id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9637	Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0	chimerax-bug-report@…	Eric Pettersen	"{{{
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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  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac14,12"",
  ""coalitionID"" : 2723,
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  ""incident"" : ""457F75AA-CAFE-46F9-BCF1-528D9F4CE493"",
  ""pid"" : 3958,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
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  ""procStartAbsTime"" : 461785838313,
  ""procExitAbsTime"" : 4562539161719,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"",
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  ""crashReporterKey"" : ""903F58DE-AEF4-B5C2-14F6-BCFBB738E9E3"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
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  ""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  "",
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  ""ktriageinfo"" : ""VM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\n"",
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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

}}}
"	defect	closed	normal		Window Toolkit		duplicate		Tom Goddard				all	ChimeraX