {
"train" : "macOS 13.5",
"build" : "22G74",
"releaseType" : "User"
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"captureTime" : "2023-08-24 23:13:22.9529 -0400",
"incident" : "457F75AA-CAFE-46F9-BCF1-528D9F4CE493",
"pid" : 3958,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-16 12:08:11.8523 -0400",
"procStartAbsTime" : 461785838313,
"procExitAbsTime" : 4562539161719,
"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":"95D9709D-3587-5D17-BEDE-FEE5F513BFD1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "903F58DE-AEF4-B5C2-14F6-BCFBB738E9E3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3,
"sleepWakeUUID" : "D27D831B-FE66-41D4-B32D-86A94980265B",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105570161917928\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 6003f8000000-600400000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3958},
"ktriageinfo" : "VM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105570161917928\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 6003f8000000-600400000000 [128.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
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/anshu_mini/Desktop/PS_Mini_Desk/BfpE_BfpD_BfpC_interacitions/BfpE_AF-
> model.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/BfpE_BfpD_BfpC_interacitions/BfpE_AF-
model.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 352 UNP A0A1C7CMT8 A0A1C7CMT8_ECOLX 1 352
BfpE_AF-model.pdb title:
Alphafold monomer V2.0 prediction for bundle-forming pilus protein BFPE
(A0A1C7CMT8) [more info...]
Chain information for BfpE_AF-model.pdb #1
---
Chain | Description
A | bundle-forming pilus protein BFPE
> open /Volumes/Pradip_Hutu/BfpE_Msl/AlphaFold_BfpD-
> E-C/BfpDEC_prediction_6/BfpDEC_best_model.pdb format pdb
Chain information for BfpDEC_best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #2 models
> select add #1
2794 atoms, 2854 bonds, 352 residues, 1 model selected
> show #2 models
> hide #1 models
> select subtract #1
Nothing selected
> select add #2
7528 atoms, 7666 bonds, 950 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.44197,0.54654,0.7113,6.0122,-0.083098,0.7646,-0.63913,0.33303,-0.89317,-0.34158,-0.29251,3.6898
> view matrix models
> #2,0.31226,0.40759,-0.85812,6.4076,-0.85951,-0.26354,-0.43794,-3.662,-0.40464,0.87431,0.26803,7.9466
> show #1 models
> view matrix models
> #2,0.31226,0.40759,-0.85812,-14.808,-0.85951,-0.26354,-0.43794,4.8152,-0.40464,0.87431,0.26803,35.298
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BfpE_AF-model.pdb, chain A (#1) with BfpDEC_best_model.pdb, chain A
(#2), sequence alignment score = 1159.1
RMSD between 218 pruned atom pairs is 0.707 angstroms; (across all 251 pairs:
7.352)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BfpE_AF-model.pdb, chain A (#1) with BfpDEC_best_model.pdb, chain A
(#2), sequence alignment score = 1159.1
RMSD between 218 pruned atom pairs is 0.707 angstroms; (across all 251 pairs:
7.352)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BfpE_AF-model.pdb, chain A (#1) with BfpDEC_best_model.pdb, chain A
(#2), sequence alignment score = 1159.1
RMSD between 218 pruned atom pairs is 0.707 angstroms; (across all 251 pairs:
7.352)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BfpE_AF-model.pdb, chain A (#1) with BfpDEC_best_model.pdb, chain A
(#2), sequence alignment score = 1159.1
RMSD between 218 pruned atom pairs is 0.707 angstroms; (across all 251 pairs:
7.352)
> color sel bychain
> ui mousemode right select
> select subtract #2
Nothing selected
> hide #1 models
> show #1 models
> hide #1 models
> select #2/A
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> select #2/A:1-114
917 atoms, 933 bonds, 114 residues, 1 model selected
> select #2/A:121-500
1053 atoms, 1077 bonds, 131 residues, 1 model selected
> renumber /A:122-251 start 189
Proposed renumbering conflicts with existing residue BfpE_AF-model.pdb #1/A
VAL 252
> renumber /A:122 start 189
Proposed renumbering conflicts with existing residue BfpE_AF-model.pdb #1/A
THR 189
> renumber #2/A:122 start 189
Proposed renumbering conflicts with existing residue BfpDEC_best_model.pdb
#2/A TYR 189
> renumber #2/A:122 start 189
Proposed renumbering conflicts with existing residue BfpDEC_best_model.pdb
#2/A TYR 189
> renumber #2/A:122 start 189 relative true
Proposed renumbering conflicts with existing residue BfpDEC_best_model.pdb
#2/A TYR 189
> renumber #2/A:122 seqStart 189
1 residues renumbered
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select add #2
7528 atoms, 7666 bonds, 950 residues, 1 model selected
> select subtract #2
Nothing selected
> ui mousemode right select
> select #2/A:1-114
917 atoms, 933 bonds, 114 residues, 1 model selected
> ui mousemode right select
> select #2/A:121
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:122
Nothing selected
> select #2/A:189
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:123
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:122
Nothing selected
> select #2/A:121
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select sequence KQMT
33 atoms, 32 bonds, 4 residues, 1 model selected
> renumber #2/A:121-251 seqStart 189
130 residues renumbered
> select #2/B
1280 atoms, 1307 bonds, 164 residues, 1 model selected
> hide sel cartoons
> select #2/C
4248 atoms, 4318 bonds, 535 residues, 1 model selected
> hide sel cartoons
> rainbow sel
> select add #2
7528 atoms, 7666 bonds, 950 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
7528 atoms, 7666 bonds, 950 residues, 1 model selected
> rainbow sel
> select subtract #2
Nothing selected
> ui mousemode right select
> renumber #2/A:309-439 seqStart 189
0 residues renumbered
> renumber #2/A start 1 relative false
131 residues renumbered
> renumber #2/A start 122-251 seqstart 189
Invalid "start" argument: Expected an integer
> renumber #2/A start 122 seqStart 189
Cannot specify both 'start' and seqStart' keywords
> renumber #2/A:122-251 seqStart 189
130 residues renumbered
> renumber #2/A start 1 relative false
130 residues renumbered
> renumber #2/A:122-251 seqStart 67
130 residues renumbered
> renumber #2/A start 1 relative false
130 residues renumbered
> renumber #2/A:122-251 seqStart 68
130 residues renumbered
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/BfpE_BfpD_BfpC_interacitions/BfpDEC_01_No_corrected.pdb
> models #2 relModel #2
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/BfpE_BfpD_BfpC_interacitions/BfpDEC_01_No_corrected.pdb
Chain information for BfpDEC_01_No_corrected.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #2 models
> color #3 bychain
> rainbow #3
> ui mousemode right select
> select sequence KQMT
66 atoms, 64 bonds, 8 residues, 2 models selected
> hide #3 models
> open
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/BfpDx2-BfpE/AF_BfpDDE.pdb
Chain information for AF_BfpDDE.pdb #4
---
Chain | Description
A | No description available
B C | No description available
> color #4 bychain
> renumber #4/A:122-251 seqStart 68
130 residues renumbered
> rainbow #4
> renumber #4/C start 108 relative false
428 residues renumbered
> renumber #4/B start 108 relative false
428 residues renumbered
> save
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/BfpDx2-BfpE/AF_BfpDDE_Num_corrected.pdb
> models #4 relModel #4
> select add #3
7561 atoms, 7698 bonds, 954 residues, 2 models selected
> select add #2
15056 atoms, 15332 bonds, 1900 residues, 2 models selected
> select subtract #2
7528 atoms, 7666 bonds, 950 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #4 models
> open
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/prediction_1_cpBfpE/AF_cpBfpE.pdb
Chain information for AF_cpBfpE.pdb #5
---
Chain | Description
A | No description available
> rainbow #5
> renumber #5/A:122-251 seqStart 68
130 residues renumbered
> save
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/prediction_1_cpBfpE/AF_cpBfpE_Num_corrected.pdb
> models #5 relModel #5
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> close #1
> close
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/BfpE_CCP4/BfpE_refmac2_ACT2-2-coot-
> PS_04.pdb format pdb
BfpE_refmac2_ACT2-2-coot-PS_04.pdb title:
\--- [more info...]
Chain information for BfpE_refmac2_ACT2-2-coot-PS_04.pdb #1
---
Chain | Description
A | No description available
Alignment identifier is 1/A
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select N
162 atoms, 114 residues, 1 model selected
> select clear
> select /A:1@CE
1 atom, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> help merge
No help found for 'merge'
> merge help
Unknown command: merge help
> merge
Unknown command: merge
> help help:user
> close
> open /Users/anshu_mini/Downloads/E2.pdb
Summary of feedback from opening /Users/anshu_mini/Downloads/E2.pdb
---
warnings | Ignored bad PDB record found on line 1
{\rtf1\ansi\ansicpg1252\cocoartf2709
Ignored bad PDB record found on line 2
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
Ignored bad PDB record found on line 3
{\colortbl;\red255\green255\blue255;}
Ignored bad PDB record found on line 4
{\\*\expandedcolortbl;;}
Ignored bad PDB record found on line 5
\margl1440\margr1440\vieww18040\viewh15420\viewkind0
3 messages similar to the above omitted
Chain information for E2.pdb #1
---
Chain | Description
E2 | No description available
> open /Users/anshu_mini/Downloads/E2.pdb
Summary of feedback from opening /Users/anshu_mini/Downloads/E2.pdb
---
warnings | Ignored bad PDB record found on line 1
{\rtf1\ansi\ansicpg1252\cocoartf2709
Ignored bad PDB record found on line 2
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
Ignored bad PDB record found on line 3
{\colortbl;\red255\green255\blue255;}
Ignored bad PDB record found on line 4
{\\*\expandedcolortbl;;}
Ignored bad PDB record found on line 5
\margl1440\margr1440\vieww18040\viewh15420\viewkind0
5 messages similar to the above omitted
Chain information for E2.pdb #2
---
Chain | Description
E1 | No description available
E2 | No description available
> hide #1 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0.pdb
Chain information for PilbPk_0817_1-coot-0.pdb #3
---
Chain | Description
A D | No description available
B C E F | No description available
> hide #2-3 atoms
> show #2-3 cartoons
> hide #2 models
> ui tool show AlphaFold
> close #1
> close #2
> alphafold search #1
Missing or invalid "sequence" argument: Sequences argument "#1" must specify 1
sequence, got 0
> alphafold match #3/A
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold A0A1F0ILZ5 from
https://alphafold.ebi.ac.uk/files/AF-A0A1F0ILZ5-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
A)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 2.01 | 384 | 384 | 100
Opened 1 AlphaFold model
> alphafold match #3/B
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
B)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
B | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 6.83 | 385 | 385 | 100
Opened 1 AlphaFold model
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> alphafold match #3/C
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
C)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
C | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 1.74 | 385 | 385 | 100
Opened 1 AlphaFold model
> alphafold match #3/D
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
D)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
D | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 2.01 | 384 | 384 | 100
Opened 1 AlphaFold model
> alphafold match #3/E
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
E)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
E | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 6.83 | 385 | 385 | 100
Opened 1 AlphaFold model
> alphafold match #3/F
1 AlphaFold model found using sequence similarity searches: A0A1F0ILZ5 (chain
F)
AlphaFold prediction matching PilbPk_0817_1-coot-0.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
F | A0A1F0ILZ5 | A0A1F0ILZ5_9PSED | 1.74 | 385 | 385 | 100
Opened 1 AlphaFold model
> open /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/0817composite_map.ccp4
Opened 0817composite_map.ccp4 as #8, grid size 226,226,226, pixel 1.08, shown
at level 3.79, step 1, values float32
> hide #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> show #!8 models
> hide #!8 models
> hide #3 models
> close #3
> close #8
> combine
> hide #3 models
> show #3 models
> hide #3 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> hide #5.1 models
> hide #!6 models
> hide #6.1 models
> hide #!7 models
> hide #7.1 models
> show #3 models
> select add #3
17954 atoms, 18212 bonds, 2308 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
17954 atoms, 18212 bonds, 2308 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
17954 atoms, 18212 bonds, 2308 residues, 1 model selected
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/AF_pilBpk_6mr.pdb
> models #3 relModel #3
> hide #3 models
> select subtract #3
Nothing selected
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #1.1 models
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/AF_pilBpk_B.pdb models
> #2 relModel #2.1
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0.pdb
Chain information for PilbPk_0817_1-coot-0.pdb #8
---
Chain | Description
A D | No description available
B C E F | No description available
> hide #8#2.1 atoms
> show #8#2.1 cartoons
> select add #8
17948 atoms, 18204 bonds, 2308 residues, 1 model selected
> select subtract #8
Nothing selected
> select #8/B
2993 atoms, 3035 bonds, 385 residues, 1 model selected
> select add #8
17948 atoms, 18204 bonds, 2308 residues, 1 model selected
> hide sel cartoons
> select #8/B
2993 atoms, 3035 bonds, 385 residues, 1 model selected
> show sel cartoons
> hide #!2 models
> hide #2.1 models
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B.pdb
> models #8 selectedOnly true relModel #8
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B2.pdb
> selectedOnly true
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO E 183
GLY E 198 1 16
Start residue of secondary structure not found: HELIX 2 2 ALA E 233 SER E 237
1 5
Start residue of secondary structure not found: HELIX 3 3 ARG E 239 VAL E 242
1 4
Start residue of secondary structure not found: HELIX 4 4 GLU E 309 LEU E 312
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA E 313 LYS E 316
1 4
130 messages similar to the above omitted
Chain information for PilbPk_0817_1-coot-0_B.pdb #9
---
Chain | Description
B | No description available
> hide #8 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B2.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_B2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 183
LYS A 197 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 230 LEU A 232
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA A 233 MET A 243
1 11
Start residue of secondary structure not found: HELIX 4 4 SER A 291 GLN A 295
1 5
Start residue of secondary structure not found: HELIX 5 5 ILE A 298 LEU A 301
1 4
33 messages similar to the above omitted
Chain information for PilbPk_0817_1-coot-0_B2.pdb #10
---
Chain | Description
B | No description available
> hide #9 models
> hide #10 models
> close #10
> show #9 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_10/0817-_real_space_refined_010.pdb
Chain information for 0817-_real_space_refined_010.pdb #10
---
Chain | Description
B | No description available
> hide #9 models
> open /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/0817composite_map.ccp4
Opened 0817composite_map.ccp4 as #11, grid size 226,226,226, pixel 1.08, shown
at level 3.79, step 1, values float32
> color #11 #b2b2b27e models
> color #11 #b2b2b24c models
> color #11 #b2b2b262 models
> color #11 #babdbf62 models
> color #11 #aeaebf62 models
> color #11 #b1afbf62 models
> volume #11 level 4.632
> select #10/B:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11
2 models selected
> select clear
> hide #!11 models
> show #!11 models
> volume #11 level 4.632
> select ::name="ARG"
5280 atoms, 4820 bonds, 480 residues, 10 models selected
> show (#10 & sel) target ab
> select ::name="LYS"
4500 atoms, 4020 bonds, 500 residues, 10 models selected
> show (#10 & sel) target ab
> select clear
> hide #!11 models
> show #3 models
> hide #3 models
> show #9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #9 models
> show #8 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0.pdb
Chain information for PilbPk_0817_1-coot-0.pdb #12
---
Chain | Description
A D | No description available
B C E F | No description available
> hide #8,10,12 atoms
> show #8,10,12 cartoons
> hide #12 models
> hide #10 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> select #8/A
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_A.pdb
> models #8 selectedOnly true
> hide #8 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_A.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO E 183
GLY E 198 1 16
Start residue of secondary structure not found: HELIX 2 2 ALA E 233 SER E 237
1 5
Start residue of secondary structure not found: HELIX 3 3 ARG E 239 VAL E 242
1 4
Start residue of secondary structure not found: HELIX 4 4 GLU E 309 LEU E 312
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA E 313 LYS E 316
1 4
137 messages similar to the above omitted
Chain information for PilbPk_0817_1-coot-0_A.pdb #13
---
Chain | Description
A | No description available
> select add #1.1
5977 atoms, 6063 bonds, 768 residues, 2 models selected
> hide #13 models
> show #8 models
> select add #8
20937 atoms, 21236 bonds, 2692 residues, 2 models selected
> select subtract #8
2989 atoms, 3032 bonds, 384 residues, 1 model selected
> hide #8 models
> select add #1
2989 atoms, 3032 bonds, 384 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1.1
2989 atoms, 3032 bonds, 384 residues, 1 model selected
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/AF_pilBpk_A.pdb models
> #1 selectedOnly true relModel #1.1
> show #13 models
> hide #13 models
> show #12 models
> hide #4.1 models
> show #!5 models
> hide #!5 models
> show #4.1 models
> hide #12 models
> select subtract #1.1
Nothing selected
> show #13 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_11/Pilbpk_0817_1-coot-0_A_real_space_refined_011.pdb
Chain information for Pilbpk_0817_1-coot-0_A_real_space_refined_011.pdb #14
---
Chain | Description
A | No description available
> hide #1.1 models
> color #14 #847d17ff
> color #14 #bfb622ff
> hide #13 models
> show #13 models
> hide #14 models
> show #14 models
> hide #4.1 models
> show #4.1 models
> hide #!1 models
> hide #13 models
> hide #14 models
> show #8 models
> select #8/c
2993 atoms, 3036 bonds, 385 residues, 1 model selected
> hide #8 models
> show #4.1 cartoons
> show #8 models
> select add #8
17948 atoms, 18204 bonds, 2308 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #8#4.1 cartoons
> select #8/c
2993 atoms, 3036 bonds, 385 residues, 1 model selected
> show sel cartoons
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!4 models
> hide #4.1 models
> show #!4 models
> show #4.1 models
> show #2.1 models
> hide #2.1 models
> select add #4
5987 atoms, 6073 bonds, 770 residues, 3 models selected
> hide #8 models
> select add #8
20942 atoms, 21241 bonds, 2693 residues, 3 models selected
> select subtract #8
2994 atoms, 3037 bonds, 385 residues, 2 models selected
> show sel cartoons
> show #8 models
> hide #!4 models
> hide #4.1 models
> select subtract #4
Nothing selected
> select add #4.1
2994 atoms, 3037 bonds, 385 residues, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4
2994 atoms, 3037 bonds, 385 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!2 models
> select #8/c
2993 atoms, 3036 bonds, 385 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_11/PilbPk_0817_1-coot-0_C.pdb
> models #8 selectedOnly true
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_C.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/PilbPk_0817_1-coot-0_C.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO E 183
GLY E 198 1 16
Start residue of secondary structure not found: HELIX 2 2 ALA E 233 SER E 237
1 5
Start residue of secondary structure not found: HELIX 3 3 ARG E 239 VAL E 242
1 4
Start residue of secondary structure not found: HELIX 4 4 GLU E 309 LEU E 312
1 4
Start residue of secondary structure not found: HELIX 5 5 ALA E 313 LYS E 316
1 4
133 messages similar to the above omitted
Chain information for PilbPk_0817_1-coot-0_C.pdb #15
---
Chain | Description
C | No description available
> hide #8 models
> show #!4 models
> show #4.1 models
> hide #15 models
> select add #8
17948 atoms, 18204 bonds, 2308 residues, 1 model selected
> select subtract #8
Nothing selected
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/AF_pilBpk_C.pdb models
> #4 displayedOnly true relModel #4
> select add #4.1
2994 atoms, 3037 bonds, 385 residues, 1 model selected
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/AF_pilBpk_C.pdb models
> #4 selectedOnly true relModel #4
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_12/Pilbpk_0817_1-coot-0_C_real_space_refined_012.pdb
Chain information for Pilbpk_0817_1-coot-0_C_real_space_refined_012.pdb #16
---
Chain | Description
C | No description available
> hide #!4 models
> hide #4.1 models
> show #15 models
> color #16 #abf40fff
> color #16 #f47a19ff
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> hide #4.1 models
> hide #15 models
> show #14 models
> show #10 models
> show #!11 models
> hide #!11 models
> combine #14 #10 #16
> hide #16 models
> hide #14 models
> hide #10 models
> show #!11 models
> save /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/0818_RSR_ABC.pdb
> models #17 relModel #11
> open /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/0818_RSR_ABC.pdb
Chain information for 0818_RSR_ABC.pdb #18
---
Chain | Description
A | No description available
B C | No description available
> close #17
> color #18 bychain
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_13/0818_ABC_real_space_refined_013.pdb
Chain information for 0818_ABC_real_space_refined_013.pdb #17
---
Chain | Description
A | No description available
B C | No description available
> hide #!11 models
> hide #18 models
> show #18 models
> hide #18 models
> color #17 bychain
> show #!11 models
> volume zone #11 nearAtoms #17 range 6.48
> color #11 #b1afbfff models
> show #8 models
> hide #!11 models
> hide #8 models
> show #10 models
> show #18 models
> hide #17 models
> hide #10 models
> show #!11 models
> color #11 #b1afbf5c models
> color #11 #b1afbf4e models
> volume #11 level 7.165
> volume #11 level 5.16
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_14/0818_ABC_rigid_real_space_refined_014.pdb
Chain information for 0818_ABC_rigid_real_space_refined_014.pdb #19
---
Chain | Description
A | No description available
B C | No description available
> hide #19 models
> hide #!11 models
> show #19 models
> hide #18 models
> show #!11 models
> hide #19 models
> show #18 models
> show #17 models
> color #17 #f5eb47ff
> hide #18 models
> hide #17 models
> show #18 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> show #17 models
> hide #17 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_15/0818_ABC_real_space_refined_015.pdb
Chain information for 0818_ABC_real_space_refined_015.pdb #20
---
Chain | Description
A | No description available
B C | No description available
> hide #!11 models
> hide #18 models
> show #!11 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_17/0818_ABC_real_space_refined_017.pdb
Chain information for 0818_ABC_real_space_refined_017.pdb #21
---
Chain | Description
A | No description available
B C | No description available
> hide #!11 models
> hide #20 models
> show #18 models
> show #!11 models
> hide #18 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_18/0818_ABC_real_space_refined_018.pdb
Chain information for 0818_ABC_real_space_refined_018.pdb #22
---
Chain | Description
A | No description available
B C | No description available
> hide #!11 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_19/0818_ABC_real_space_refined_019.pdb
Chain information for 0818_ABC_real_space_refined_019.pdb #23
---
Chain | Description
A | No description available
B C | No description available
> hide #21 models
> hide #22 models
> show #18 models
> show #!11 models
> hide #18 models
> hide #23 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_20/0818_ABC_real_space_refined_020.pdb
Chain information for 0818_ABC_real_space_refined_020.pdb #24
---
Chain | Description
A | No description available
B C | No description available
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #18 models
> volume #11 color #b1afbd4e
> volume #11 color #6bbd234e
> volume #11 color #a7bd0d4e
> volume #11 color #a2b80d74
> select #18/C:212
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #18/C:213
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #11
2 models selected
> select #11
2 models selected
> select clear
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_24/0818_ABC_real_space_refined_024.pdb
Chain information for 0818_ABC_real_space_refined_024.pdb #25
---
Chain | Description
A | No description available
B C | No description available
> hide #24 models
> hide #!11 models
> hide #18 models
> show #!11 models
> show #18 models
> hide #!11 models
> color #25 #a3a51cff
> color #25 #9da512ff
> color #25 #a5a102ff
> color #25 #ece603ff
> show #!11 models
> hide #18 models
> color #11 #5c640674 models
> color #11 #5c645b74 models
> color #11 #35646374 models
> color #11 #4b476474 models
> color #11 #642e2f74 models
> color #11 #641f1a74 models
> color #11 #64363074 models
> color #11 #fb877974 models
> color #11 #ff8a7b74 models
> color #11 #f4837674 models
> color #11 #f4b4c474 models
> color #11 #f49eb074 models
> close #1
> close #2
> close #4
> close #5
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_25/0818_ABC_real_space_refined_025.pdb
Chain information for 0818_ABC_real_space_refined_025.pdb #1
---
Chain | Description
A | No description available
B C | No description available
> hide #25 models
> show #24 models
> hide #24 models
> hide #!11 models
> show #!11 models
> hide #1 models
> show #25 models
> show #24 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_25/0818_ABC_real_space_refined_025.pdb
Chain information for 0818_ABC_real_space_refined_025.pdb #2
---
Chain | Description
A | No description available
B C | No description available
> show #1 models
> close #1
> hide #24 models
> hide #25 models
> hide #2 models
> show #25 models
> hide #!11 models
> show #18 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_26/0818_ABC_real_space_refined_026.pdb
Chain information for 0818_ABC_real_space_refined_026.pdb #1
---
Chain | Description
A | No description available
B C | No description available
> hide #1 models
> show #1 models
> hide #1 models
> show #24 models
> hide #24 models
> hide #18 models
> show #!11 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/CryoFit_J184/RealSpaceRefine_27/0818_ABC_real_space_refined_027.pdb
Chain information for 0818_ABC_real_space_refined_027.pdb #4
---
Chain | Description
A | No description available
B C | No description available
> hide #25 models
> hide #!11 models
> show #18 models
> show #25 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/RealSpaceRefine_44/0818_RSR_ABC-
> coot-0_real_space_refined_044.pdb
Chain information for 0818_RSR_ABC-coot-0_real_space_refined_044.pdb #5
---
Chain | Description
A | No description available
B C | No description available
> close #25
> close #24
> close #23
> close #22
> close #21
> close #20
> close #19
> close #1
> close #2
> close #4
> color #18 #2df53dff
> show #!11 models
> color #11 #636af874 models
> color #11 #26e5f874 models
> color #11 #9065f874 models
> color #11 #4e50f874 models
> color #11 #1b3ff874 models
> color #11 #5260f874 models
> color #11 #7a76f874 models
> color #11 #f1f80274 models
> color #11 #9e85f874 models
> color #11 #ac81f874 models
> color #11 #47356774 models
> color #11 #235f6774 models
> color #11 #3a9ca974 models
> color #11 #bfbfbfff models
> color #11 #919191ff models
> color #11 #91919190 models
> ui tool show AlphaFold
> hide #!11 models
> hide #5 models
> select add #18
8974 atoms, 9105 bonds, 1154 residues, 1 model selected
Alignment identifier is 18/A
Alignment identifier is 1
> alphafold predict
> PVVRFVNKMLLDAIKGGSSDLHFEPYEKIYRVRFRTDGMLHEVAKPPIQLASRISARLKVMAGLDISERRKPQDGRIKMRVSKTKSIDFRVNTLPTLWGEKIVMRILDSSSAQMGIDALGYEEDQKELYLAALKQPQGMILVTGPTGSGKTVSLYTGLNILNTTDINISTAEDPVEINLEGINQVNVNPRQGMDFSQALRAFLRQDPDVIMVGEIRDLETAEIAIKAAQTGHMVMSTLHTNSAAETLTRLLNMGVPAFNLATSVNLIIAQRLARKLCSHCKKEHDVPKETLLHEGFPEELIGTFKLYSPVGCDHCKNGYKGRVGIYEVVKNTPALQRIIMEEGNSIEIAEQARKEGFNDLRTSGLLKAMQGITSLEEVNRVTKD,PVVRFVNKMLLDAIKGGSSDLHFEPYEKIYRVRFRTDGMLHEVAKPPIQLASRISARLKVMAGLDISERRKPQDGRIKMRVSKTKSIDFRVNTLPTLWGEKIVMRILDSSSAQMGIDALGYEEDQKELYLAALKQPQGMILVTGPTGSGKTVSLYTGLNILNTTDINISTAEDPVEINLEGINQVNVNPRQGMDFSQALRAFLRQDPDVIMVGEIRDLETAEIAIKAAQTGHMVMSTLHTNSAAETLTRLLNMGVPAFNLATSVNLIIAQRLARKLCSHCKKEHDVPKETLLHEGFPEELIGTFKLYSPVGCDHCKNGYKGRVGIYEVVKNTPALQRIIMEEGNSIEIAEQARKEGFNDLRTSGLLKAMQGITSLEEVNRVTKD,PVVRFVNKMLLDAIKGGSSDLHFEPYEKIYRVRFRTDGMLHEVAKPPIQLASRISARLKVMAGLDISERRKPQDGRIKMRVSKTKSIDFRVNTLPTLWGEKIVMRILDSSSAQMGIDALGYEEDQKELYLAALKQPQGMILVTGPTGSGKTVSLYTGLNILNTTDINISTAEDPVEINLEGINQVNVNPRQGMDFSQALRAFLRQDPDVIMVGEIRDLETAEIAIKAAQTGHMVMSTLHTNSAAETLTRLLNMGVPAFNLATSVNLIIAQRLARKLCSHCKKEHDVPKETLLHEGFPEELIGTFKLYSPVGCDHCKNGYKGRVGIYEVVKNTPALQRIIMEEGNSIEIAEQARKEGFNDLRTSGLLKAMQGITSLEEVNRVTKD
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #1 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 combination, chain A (#3) with best_model.pdb, chain C (#1),
sequence alignment score = 1943.7
RMSD between 384 pruned atom pairs is 0.471 angstroms; (across all 384 pairs:
0.471)
> matchmaker #1 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 combination, chain A (#3) with best_model.pdb, chain C (#1),
sequence alignment score = 1943.7
RMSD between 384 pruned atom pairs is 0.471 angstroms; (across all 384 pairs:
0.471)
> color sel bychain
> select clear
> hide #1 models
> show #!11 models
> hide #!11 models
> set bgColor white
> set bgColor #ffffff00
> show #!11 models
> color #11 #bfbfbfff models
> color #11 white models
> color #11 grey models
> color #11 #80808039 models
> color #11 #8080803a models
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #17 models
> show #5 models
> hide #5 models
> show #5 models
> color #5 grey
> color #5 white
> color #5 #bfbfbfff
> color #5 #aa7942ff
> color #5 #0433ffff
> color #5 #76d6ffff
> show #1 models
> hide #18 models
> hide #5 models
> color #11 #8080805e models
> select #1/A
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> hide sel cartoons
> select add #1
8964 atoms, 9093 bonds, 1152 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
8964 atoms, 9093 bonds, 1152 residues, 1 model selected
> color sel bychain
> select clear
> select #1/B:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:108-600
2121 atoms, 2148 bonds, 277 residues, 1 model selected
> hide sel cartoons
> select ::name="ARG"
10032 atoms, 9158 bonds, 912 residues, 15 models selected
> style sel & #1 stick
Changed 792 atom styles
> style sel & #1 stick
Changed 792 atom styles
> show sel & #1 atoms
> select clear
> hide #1 atoms
> select #1/B:108-600
2121 atoms, 2148 bonds, 277 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/A
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> show sel cartoons
> select #1/A, #1/B: 107-600
Expected an objects specifier or a keyword
> hide sel cartoons
> select #1/A #1/B: 107-600
5117 atoms, 5187 bonds, 662 residues, 1 model selected
> hide sel cartoons
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/BfpE_BfpD_BfpC_interacitions/BfpDEC_01_No_corrected.pdb
Chain information for BfpDEC_01_No_corrected.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #1 models
> hide #2 models
> hide #!11 models
> select add #1
8964 atoms, 9093 bonds, 1152 residues, 1 model selected
> select subtract #1
Nothing selected
> show #2 models
> color #2 bychain
> select #2/A
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> hide #2 models
> open
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/BfpDx2-BfpE/AF_BfpDDE_Num_corrected.pdb
Chain information for AF_BfpDDE_Num_corrected.pdb #4
---
Chain | Description
A | No description available
B C | No description available
> color #4 bychain
> select #4/A
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> rainbow sel
> select #4/b
3373 atoms, 3429 bonds, 428 residues, 1 model selected
> select #4/A
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> select #4/B
3373 atoms, 3429 bonds, 428 residues, 1 model selected
> select #4/C
3373 atoms, 3429 bonds, 428 residues, 1 model selected
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-100
799 atoms, 814 bonds, 100 residues, 1 model selected
> style sel stick
Changed 799 atom styles
> show sel atoms
> hide sel atoms
> select #4/B
3373 atoms, 3429 bonds, 428 residues, 1 model selected
> select add #4
8746 atoms, 8899 bonds, 1107 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #4/a
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select add #4
8746 atoms, 8899 bonds, 1107 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #4/a
2000 atoms, 2041 bonds, 251 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> ui mousemode right distance
> hide sel surfaces
> ui mousemode right select
> select add #4
8746 atoms, 8899 bonds, 1107 residues, 2 models selected
> select subtract #4
1 model selected
> ui mousemode right select
> ui mousemode right distance
> open /Volumes/Pradip_Hutu/BfpE_Msl/BfpD/8dzg.cif
8dzg.cif title:
Cryo-EM structure of bundle-forming pilus extension ATPase from E.coli in the
presence of ADP [more info...]
Chain information for 8dzg.cif #19
---
Chain | Description | UniProt
A B C D E F | BfpD | Q47070_ECOLX 3-534
Non-standard residues in 8dzg.cif #19
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
> hide #!4 models
> hide #!19 atoms
> show #!19 cartoons
> show #!19 surfaces
> select add #19
19758 atoms, 20088 bonds, 42 pseudobonds, 2538 residues, 3 models selected
> hide sel surfaces
> select subtract #19
6 models selected
> close #19
> show #18 models
> show #1 models
> close #2
> close #4
> show #5 models
> hide #5 models
> select add #1
8964 atoms, 9093 bonds, 1152 residues, 1 model selected
> show sel cartoons
> color #1 #ff40ffff
> ui mousemode right select
> select clear
> hide #18 models
> color #1 bychain
> show #!11 models
> hide #!11 models
> select #5/A
2988 atoms, 3033 bonds, 384 residues, 1 model selected
> select #1/A
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> select #1/A,B
5976 atoms, 6062 bonds, 768 residues, 1 model selected
> select #1/A,B:107-600
4258 atoms, 4312 bonds, 556 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_model.pdb
> models #1 selectedOnly true
> select clear
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_model.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 2
GLY A 16 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 48 LEU A 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA A 51 ALA A 62 1
12
Start residue of secondary structure not found: HELIX 20 20 VAL B 2 LYS B 15 1
14
Start residue of secondary structure not found: HELIX 21 21 ILE B 48 LEU B 50
1 3
47 messages similar to the above omitted
Chain information for AF_pilBpk_0821_half_model.pdb #2
---
Chain | Description
A B | No description available
> hide #1 models
> color #2 bychain
> show #!11 models
> select add #2
4258 atoms, 4312 bonds, 556 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-3.0916,0,1,0,-16.104,0,0,1,-2.7382
> view matrix models #2,1,0,0,0.41222,0,1,0,-19.421,0,0,1,5.8453
> fitmap #2 inMap #11
Fit molecule AF_pilBpk_0821_half_model.pdb (#2) to map 0817composite_map.ccp4
(#11) using 4258 atoms
average map value = 1.851, steps = 112
shifted from previous position = 4.75
rotated from previous position = 16.6 degrees
atoms outside contour = 3558, contour level = 5.1599
Position of AF_pilBpk_0821_half_model.pdb (#2) relative to
0817composite_map.ccp4 (#11) coordinates:
Matrix rotation and translation
0.95935902 -0.12674214 0.25212437 -5.83942460
0.11593569 0.99160096 0.05732757 -38.19985582
-0.25727259 -0.02576750 0.96599526 42.04476201
Axis -0.14569507 0.89315318 0.42550012
Axis point 180.77039320 0.00000000 61.18621323
Rotation angle (degrees) 16.56887614
Shift along axis -15.37749586
> view matrix models
> #2,0.95936,-0.12674,0.25212,-13.183,0.11594,0.9916,0.057328,-34.417,-0.25727,-0.025768,0.966,44.322
> view matrix models
> #2,0.95936,-0.12674,0.25212,-13.215,0.11594,0.9916,0.057328,-34.945,-0.25727,-0.025768,0.966,44.294
> view matrix models
> #2,0.86421,-0.33504,0.37535,15.635,-0.0021476,0.74357,0.66865,-51.215,-0.50312,-0.57867,0.64188,191.83
> view matrix models
> #2,0.86421,-0.33504,0.37535,25.083,-0.0021476,0.74357,0.66865,-57.68,-0.50312,-0.57867,0.64188,188.79
> view matrix models
> #2,0.86421,-0.33504,0.37535,25.548,-0.0021476,0.74357,0.66865,-59.416,-0.50312,-0.57867,0.64188,197.13
> view matrix models
> #2,0.91706,-0.21678,0.33469,6.0612,-0.089259,0.70643,0.70213,-48.721,-0.38864,-0.67377,0.62849,202.62
> view matrix models
> #2,0.91706,-0.21678,0.33469,7.2622,-0.089259,0.70643,0.70213,-47.785,-0.38864,-0.67377,0.62849,202.52
> view matrix models
> #2,0.91706,-0.21678,0.33469,4.6353,-0.089259,0.70643,0.70213,-50.904,-0.38864,-0.67377,0.62849,203.65
> view matrix models
> #2,0.91706,-0.21678,0.33469,4.9036,-0.089259,0.70643,0.70213,-45.044,-0.38864,-0.67377,0.62849,202.45
> view matrix models
> #2,0.91706,-0.21678,0.33469,5.4725,-0.089259,0.70643,0.70213,-44.904,-0.38864,-0.67377,0.62849,202.4
> view matrix models
> #2,0.91511,-0.17184,0.36476,-4.7977,-0.13891,0.71489,0.6853,-39.575,-0.37852,-0.67779,0.63033,201.85
> view matrix models
> #2,0.91511,-0.17184,0.36476,-7.156,-0.13891,0.71489,0.6853,-41.689,-0.37852,-0.67779,0.63033,202.4
> view matrix models
> #2,0.9119,-0.15924,0.37825,-10.334,-0.15216,0.72477,0.67197,-40.51,-0.38115,-0.67033,0.63669,200.77
> view matrix models
> #2,0.88658,-0.041607,0.46071,-35.665,-0.27291,0.7571,0.59356,-25.3,-0.3735,-0.65197,0.65987,194.55
> view matrix models
> #2,0.88658,-0.041607,0.46071,-37.847,-0.27291,0.7571,0.59356,-26.389,-0.3735,-0.65197,0.65987,193.71
> view matrix models
> #2,0.91635,-0.0067351,0.40032,-39.651,-0.237,0.79674,0.55591,-32.047,-0.3227,-0.60429,0.7285,173.63
> view matrix models
> #2,0.9075,-0.016421,0.41974,-39.384,-0.24997,0.78195,0.57103,-30.096,-0.33759,-0.62312,0.70551,180.61
> view matrix models
> #2,0.9075,-0.016421,0.41974,-36.975,-0.24997,0.78195,0.57103,-27.585,-0.33759,-0.62312,0.70551,180
> fitmap #2 inMap #11
Fit molecule AF_pilBpk_0821_half_model.pdb (#2) to map 0817composite_map.ccp4
(#11) using 4258 atoms
average map value = 5.007, steps = 148
shifted from previous position = 4.23
rotated from previous position = 35.3 degrees
atoms outside contour = 2354, contour level = 5.1599
Position of AF_pilBpk_0821_half_model.pdb (#2) relative to
0817composite_map.ccp4 (#11) coordinates:
Matrix rotation and translation
0.96362136 0.26700175 0.01199772 -47.71429391
-0.16021505 0.54112783 0.82553728 -26.12357722
0.21392760 -0.79742757 0.56422004 163.74708905
Axis -0.96013175 -0.11945994 -0.25273771
Axis point 0.00000000 146.53009025 112.00040944
Rotation angle (degrees) 57.69103420
Shift along axis 7.54766550
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> select #1/A
2988 atoms, 3031 bonds, 384 residues, 1 model selected
> select #2/A
2129 atoms, 2156 bonds, 278 residues, 1 model selected
> hide sel cartoons
> show #18 models
> color #18 #fffc79ff
> color #18 #919191ff
> color #18 #797979ff
> color #18 white
> color #18 #ff2f92ff
> show #1 models
> hide #18 models
> hide #1 models
> show #18 models
> hide #2 models
> hide #18 models
> show #2 models
> show #1 models
> hide #2 models
> select add #2
4258 atoms, 4312 bonds, 556 residues, 1 model selected
> select subtract #2
Nothing selected
> select #1/A, B:1-107
1734 atoms, 1764 bonds, 214 residues, 1 model selected
> select #1/C, B:1-107
1734 atoms, 1764 bonds, 214 residues, 1 model selected
> select #1/C #1/ B:1-107
3855 atoms, 3913 bonds, 491 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
> models #1 selectedOnly true relModel #11
> hide #1 models
> select add #1
8964 atoms, 9093 bonds, 1152 residues, 1 model selected
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 2
GLY A 16 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 48 LEU A 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA A 51 ALA A 62 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 109 GLN A 113
1 5
Start residue of secondary structure not found: HELIX 5 5 ILE A 116 ALA A 118
1 3
54 messages similar to the above omitted
Chain information for AF_pilBpk_0821_half_1_model.pdb #4
---
Chain | Description
B C | No description available
> color #4 bychain
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #2 models
> hide #2 models
> hide #4 models
> show #18 models
> color #18 bychain
> hide #!11 models
> select #18/C #1/ B:295-600
3693 atoms, 3745 bonds, 475 residues, 2 models selected
> select #18/C #18/ B:295-600
5083 atoms, 5154 bonds, 657 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0818_RSR_part2.pdb
> models #18 selectedOnly true relModel #11
> hide #18 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0818_RSR_part2.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0818_RSR_part2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 183
LYS A 197 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 230 LEU A 232
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA A 233 MET A 243
1 11
Start residue of secondary structure not found: HELIX 4 4 SER A 291 GLN A 295
1 5
Start residue of secondary structure not found: HELIX 5 5 ILE A 298 LEU A 301
1 4
43 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (459 )
Cannot find LINK/SSBOND residue CYS (462 )
Chain information for 0818_RSR_part2.pdb #19
---
Chain | Description
B C | No description available
> show #4 models
> show #!11 models
> show #2 models
> hide #2 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0818_RSR_part2-coot-0.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0818_RSR_part2-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 183
LYS A 197 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 230 LEU A 232
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA A 233 MET A 243
1 11
Start residue of secondary structure not found: HELIX 4 4 SER A 291 GLN A 295
1 5
Start residue of secondary structure not found: HELIX 5 5 ILE A 298 LEU A 301
1 4
43 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (459 )
Cannot find LINK/SSBOND residue CYS (462 )
Chain information for 0818_RSR_part2-coot-0.pdb #20
---
Chain | Description
B C | No description available
> hide #19 models
> select add #18
8974 atoms, 9105 bonds, 1154 residues, 1 model selected
> select subtract #18
Nothing selected
> hide #!11 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> ui mousemode right select
Drag select of 1148 residues
> combine sel
Remapping chain ID 'B' in 0818_RSR_part2-coot-0.pdb #20 to 'D'
Remapping chain ID 'C' in 0818_RSR_part2-coot-0.pdb #20 to 'E'
> hide #4 models
> hide #20 models
> select add #20
8938 atoms, 5154 bonds, 1148 residues, 2 models selected
> select add #4
8938 atoms, 9067 bonds, 1148 residues, 2 models selected
> select subtract #4
5083 atoms, 5154 bonds, 657 residues, 1 model selected
> select subtract #20
Nothing selected
> select add #21
8938 atoms, 9067 bonds, 1148 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_01.pdb
> models #21 selectedOnly true relModel #11
> show #18 models
> hide #21 models
> select subtract #21
Nothing selected
> hide #18 models
> show #19 models
> show #1 models
> hide #19 models
> show #2 models
> hide #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #1 models
> show #4 models
> show #1 models
> hide #4 models
> select #1/C #1/B:1-112
3886 atoms, 3944 bonds, 496 residues, 1 model selected
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
> models #1 selectedOnly true relModel #11
> close #4
> hide #1 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/AF_pilBpk_0821_half_1_model.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 2
GLY A 16 1 15
Start residue of secondary structure not found: HELIX 2 2 ILE A 48 LEU A 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA A 51 ALA A 62 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 109 GLN A 113
1 5
Start residue of secondary structure not found: HELIX 5 5 ILE A 116 ALA A 118
1 3
14 messages similar to the above omitted
End residue of secondary structure not found: HELIX 23 23 SER B 109 GLN B 113
1 5
Start residue of secondary structure not found: HELIX 24 24 ILE B 116 ALA B
118 1 3
Start residue of secondary structure not found: HELIX 25 25 GLU B 123 LEU B
133 1 11
Start residue of secondary structure not found: HELIX 26 26 LYS B 150 LEU B
161 1 12
Start residue of secondary structure not found: HELIX 27 27 PRO B 189 GLN B
191 1 3
Start residue of secondary structure not found: HELIX 28 28 PHE B 195 ALA B
201 1 7
34 messages similar to the above omitted
Chain information for AF_pilBpk_0821_half_1_model.pdb #4
---
Chain | Description
B C | No description available
> color #4 bychain
> show #20 models
> show #!11 models
> hide #!11 models
Drag select of 1153 residues
> select clear
Drag select of 1153 residues
> combine sel
Remapping chain ID 'B' in 0818_RSR_part2-coot-0.pdb #20 to 'D'
Remapping chain ID 'C' in 0818_RSR_part2-coot-0.pdb #20 to 'E'
> close #21
> hide #20 models
> select add #20
8969 atoms, 5154 bonds, 1153 residues, 2 models selected
> hide #4 models
> select subtract #20
3886 atoms, 496 residues, 1 model selected
> select add #4
3886 atoms, 3944 bonds, 496 residues, 1 model selected
> select add #22
12855 atoms, 13042 bonds, 1649 residues, 2 models selected
> select subtract #22
3886 atoms, 3944 bonds, 496 residues, 1 model selected
> select add #22
12855 atoms, 13042 bonds, 1649 residues, 2 models selected
> select clear
> select add #22
8969 atoms, 9098 bonds, 1153 residues, 1 model selected
> hide #22 models
> show #22 models
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_01.pdb
> models #22 selectedOnly true relModel #11
> close #22
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_01.pdb
Chain information for 0821_Model_01.pdb #21
---
Chain | Description
B C | No description available
D E | No description available
> color #21 bychain
> show #18 models
> close #21
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_01.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_01.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL B 2
LYS B 15 1 14
Start residue of secondary structure not found: HELIX 2 2 ILE B 48 LEU B 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA B 51 ALA B 62 1
12
Start residue of secondary structure not found: HELIX 4 4 VAL C 2 LYS C 15 1
14
Start residue of secondary structure not found: HELIX 5 5 ILE C 48 LEU C 50 1
3
104 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (462 )
Chain information for 0821_Model_01.pdb #21
---
Chain | Description
A B | No description available
C | No description available
> hide #18 models
> color #21 bychain
Drag select of 87 residues
> select clear
> show #!11 models
Drag select of 11 0817composite_map.ccp4 , 2 residues
> select #11
2 models selected
> select clear
> select add #21
8969 atoms, 9097 bonds, 1153 residues, 1 model selected
> select add #11
8969 atoms, 9097 bonds, 1153 residues, 3 models selected
> fitmap #21 inMap #11
Fit molecule 0821_Model_01.pdb (#21) to map 0817composite_map.ccp4 (#11) using
8969 atoms
average map value = 6.017, steps = 64
shifted from previous position = 0.17
rotated from previous position = 0.335 degrees
atoms outside contour = 4127, contour level = 5.1599
Position of 0821_Model_01.pdb (#21) relative to 0817composite_map.ccp4 (#11)
coordinates:
Matrix rotation and translation
0.99998373 0.00090556 0.00563240 -0.90200986
-0.00089820 0.99999874 -0.00130973 0.19577333
-0.00563357 0.00130465 0.99998328 0.30217848
Axis 0.22335335 0.96247946 -0.15409921
Axis point 51.53972336 0.00000000 157.93202691
Rotation angle (degrees) 0.33532986
Shift along axis -0.05960459
Drag select of 11 0817composite_map.ccp4 , 1 residues
> select clear
> hide #21 models
> show #21 models
> ui tool show "Fit in Map"
> close #21
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_02.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_02.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL B 2
LYS B 15 1 14
Start residue of secondary structure not found: HELIX 2 2 ILE B 48 LEU B 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA B 51 ALA B 62 1
12
Start residue of secondary structure not found: HELIX 4 4 VAL C 2 LYS C 15 1
14
Start residue of secondary structure not found: HELIX 5 5 ILE C 48 LEU C 50 1
3
104 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (462 )
Chain information for 0821_Model_02.pdb #21
---
Chain | Description
A B | No description available
C | No description available
> color #21 bychain
> fitmap #21 inMap #11
Fit molecule 0821_Model_02.pdb (#21) to map 0817composite_map.ccp4 (#11) using
8969 atoms
average map value = 6.017, steps = 64
shifted from previous position = 0.17
rotated from previous position = 0.335 degrees
atoms outside contour = 4127, contour level = 5.1599
Position of 0821_Model_02.pdb (#21) relative to 0817composite_map.ccp4 (#11)
coordinates:
Matrix rotation and translation
0.99998373 0.00090556 0.00563240 -0.90200986
-0.00089820 0.99999874 -0.00130973 0.19577333
-0.00563357 0.00130465 0.99998328 0.30217848
Axis 0.22335335 0.96247946 -0.15409921
Axis point 51.53972336 0.00000000 157.93202691
Rotation angle (degrees) 0.33532986
Shift along axis -0.05960459
> fitmap #21 inMap #11
Fit molecule 0821_Model_02.pdb (#21) to map 0817composite_map.ccp4 (#11) using
8969 atoms
average map value = 6.017, steps = 44
shifted from previous position = 0.0106
rotated from previous position = 0.0155 degrees
atoms outside contour = 4129, contour level = 5.1599
Position of 0821_Model_02.pdb (#21) relative to 0817composite_map.ccp4 (#11)
coordinates:
Matrix rotation and translation
0.99998322 0.00070382 0.00575009 -0.89696693
-0.00069553 0.99999872 -0.00144415 0.19645115
-0.00575109 0.00144013 0.99998243 0.29709300
Axis 0.24157197 0.96327907 -0.11720249
Axis point 49.92046642 0.00000000 153.52174636
Rotation angle (degrees) 0.34204676
Shift along axis -0.06226483
> fitmap #21 inMap #11
Fit molecule 0821_Model_02.pdb (#21) to map 0817composite_map.ccp4 (#11) using
8969 atoms
average map value = 6.017, steps = 28
shifted from previous position = 0.0097
rotated from previous position = 0.0066 degrees
atoms outside contour = 4134, contour level = 5.1599
Position of 0821_Model_02.pdb (#21) relative to 0817composite_map.ccp4 (#11)
coordinates:
Matrix rotation and translation
0.99998318 0.00081738 0.00574205 -0.90336079
-0.00080900 0.99999860 -0.00146290 0.21570761
-0.00574323 0.00145823 0.99998244 0.29377041
Axis 0.24420092 0.96014596 -0.13596195
Axis point 49.41137932 0.00000000 155.19620723
Rotation angle (degrees) 0.34268847
Shift along axis -0.05343235
> fitmap #21 inMap #11
Fit molecule 0821_Model_02.pdb (#21) to map 0817composite_map.ccp4 (#11) using
8969 atoms
average map value = 6.016, steps = 48
shifted from previous position = 0.0237
rotated from previous position = 0.00984 degrees
atoms outside contour = 4131, contour level = 5.1599
Position of 0821_Model_02.pdb (#21) relative to 0817composite_map.ccp4 (#11)
coordinates:
Matrix rotation and translation
0.99998393 0.00088075 0.00560031 -0.91581586
-0.00087298 0.99999865 -0.00138978 0.20421055
-0.00560152 0.00138487 0.99998335 0.28551226
Axis 0.23770088 0.95964897 -0.15024031
Axis point 48.75913369 0.00000000 160.92696818
Rotation angle (degrees) 0.33440414
Shift along axis -0.06461525
> save
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0817composite_map_aligned.ccp4
> models #11
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/Douse_2/douse_000.pdb
Chain information for douse_000.pdb #22
---
Chain | Description
A B | No description available
C | No description available
> hide #21 models
> show #21 models
> hide #21 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_02-coot-0.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0821_Model_02-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL B 2
LYS B 15 1 14
Start residue of secondary structure not found: HELIX 2 2 ILE B 48 LEU B 50 1
3
Start residue of secondary structure not found: HELIX 3 3 ALA B 51 ALA B 62 1
12
Start residue of secondary structure not found: HELIX 4 4 VAL C 2 LYS C 15 1
14
Start residue of secondary structure not found: HELIX 5 5 ILE C 48 LEU C 50 1
3
104 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (462 )
Chain information for 0821_Model_02-coot-0.pdb #23
---
Chain | Description
A B | No description available
C | No description available
> hide #22 models
> show #22 models
> hide #!11 models
> hide #23 models
> color #22 bychain
> show #23 models
> hide #23 models
> show #23 models
> hide #22 models
> hide #23 models
> show #22 models
> show #21 models
> hide #22 models
> show #23 models
> color #23 black
> hide #23 models
> show #23 models
> hide #21 models
> show #21 models
> hide #23 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/RealSpaceRefine_6/Model_2_real_space_refined_006.pdb
Chain information for Model_2_real_space_refined_006.pdb #24
---
Chain | Description
A B | No description available
C | No description available
> show #!11 models
> hide #21 models
> show #21 models
> hide #!11 models
> show #!11 models
> hide #21 models
> hide #24 models
> show #21 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/Model_2_Mix_real_space_refined_006.pdb
Summary of feedback from opening
/Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/Model_2_Mix_real_space_refined_006.pdb
---
warnings | Ignored bad PDB record found on line 60
Ignored bad PDB record found on line 959
Chain information for Model_2_Mix_real_space_refined_006.pdb #25
---
Chain | Description
A B | No description available
C | No description available
> show #24 models
> hide #21 models
> hide #24 models
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/RealSpaceRefine_11/Model_2Mix__real_space_refined_011.pdb
Chain information for Model_2Mix__real_space_refined_011.pdb #26
---
Chain | Description
A B | No description available
C | No description available
> show #23 models
> hide #25 models
> hide #26 models
> select clear
> open
> /Users/anshu_mini/Desktop/PS_Mini_Desk/PilB_0817/From_AF_model/0817composite_map_aligned.ccp4
Opened 0817composite_map_aligned.ccp4 as #27, grid size 226,226,226, pixel
1.08, shown at level 3.79, step 1, values float32
> open
> /Users/anshu_mini/Downloads/ChimeraX/AlphaFold/BfpDx2-BfpE/AF_BfpDDE_Num_corrected.pdb
Chain information for AF_BfpDDE_Num_corrected.pdb #28
---
Chain | Description
A | No description available
B C | No description available
> hide #!11 models
> hide #23 models
> hide #!27 models
> hide #28 models
> show #28 models
> color #28 bychain
> interfaces #28 & ~solvent
3 buried areas: B C 1484, C A 771, B A 522
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> hbonds sel reveal true
63 hydrogen bonds found
> select add #28
8746 atoms, 8899 bonds, 63 pseudobonds, 1107 residues, 3 models selected
> select subtract #29
8746 atoms, 8899 bonds, 1107 residues, 2 models selected
> show sel cartoons
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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
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: Mac mini
Model Identifier: Mac14,12
Model Number: MNH73LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 9 days, 9 hours, 35 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL S2721QS:
Resolution: 4608 x 2592
UI Looks like: 2304 x 1296 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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-Clipper: 0.21.0
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: 2022.2.22
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 , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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