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#17928 closed defect (can't reproduce)

Cannot instantiate sseq.structure

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Z:/Aorta/Anne/Experiments/AlphaFold/test_f69a7_1.result.zip

Unrecognized file suffix '.zip'  

> open
> Z:/Aorta/Anne/Experiments/AlphaFold/G259V/test_f69a7_1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb

Chain information for
test_f69a7_1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open
> Z:/Aorta/Anne/Experiments/AlphaFold/WT/WT_1bb03/WT_1bb03_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for
WT_1bb03_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #2  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> ui tool show "Selection Inspector"

QWindowsWindow::setGeometry: Unable to set geometry 379x335+1011+546 (frame:
397x382+1002+508) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 377x327+1012+553 (frame:
395x374+1003+515) margins: 9, 38, 9, 9 minimum size: 159x84 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=217, y=152)))  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie1.mp4

Movie saved to C:\ProgramData\ChimeraX\movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie2.mp4

Movie saved to C:\ProgramData\ChimeraX\movie2.mp4  
  

> show atoms

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie3.mp4

Movie saved to C:\ProgramData\ChimeraX\movie3.mp4  
  

> save C:\ProgramData\ChimeraX\image1.png supersample 3

> show atoms

> style ball

Changed 5867 atom styles  

> style ball

Changed 5867 atom styles  

> style stick

Changed 5867 atom styles  

> style stick

Changed 5867 atom styles  

> show cartoons

> show atoms

[Repeated 1 time(s)]

> hide target m

[Repeated 1 time(s)]

> show #1 models

> show #1 cartoons

> style #1 stick

Changed 2935 atom styles  

> style #1 stick

Changed 2935 atom styles  

> style #1 sphere

Changed 2935 atom styles  

> style #1 sphere

Changed 2935 atom styles  

> undo

[Repeated 9 time(s)]

> hide atoms

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> set bgColor black

> set bgColor transparent

> lighting simple

> ui tool show "Selection Inspector"

QWindowsWindow::setGeometry: Unable to set geometry 379x335+1011+546 (frame:
397x382+1002+508) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 377x327+1012+553 (frame:
395x374+1003+515) margins: 9, 38, 9, 9 minimum size: 159x84 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=217, y=152)))  

> view

> ui tool show "Command Line Interface"

> align #1 toAtoms #2

Unequal number of atoms to pair, 2935 and 2932  

> align #1 toAtoms #2

Unequal number of atoms to pair, 2935 and 2932  

> matchmaker #1 to #2

Computing secondary structure  
[Repeated 1 time(s)]  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 WT_1bb03_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#2) with
test_f69a7_1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#1), sequence alignment score = 1564  
RMSD between 158 pruned atom pairs is 0.989 angstroms; (across all 368 pairs:
16.625)  
  

> color byattribute pldd

No known/registered numeric attribute pldd  

> color byattribute pldd

No known/registered numeric attribute pldd  

> color bfactor palette rainbow target r

736 residues, atom bfactor range 22.2 to 98.9  

> color bfactor palette rainbow target r key true

> key rainbow :22.2 :41.4 :60.6 :79.7 :98.9 showTool true

> ui mousemode right "color key"

736 residues, atom bfactor range 22.2 to 98.9  

> ui windowfill toggle

[Repeated 2 time(s)]

> ui mousemode right translate

> color bfactor palette rainbow target r key true models #1,2

> color byattribute bfactor palette rainbow target r key true models #1,2

Expected a keyword  

> color bfactor palette rainbow target r key true models

> color byattribute bfactor palette rainbow target r key true models

Expected a keyword  

> cartoon style tube

Expected an atoms specifier or a keyword  

> hide atoms

> show cartoons

[Repeated 2 time(s)]

> select #1:259, #2:259

Expected an objects specifier or a keyword  

> ui windowfill toggle

> color bfactor palette rainbow key true target r models #1,2

> color byattribute bfactor palette rainbow key true target r models #1,2

Expected a keyword  

> color bfactor palette rainbow target r models #1, #2

> color byattribute bfactor palette rainbow target r models #1, #2

Expected a keyword  
Fetching compressed palette true from
https://www.colourlovers.com/api/palettes?keywords=true&format=json&numResults=100  
Could not find palette true at COLOURlovers.com using keyword search  
Could not find palette true at COLOURlovers.com using keyword search  

> hide atoms

> cartoon style tube

Expected an atoms specifier or a keyword  

> show cartoons

[Repeated 1 time(s)]

> cartoon style tube

Expected an atoms specifier or a keyword  

> select #1:259

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> color sel hot pink

> label atoms sel

Expected a keyword  

> ui tool show "Command Line Interface"

> matchmaker #1 to #2

Computing secondary structure  
[Repeated 1 time(s)]  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 WT_1bb03_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#2) with
test_f69a7_1_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#1), sequence alignment score = 1564  
RMSD between 158 pruned atom pairs is 0.989 angstroms; (across all 368 pairs:
16.625)  
  

> hide atoms

> cartoon style tube

Expected an atoms specifier or a keyword  

> show cartoons

> color byattribute bfactor palette rainbow target r models #1, #2

Expected a keyword  

> key showTool true

> ui mousemode right "color key"

> select #1:259

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> color sel hot pink

> label atoms sel

Expected a keyword  

> select add #2:259

11 atoms, 9 bonds, 2 residues, 2 models selected  

> style sel stick

Changed 11 atom styles  

> color sel cyan

> label atoms sel

Expected a keyword  

> focus #1:259

Unknown command: focus #1:259  

> ~select

Nothing selected  

> ui mousemode right translate

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> close session

> cd Z:/Aorta/Anne/Experiments/AlphaFold

Current working directory is: Z:\Aorta\Anne\Experiments\AlphaFold  

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open biglycan_wt.pdb

No such file/path: biglycan_wt.pdb  

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> copy #1 model #2

Unknown command: copy #1 model #2  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show "File History"

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> swapaa E :147 model #2

Missing or invalid "residues" argument: invalid residues specifier  
Computing secondary structure  

> select :140-150

190 atoms, 192 bonds, 22 residues, 2 models selected  

> ~label

> label sel

> select #2/A:1-368

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> swapaa E :147.A model #2

Missing or invalid "residues" argument: invalid residues specifier  
Computing secondary structure  

> showattr #2 rnumber chain

Unknown command: showattr #2 rnumber chain  

> showattr rnumber chain

Unknown command: showattr rnumber chain  

> hide #2 models

> select add #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> showattr rnumber chain

Unknown command: showattr rnumber chain  

> select #2/A:1-368

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> swapaa /A:147 glu model #2

Expected ',' or a keyword  
Computing secondary structure  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> swapaa glu /A:147 target #2

Missing or invalid "residues" argument: invalid residues specifier  
Computing secondary structure  

> close session

> select :140-150

Nothing selected  

> label sel

> open Z:\Aorta\Anne\Experiments\AlphaFold\BGN_WT.pdb format pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> label sel

> select /A:1-368

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> swapaa glu /A:147 target #2

Missing or invalid "residues" argument: invalid residues specifier  
Computing secondary structure  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select model #1

Expected an objects specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa glu :147 target #2

Missing or invalid "residues" argument: invalid residues specifier  
Computing secondary structure  

> color sel bynucleotide

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

QWindowsWindow::setGeometry: Unable to set geometry 343x334+1029+548 (frame:
361x381+1020+510) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 341x326+1030+555 (frame:
359x373+1021+517) margins: 9, 38, 9, 9 minimum size: 184x133 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=248, y=213)))  

> ui tool show "Selection Inspector"

QWindowsWindow::setGeometry: Unable to set geometry 379x395+1011+516 (frame:
397x442+1002+478) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 377x387+1012+523 (frame:
395x434+1003+485) margins: 9, 38, 9, 9 minimum size: 159x174 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=217, y=265)))  

> ui tool show AlphaFold

> alphafold predict #1

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  

QWindowsWindow::setGeometry: Unable to set geometry 1000x626+700+401 (frame:
1018x673+691+363) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 998x618+701+408 (frame:
1016x665+692+370) margins: 9, 38, 9, 9 minimum size: 82x1 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=121, y=48)))  

Running AlphaFold prediction  

> select ::name="LYS"

416 atoms, 372 bonds, 46 residues, 2 models selected  

> select #1/A#2/A

5866 atoms, 6004 bonds, 736 residues, 2 models selected  

> select #1/A#2/A

5866 atoms, 6004 bonds, 736 residues, 2 models selected  

> ui mousemode right label

[Repeated 3 time(s)]

> view clip false

> ui mousemode right label

> select sequence L147

Nothing selected  

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

[Repeated 1 time(s)]

> info residues

residue id #1/A:1 name MET index 0  
residue id #1/A:2 name TRP index 1  
residue id #1/A:3 name PRO index 2  
residue id #1/A:4 name LEU index 3  
residue id #1/A:5 name TRP index 4  
residue id #1/A:6 name ARG index 5  
residue id #1/A:7 name LEU index 6  
residue id #1/A:8 name VAL index 7  
residue id #1/A:9 name SER index 8  
residue id #1/A:10 name LEU index 9  
residue id #1/A:11 name LEU index 10  
residue id #1/A:12 name ALA index 11  
residue id #1/A:13 name LEU index 12  
residue id #1/A:14 name SER index 13  
residue id #1/A:15 name GLN index 14  
residue id #1/A:16 name ALA index 15  
residue id #1/A:17 name LEU index 16  
residue id #1/A:18 name PRO index 17  
residue id #1/A:19 name PHE index 18  
residue id #1/A:20 name GLU index 19  
residue id #1/A:21 name GLN index 20  
residue id #1/A:22 name ARG index 21  
residue id #1/A:23 name GLY index 22  
residue id #1/A:24 name PHE index 23  
residue id #1/A:25 name TRP index 24  
residue id #1/A:26 name ASP index 25  
residue id #1/A:27 name PHE index 26  
residue id #1/A:28 name THR index 27  
residue id #1/A:29 name LEU index 28  
residue id #1/A:30 name ASP index 29  
residue id #1/A:31 name ASP index 30  
residue id #1/A:32 name GLY index 31  
residue id #1/A:33 name PRO index 32  
residue id #1/A:34 name PHE index 33  
residue id #1/A:35 name MET index 34  
residue id #1/A:36 name MET index 35  
residue id #1/A:37 name ASN index 36  
residue id #1/A:38 name ASP index 37  
residue id #1/A:39 name GLU index 38  
residue id #1/A:40 name GLU index 39  
residue id #1/A:41 name ALA index 40  
residue id #1/A:42 name SER index 41  
residue id #1/A:43 name GLY index 42  
residue id #1/A:44 name ALA index 43  
residue id #1/A:45 name ASP index 44  
residue id #1/A:46 name THR index 45  
residue id #1/A:47 name SER index 46  
residue id #1/A:48 name GLY index 47  
residue id #1/A:49 name VAL index 48  
residue id #1/A:50 name LEU index 49  
residue id #1/A:51 name ASP index 50  
residue id #1/A:52 name PRO index 51  
residue id #1/A:53 name ASP index 52  
residue id #1/A:54 name SER index 53  
residue id #1/A:55 name VAL index 54  
residue id #1/A:56 name THR index 55  
residue id #1/A:57 name PRO index 56  
residue id #1/A:58 name THR index 57  
residue id #1/A:59 name TYR index 58  
residue id #1/A:60 name SER index 59  
residue id #1/A:61 name ALA index 60  
residue id #1/A:62 name MET index 61  
residue id #1/A:63 name CYS index 62  
residue id #1/A:64 name PRO index 63  
residue id #1/A:65 name PHE index 64  
residue id #1/A:66 name GLY index 65  
residue id #1/A:67 name CYS index 66  
residue id #1/A:68 name HIS index 67  
residue id #1/A:69 name CYS index 68  
residue id #1/A:70 name HIS index 69  
residue id #1/A:71 name LEU index 70  
residue id #1/A:72 name ARG index 71  
residue id #1/A:73 name VAL index 72  
residue id #1/A:74 name VAL index 73  
residue id #1/A:75 name GLN index 74  
residue id #1/A:76 name CYS index 75  
residue id #1/A:77 name SER index 76  
residue id #1/A:78 name ASP index 77  
residue id #1/A:79 name LEU index 78  
residue id #1/A:80 name GLY index 79  
residue id #1/A:81 name LEU index 80  
residue id #1/A:82 name LYS index 81  
residue id #1/A:83 name SER index 82  
residue id #1/A:84 name VAL index 83  
residue id #1/A:85 name PRO index 84  
residue id #1/A:86 name LYS index 85  
residue id #1/A:87 name GLU index 86  
residue id #1/A:88 name ILE index 87  
residue id #1/A:89 name SER index 88  
residue id #1/A:90 name PRO index 89  
residue id #1/A:91 name ASP index 90  
residue id #1/A:92 name THR index 91  
residue id #1/A:93 name THR index 92  
residue id #1/A:94 name LEU index 93  
residue id #1/A:95 name LEU index 94  
residue id #1/A:96 name ASP index 95  
residue id #1/A:97 name LEU index 96  
residue id #1/A:98 name GLN index 97  
residue id #1/A:99 name ASN index 98  
residue id #1/A:100 name ASN index 99  
residue id #1/A:101 name ASP index 100  
residue id #1/A:102 name ILE index 101  
residue id #1/A:103 name SER index 102  
residue id #1/A:104 name GLU index 103  
residue id #1/A:105 name LEU index 104  
residue id #1/A:106 name ARG index 105  
residue id #1/A:107 name LYS index 106  
residue id #1/A:108 name ASP index 107  
residue id #1/A:109 name ASP index 108  
residue id #1/A:110 name PHE index 109  
residue id #1/A:111 name LYS index 110  
residue id #1/A:112 name GLY index 111  
residue id #1/A:113 name LEU index 112  
residue id #1/A:114 name GLN index 113  
residue id #1/A:115 name HIS index 114  
residue id #1/A:116 name LEU index 115  
residue id #1/A:117 name TYR index 116  
residue id #1/A:118 name ALA index 117  
residue id #1/A:119 name LEU index 118  
residue id #1/A:120 name VAL index 119  
residue id #1/A:121 name LEU index 120  
residue id #1/A:122 name VAL index 121  
residue id #1/A:123 name ASN index 122  
residue id #1/A:124 name ASN index 123  
residue id #1/A:125 name LYS index 124  
residue id #1/A:126 name ILE index 125  
residue id #1/A:127 name SER index 126  
residue id #1/A:128 name LYS index 127  
residue id #1/A:129 name ILE index 128  
residue id #1/A:130 name HIS index 129  
residue id #1/A:131 name GLU index 130  
residue id #1/A:132 name LYS index 131  
residue id #1/A:133 name ALA index 132  
residue id #1/A:134 name PHE index 133  
residue id #1/A:135 name SER index 134  
residue id #1/A:136 name PRO index 135  
residue id #1/A:137 name LEU index 136  
residue id #1/A:138 name ARG index 137  
residue id #1/A:139 name LYS index 138  
residue id #1/A:140 name LEU index 139  
residue id #1/A:141 name GLN index 140  
residue id #1/A:142 name LYS index 141  
residue id #1/A:143 name LEU index 142  
residue id #1/A:144 name TYR index 143  
residue id #1/A:145 name ILE index 144  
residue id #1/A:146 name SER index 145  
residue id #1/A:147 name LYS index 146  
residue id #1/A:148 name ASN index 147  
residue id #1/A:149 name HIS index 148  
residue id #1/A:150 name LEU index 149  
residue id #1/A:151 name VAL index 150  
residue id #1/A:152 name GLU index 151  
residue id #1/A:153 name ILE index 152  
residue id #1/A:154 name PRO index 153  
residue id #1/A:155 name PRO index 154  
residue id #1/A:156 name ASN index 155  
residue id #1/A:157 name LEU index 156  
residue id #1/A:158 name PRO index 157  
residue id #1/A:159 name SER index 158  
residue id #1/A:160 name SER index 159  
residue id #1/A:161 name LEU index 160  
residue id #1/A:162 name VAL index 161  
residue id #1/A:163 name GLU index 162  
residue id #1/A:164 name LEU index 163  
residue id #1/A:165 name ARG index 164  
residue id #1/A:166 name ILE index 165  
residue id #1/A:167 name HIS index 166  
residue id #1/A:168 name ASP index 167  
residue id #1/A:169 name ASN index 168  
residue id #1/A:170 name ARG index 169  
residue id #1/A:171 name ILE index 170  
residue id #1/A:172 name ARG index 171  
residue id #1/A:173 name LYS index 172  
residue id #1/A:174 name VAL index 173  
residue id #1/A:175 name PRO index 174  
residue id #1/A:176 name LYS index 175  
residue id #1/A:177 name GLY index 176  
residue id #1/A:178 name VAL index 177  
residue id #1/A:179 name PHE index 178  
residue id #1/A:180 name SER index 179  
residue id #1/A:181 name GLY index 180  
residue id #1/A:182 name LEU index 181  
residue id #1/A:183 name ARG index 182  
residue id #1/A:184 name ASN index 183  
residue id #1/A:185 name MET index 184  
residue id #1/A:186 name ASN index 185  
residue id #1/A:187 name CYS index 186  
residue id #1/A:188 name ILE index 187  
residue id #1/A:189 name GLU index 188  
residue id #1/A:190 name MET index 189  
residue id #1/A:191 name GLY index 190  
residue id #1/A:192 name GLY index 191  
residue id #1/A:193 name ASN index 192  
residue id #1/A:194 name PRO index 193  
residue id #1/A:195 name LEU index 194  
residue id #1/A:196 name GLU index 195  
residue id #1/A:197 name ASN index 196  
residue id #1/A:198 name SER index 197  
residue id #1/A:199 name GLY index 198  
residue id #1/A:200 name PHE index 199  
residue id #1/A:201 name GLU index 200  
residue id #1/A:202 name PRO index 201  
residue id #1/A:203 name GLY index 202  
residue id #1/A:204 name ALA index 203  
residue id #1/A:205 name PHE index 204  
residue id #1/A:206 name ASP index 205  
residue id #1/A:207 name GLY index 206  
residue id #1/A:208 name LEU index 207  
residue id #1/A:209 name LYS index 208  
residue id #1/A:210 name LEU index 209  
residue id #1/A:211 name ASN index 210  
residue id #1/A:212 name TYR index 211  
residue id #1/A:213 name LEU index 212  
residue id #1/A:214 name ARG index 213  
residue id #1/A:215 name ILE index 214  
residue id #1/A:216 name SER index 215  
residue id #1/A:217 name GLU index 216  
residue id #1/A:218 name ALA index 217  
residue id #1/A:219 name LYS index 218  
residue id #1/A:220 name LEU index 219  
residue id #1/A:221 name THR index 220  
residue id #1/A:222 name GLY index 221  
residue id #1/A:223 name ILE index 222  
residue id #1/A:224 name PRO index 223  
residue id #1/A:225 name LYS index 224  
residue id #1/A:226 name ASP index 225  
residue id #1/A:227 name LEU index 226  
residue id #1/A:228 name PRO index 227  
residue id #1/A:229 name GLU index 228  
residue id #1/A:230 name THR index 229  
residue id #1/A:231 name LEU index 230  
residue id #1/A:232 name ASN index 231  
residue id #1/A:233 name GLU index 232  
residue id #1/A:234 name LEU index 233  
residue id #1/A:235 name HIS index 234  
residue id #1/A:236 name LEU index 235  
residue id #1/A:237 name ASP index 236  
residue id #1/A:238 name HIS index 237  
residue id #1/A:239 name ASN index 238  
residue id #1/A:240 name LYS index 239  
residue id #1/A:241 name ILE index 240  
residue id #1/A:242 name GLN index 241  
residue id #1/A:243 name ALA index 242  
residue id #1/A:244 name ILE index 243  
residue id #1/A:245 name GLU index 244  
residue id #1/A:246 name LEU index 245  
residue id #1/A:247 name GLU index 246  
residue id #1/A:248 name ASP index 247  
residue id #1/A:249 name LEU index 248  
residue id #1/A:250 name LEU index 249  
residue id #1/A:251 name ARG index 250  
residue id #1/A:252 name TYR index 251  
residue id #1/A:253 name SER index 252  
residue id #1/A:254 name LYS index 253  
residue id #1/A:255 name LEU index 254  
residue id #1/A:256 name TYR index 255  
residue id #1/A:257 name ARG index 256  
residue id #1/A:258 name LEU index 257  
residue id #1/A:259 name GLY index 258  
residue id #1/A:260 name LEU index 259  
residue id #1/A:261 name GLY index 260  
residue id #1/A:262 name HIS index 261  
residue id #1/A:263 name ASN index 262  
residue id #1/A:264 name GLN index 263  
residue id #1/A:265 name ILE index 264  
residue id #1/A:266 name ARG index 265  
residue id #1/A:267 name MET index 266  
residue id #1/A:268 name ILE index 267  
residue id #1/A:269 name GLU index 268  
residue id #1/A:270 name ASN index 269  
residue id #1/A:271 name GLY index 270  
residue id #1/A:272 name SER index 271  
residue id #1/A:273 name LEU index 272  
residue id #1/A:274 name SER index 273  
residue id #1/A:275 name PHE index 274  
residue id #1/A:276 name LEU index 275  
residue id #1/A:277 name PRO index 276  
residue id #1/A:278 name THR index 277  
residue id #1/A:279 name LEU index 278  
residue id #1/A:280 name ARG index 279  
residue id #1/A:281 name GLU index 280  
residue id #1/A:282 name LEU index 281  
residue id #1/A:283 name HIS index 282  
residue id #1/A:284 name LEU index 283  
residue id #1/A:285 name ASP index 284  
residue id #1/A:286 name ASN index 285  
residue id #1/A:287 name ASN index 286  
residue id #1/A:288 name LYS index 287  
residue id #1/A:289 name LEU index 288  
residue id #1/A:290 name ALA index 289  
residue id #1/A:291 name ARG index 290  
residue id #1/A:292 name VAL index 291  
residue id #1/A:293 name PRO index 292  
residue id #1/A:294 name SER index 293  
residue id #1/A:295 name GLY index 294  
residue id #1/A:296 name LEU index 295  
residue id #1/A:297 name PRO index 296  
residue id #1/A:298 name ASP index 297  
residue id #1/A:299 name LEU index 298  
residue id #1/A:300 name LYS index 299  
residue id #1/A:301 name LEU index 300  
residue id #1/A:302 name LEU index 301  
residue id #1/A:303 name GLN index 302  
residue id #1/A:304 name VAL index 303  
residue id #1/A:305 name VAL index 304  
residue id #1/A:306 name TYR index 305  
residue id #1/A:307 name LEU index 306  
residue id #1/A:308 name HIS index 307  
residue id #1/A:309 name SER index 308  
residue id #1/A:310 name ASN index 309  
residue id #1/A:311 name ASN index 310  
residue id #1/A:312 name ILE index 311  
residue id #1/A:313 name THR index 312  
residue id #1/A:314 name LYS index 313  
residue id #1/A:315 name VAL index 314  
residue id #1/A:316 name GLY index 315  
residue id #1/A:317 name VAL index 316  
residue id #1/A:318 name ASN index 317  
residue id #1/A:319 name ASP index 318  
residue id #1/A:320 name PHE index 319  
residue id #1/A:321 name CYS index 320  
residue id #1/A:322 name PRO index 321  
residue id #1/A:323 name MET index 322  
residue id #1/A:324 name GLY index 323  
residue id #1/A:325 name PHE index 324  
residue id #1/A:326 name GLY index 325  
residue id #1/A:327 name VAL index 326  
residue id #1/A:328 name LYS index 327  
residue id #1/A:329 name ARG index 328  
residue id #1/A:330 name ALA index 329  
residue id #1/A:331 name TYR index 330  
residue id #1/A:332 name TYR index 331  
residue id #1/A:333 name ASN index 332  
residue id #1/A:334 name GLY index 333  
residue id #1/A:335 name ILE index 334  
residue id #1/A:336 name SER index 335  
residue id #1/A:337 name LEU index 336  
residue id #1/A:338 name PHE index 337  
residue id #1/A:339 name ASN index 338  
residue id #1/A:340 name ASN index 339  
residue id #1/A:341 name PRO index 340  
residue id #1/A:342 name VAL index 341  
residue id #1/A:343 name PRO index 342  
residue id #1/A:344 name TYR index 343  
residue id #1/A:345 name TRP index 344  
residue id #1/A:346 name GLU index 345  
residue id #1/A:347 name VAL index 346  
residue id #1/A:348 name GLN index 347  
residue id #1/A:349 name PRO index 348  
residue id #1/A:350 name ALA index 349  
residue id #1/A:351 name THR index 350  
residue id #1/A:352 name PHE index 351  
residue id #1/A:353 name ARG index 352  
residue id #1/A:354 name CYS index 353  
residue id #1/A:355 name VAL index 354  
residue id #1/A:356 name THR index 355  
residue id #1/A:357 name ASP index 356  
residue id #1/A:358 name ARG index 357  
residue id #1/A:359 name LEU index 358  
residue id #1/A:360 name ALA index 359  
residue id #1/A:361 name ILE index 360  
residue id #1/A:362 name GLN index 361  
residue id #1/A:363 name PHE index 362  
residue id #1/A:364 name GLY index 363  
residue id #1/A:365 name ASN index 364  
residue id #1/A:366 name TYR index 365  
residue id #1/A:367 name LYS index 366  
residue id #1/A:368 name LYS index 367  
residue id #2/A:1 name MET index 0  
residue id #2/A:2 name TRP index 1  
residue id #2/A:3 name PRO index 2  
residue id #2/A:4 name LEU index 3  
residue id #2/A:5 name TRP index 4  
residue id #2/A:6 name ARG index 5  
residue id #2/A:7 name LEU index 6  
residue id #2/A:8 name VAL index 7  
residue id #2/A:9 name SER index 8  
residue id #2/A:10 name LEU index 9  
residue id #2/A:11 name LEU index 10  
residue id #2/A:12 name ALA index 11  
residue id #2/A:13 name LEU index 12  
residue id #2/A:14 name SER index 13  
residue id #2/A:15 name GLN index 14  
residue id #2/A:16 name ALA index 15  
residue id #2/A:17 name LEU index 16  
residue id #2/A:18 name PRO index 17  
residue id #2/A:19 name PHE index 18  
residue id #2/A:20 name GLU index 19  
residue id #2/A:21 name GLN index 20  
residue id #2/A:22 name ARG index 21  
residue id #2/A:23 name GLY index 22  
residue id #2/A:24 name PHE index 23  
residue id #2/A:25 name TRP index 24  
residue id #2/A:26 name ASP index 25  
residue id #2/A:27 name PHE index 26  
residue id #2/A:28 name THR index 27  
residue id #2/A:29 name LEU index 28  
residue id #2/A:30 name ASP index 29  
residue id #2/A:31 name ASP index 30  
residue id #2/A:32 name GLY index 31  
residue id #2/A:33 name PRO index 32  
residue id #2/A:34 name PHE index 33  
residue id #2/A:35 name MET index 34  
residue id #2/A:36 name MET index 35  
residue id #2/A:37 name ASN index 36  
residue id #2/A:38 name ASP index 37  
residue id #2/A:39 name GLU index 38  
residue id #2/A:40 name GLU index 39  
residue id #2/A:41 name ALA index 40  
residue id #2/A:42 name SER index 41  
residue id #2/A:43 name GLY index 42  
residue id #2/A:44 name ALA index 43  
residue id #2/A:45 name ASP index 44  
residue id #2/A:46 name THR index 45  
residue id #2/A:47 name SER index 46  
residue id #2/A:48 name GLY index 47  
residue id #2/A:49 name VAL index 48  
residue id #2/A:50 name LEU index 49  
residue id #2/A:51 name ASP index 50  
residue id #2/A:52 name PRO index 51  
residue id #2/A:53 name ASP index 52  
residue id #2/A:54 name SER index 53  
residue id #2/A:55 name VAL index 54  
residue id #2/A:56 name THR index 55  
residue id #2/A:57 name PRO index 56  
residue id #2/A:58 name THR index 57  
residue id #2/A:59 name TYR index 58  
residue id #2/A:60 name SER index 59  
residue id #2/A:61 name ALA index 60  
residue id #2/A:62 name MET index 61  
residue id #2/A:63 name CYS index 62  
residue id #2/A:64 name PRO index 63  
residue id #2/A:65 name PHE index 64  
residue id #2/A:66 name GLY index 65  
residue id #2/A:67 name CYS index 66  
residue id #2/A:68 name HIS index 67  
residue id #2/A:69 name CYS index 68  
residue id #2/A:70 name HIS index 69  
residue id #2/A:71 name LEU index 70  
residue id #2/A:72 name ARG index 71  
residue id #2/A:73 name VAL index 72  
residue id #2/A:74 name VAL index 73  
residue id #2/A:75 name GLN index 74  
residue id #2/A:76 name CYS index 75  
residue id #2/A:77 name SER index 76  
residue id #2/A:78 name ASP index 77  
residue id #2/A:79 name LEU index 78  
residue id #2/A:80 name GLY index 79  
residue id #2/A:81 name LEU index 80  
residue id #2/A:82 name LYS index 81  
residue id #2/A:83 name SER index 82  
residue id #2/A:84 name VAL index 83  
residue id #2/A:85 name PRO index 84  
residue id #2/A:86 name LYS index 85  
residue id #2/A:87 name GLU index 86  
residue id #2/A:88 name ILE index 87  
residue id #2/A:89 name SER index 88  
residue id #2/A:90 name PRO index 89  
residue id #2/A:91 name ASP index 90  
residue id #2/A:92 name THR index 91  
residue id #2/A:93 name THR index 92  
residue id #2/A:94 name LEU index 93  
residue id #2/A:95 name LEU index 94  
residue id #2/A:96 name ASP index 95  
residue id #2/A:97 name LEU index 96  
residue id #2/A:98 name GLN index 97  
residue id #2/A:99 name ASN index 98  
residue id #2/A:100 name ASN index 99  
residue id #2/A:101 name ASP index 100  
residue id #2/A:102 name ILE index 101  
residue id #2/A:103 name SER index 102  
residue id #2/A:104 name GLU index 103  
residue id #2/A:105 name LEU index 104  
residue id #2/A:106 name ARG index 105  
residue id #2/A:107 name LYS index 106  
residue id #2/A:108 name ASP index 107  
residue id #2/A:109 name ASP index 108  
residue id #2/A:110 name PHE index 109  
residue id #2/A:111 name LYS index 110  
residue id #2/A:112 name GLY index 111  
residue id #2/A:113 name LEU index 112  
residue id #2/A:114 name GLN index 113  
residue id #2/A:115 name HIS index 114  
residue id #2/A:116 name LEU index 115  
residue id #2/A:117 name TYR index 116  
residue id #2/A:118 name ALA index 117  
residue id #2/A:119 name LEU index 118  
residue id #2/A:120 name VAL index 119  
residue id #2/A:121 name LEU index 120  
residue id #2/A:122 name VAL index 121  
residue id #2/A:123 name ASN index 122  
residue id #2/A:124 name ASN index 123  
residue id #2/A:125 name LYS index 124  
residue id #2/A:126 name ILE index 125  
residue id #2/A:127 name SER index 126  
residue id #2/A:128 name LYS index 127  
residue id #2/A:129 name ILE index 128  
residue id #2/A:130 name HIS index 129  
residue id #2/A:131 name GLU index 130  
residue id #2/A:132 name LYS index 131  
residue id #2/A:133 name ALA index 132  
residue id #2/A:134 name PHE index 133  
residue id #2/A:135 name SER index 134  
residue id #2/A:136 name PRO index 135  
residue id #2/A:137 name LEU index 136  
residue id #2/A:138 name ARG index 137  
residue id #2/A:139 name LYS index 138  
residue id #2/A:140 name LEU index 139  
residue id #2/A:141 name GLN index 140  
residue id #2/A:142 name LYS index 141  
residue id #2/A:143 name LEU index 142  
residue id #2/A:144 name TYR index 143  
residue id #2/A:145 name ILE index 144  
residue id #2/A:146 name SER index 145  
residue id #2/A:147 name LYS index 146  
residue id #2/A:148 name ASN index 147  
residue id #2/A:149 name HIS index 148  
residue id #2/A:150 name LEU index 149  
residue id #2/A:151 name VAL index 150  
residue id #2/A:152 name GLU index 151  
residue id #2/A:153 name ILE index 152  
residue id #2/A:154 name PRO index 153  
residue id #2/A:155 name PRO index 154  
residue id #2/A:156 name ASN index 155  
residue id #2/A:157 name LEU index 156  
residue id #2/A:158 name PRO index 157  
residue id #2/A:159 name SER index 158  
residue id #2/A:160 name SER index 159  
residue id #2/A:161 name LEU index 160  
residue id #2/A:162 name VAL index 161  
residue id #2/A:163 name GLU index 162  
residue id #2/A:164 name LEU index 163  
residue id #2/A:165 name ARG index 164  
residue id #2/A:166 name ILE index 165  
residue id #2/A:167 name HIS index 166  
residue id #2/A:168 name ASP index 167  
residue id #2/A:169 name ASN index 168  
residue id #2/A:170 name ARG index 169  
residue id #2/A:171 name ILE index 170  
residue id #2/A:172 name ARG index 171  
residue id #2/A:173 name LYS index 172  
residue id #2/A:174 name VAL index 173  
residue id #2/A:175 name PRO index 174  
residue id #2/A:176 name LYS index 175  
residue id #2/A:177 name GLY index 176  
residue id #2/A:178 name VAL index 177  
residue id #2/A:179 name PHE index 178  
residue id #2/A:180 name SER index 179  
residue id #2/A:181 name GLY index 180  
residue id #2/A:182 name LEU index 181  
residue id #2/A:183 name ARG index 182  
residue id #2/A:184 name ASN index 183  
residue id #2/A:185 name MET index 184  
residue id #2/A:186 name ASN index 185  
residue id #2/A:187 name CYS index 186  
residue id #2/A:188 name ILE index 187  
residue id #2/A:189 name GLU index 188  
residue id #2/A:190 name MET index 189  
residue id #2/A:191 name GLY index 190  
residue id #2/A:192 name GLY index 191  
residue id #2/A:193 name ASN index 192  
residue id #2/A:194 name PRO index 193  
residue id #2/A:195 name LEU index 194  
residue id #2/A:196 name GLU index 195  
residue id #2/A:197 name ASN index 196  
residue id #2/A:198 name SER index 197  
residue id #2/A:199 name GLY index 198  
residue id #2/A:200 name PHE index 199  
residue id #2/A:201 name GLU index 200  
residue id #2/A:202 name PRO index 201  
residue id #2/A:203 name GLY index 202  
residue id #2/A:204 name ALA index 203  
residue id #2/A:205 name PHE index 204  
residue id #2/A:206 name ASP index 205  
residue id #2/A:207 name GLY index 206  
residue id #2/A:208 name LEU index 207  
residue id #2/A:209 name LYS index 208  
residue id #2/A:210 name LEU index 209  
residue id #2/A:211 name ASN index 210  
residue id #2/A:212 name TYR index 211  
residue id #2/A:213 name LEU index 212  
residue id #2/A:214 name ARG index 213  
residue id #2/A:215 name ILE index 214  
residue id #2/A:216 name SER index 215  
residue id #2/A:217 name GLU index 216  
residue id #2/A:218 name ALA index 217  
residue id #2/A:219 name LYS index 218  
residue id #2/A:220 name LEU index 219  
residue id #2/A:221 name THR index 220  
residue id #2/A:222 name GLY index 221  
residue id #2/A:223 name ILE index 222  
residue id #2/A:224 name PRO index 223  
residue id #2/A:225 name LYS index 224  
residue id #2/A:226 name ASP index 225  
residue id #2/A:227 name LEU index 226  
residue id #2/A:228 name PRO index 227  
residue id #2/A:229 name GLU index 228  
residue id #2/A:230 name THR index 229  
residue id #2/A:231 name LEU index 230  
residue id #2/A:232 name ASN index 231  
residue id #2/A:233 name GLU index 232  
residue id #2/A:234 name LEU index 233  
residue id #2/A:235 name HIS index 234  
residue id #2/A:236 name LEU index 235  
residue id #2/A:237 name ASP index 236  
residue id #2/A:238 name HIS index 237  
residue id #2/A:239 name ASN index 238  
residue id #2/A:240 name LYS index 239  
residue id #2/A:241 name ILE index 240  
residue id #2/A:242 name GLN index 241  
residue id #2/A:243 name ALA index 242  
residue id #2/A:244 name ILE index 243  
residue id #2/A:245 name GLU index 244  
residue id #2/A:246 name LEU index 245  
residue id #2/A:247 name GLU index 246  
residue id #2/A:248 name ASP index 247  
residue id #2/A:249 name LEU index 248  
residue id #2/A:250 name LEU index 249  
residue id #2/A:251 name ARG index 250  
residue id #2/A:252 name TYR index 251  
residue id #2/A:253 name SER index 252  
residue id #2/A:254 name LYS index 253  
residue id #2/A:255 name LEU index 254  
residue id #2/A:256 name TYR index 255  
residue id #2/A:257 name ARG index 256  
residue id #2/A:258 name LEU index 257  
residue id #2/A:259 name GLY index 258  
residue id #2/A:260 name LEU index 259  
residue id #2/A:261 name GLY index 260  
residue id #2/A:262 name HIS index 261  
residue id #2/A:263 name ASN index 262  
residue id #2/A:264 name GLN index 263  
residue id #2/A:265 name ILE index 264  
residue id #2/A:266 name ARG index 265  
residue id #2/A:267 name MET index 266  
residue id #2/A:268 name ILE index 267  
residue id #2/A:269 name GLU index 268  
residue id #2/A:270 name ASN index 269  
residue id #2/A:271 name GLY index 270  
residue id #2/A:272 name SER index 271  
residue id #2/A:273 name LEU index 272  
residue id #2/A:274 name SER index 273  
residue id #2/A:275 name PHE index 274  
residue id #2/A:276 name LEU index 275  
residue id #2/A:277 name PRO index 276  
residue id #2/A:278 name THR index 277  
residue id #2/A:279 name LEU index 278  
residue id #2/A:280 name ARG index 279  
residue id #2/A:281 name GLU index 280  
residue id #2/A:282 name LEU index 281  
residue id #2/A:283 name HIS index 282  
residue id #2/A:284 name LEU index 283  
residue id #2/A:285 name ASP index 284  
residue id #2/A:286 name ASN index 285  
residue id #2/A:287 name ASN index 286  
residue id #2/A:288 name LYS index 287  
residue id #2/A:289 name LEU index 288  
residue id #2/A:290 name ALA index 289  
residue id #2/A:291 name ARG index 290  
residue id #2/A:292 name VAL index 291  
residue id #2/A:293 name PRO index 292  
residue id #2/A:294 name SER index 293  
residue id #2/A:295 name GLY index 294  
residue id #2/A:296 name LEU index 295  
residue id #2/A:297 name PRO index 296  
residue id #2/A:298 name ASP index 297  
residue id #2/A:299 name LEU index 298  
residue id #2/A:300 name LYS index 299  
residue id #2/A:301 name LEU index 300  
residue id #2/A:302 name LEU index 301  
residue id #2/A:303 name GLN index 302  
residue id #2/A:304 name VAL index 303  
residue id #2/A:305 name VAL index 304  
residue id #2/A:306 name TYR index 305  
residue id #2/A:307 name LEU index 306  
residue id #2/A:308 name HIS index 307  
residue id #2/A:309 name SER index 308  
residue id #2/A:310 name ASN index 309  
residue id #2/A:311 name ASN index 310  
residue id #2/A:312 name ILE index 311  
residue id #2/A:313 name THR index 312  
residue id #2/A:314 name LYS index 313  
residue id #2/A:315 name VAL index 314  
residue id #2/A:316 name GLY index 315  
residue id #2/A:317 name VAL index 316  
residue id #2/A:318 name ASN index 317  
residue id #2/A:319 name ASP index 318  
residue id #2/A:320 name PHE index 319  
residue id #2/A:321 name CYS index 320  
residue id #2/A:322 name PRO index 321  
residue id #2/A:323 name MET index 322  
residue id #2/A:324 name GLY index 323  
residue id #2/A:325 name PHE index 324  
residue id #2/A:326 name GLY index 325  
residue id #2/A:327 name VAL index 326  
residue id #2/A:328 name LYS index 327  
residue id #2/A:329 name ARG index 328  
residue id #2/A:330 name ALA index 329  
residue id #2/A:331 name TYR index 330  
residue id #2/A:332 name TYR index 331  
residue id #2/A:333 name ASN index 332  
residue id #2/A:334 name GLY index 333  
residue id #2/A:335 name ILE index 334  
residue id #2/A:336 name SER index 335  
residue id #2/A:337 name LEU index 336  
residue id #2/A:338 name PHE index 337  
residue id #2/A:339 name ASN index 338  
residue id #2/A:340 name ASN index 339  
residue id #2/A:341 name PRO index 340  
residue id #2/A:342 name VAL index 341  
residue id #2/A:343 name PRO index 342  
residue id #2/A:344 name TYR index 343  
residue id #2/A:345 name TRP index 344  
residue id #2/A:346 name GLU index 345  
residue id #2/A:347 name VAL index 346  
residue id #2/A:348 name GLN index 347  
residue id #2/A:349 name PRO index 348  
residue id #2/A:350 name ALA index 349  
residue id #2/A:351 name THR index 350  
residue id #2/A:352 name PHE index 351  
residue id #2/A:353 name ARG index 352  
residue id #2/A:354 name CYS index 353  
residue id #2/A:355 name VAL index 354  
residue id #2/A:356 name THR index 355  
residue id #2/A:357 name ASP index 356  
residue id #2/A:358 name ARG index 357  
residue id #2/A:359 name LEU index 358  
residue id #2/A:360 name ALA index 359  
residue id #2/A:361 name ILE index 360  
residue id #2/A:362 name GLN index 361  
residue id #2/A:363 name PHE index 362  
residue id #2/A:364 name GLY index 363  
residue id #2/A:365 name ASN index 364  
residue id #2/A:366 name TYR index 365  
residue id #2/A:367 name LYS index 366  
residue id #2/A:368 name LYS index 367  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu target #2

Expected ',' or a keyword  
Computing secondary structure  

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu #2

Expected ',' or a keyword  
Computing secondary structure  

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> hide atoms

> cartoon style tube

Expected an atoms specifier or a keyword  

> select add #2

5869 atoms, 6007 bonds, 736 residues, 2 models selected  

> select add #3

5872 atoms, 6010 bonds, 736 residues, 2 models selected  

QWindowsWindow::setGeometry: Unable to set geometry 1058x1096+671+166 (frame:
1076x1143+662+128) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1088+672+173 (frame:
1074x1135+663+135) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> hide atoms

> cartoon style tube #1, #2, #3

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube #1, #2, #3

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube sel

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube #1, #2, #3

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube #1 #2 #3

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style tube shown

Expected an atoms specifier or a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube #1 #2 #3

Expected a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube #1, #2, #3

Expected a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube

> show cartoons

> color byattribute bfactor palette rainbow target r models #1, #2, #3

Expected a keyword  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube

> show cartoons

> color byattribute bfactor palette rainbow target r

1104 residues, atom bfactor range 28.9 to 98.8  

> key showTool true

> ui mousemode right "color key"

> focus #1:140-270

Unknown command: focus #1:140-270  

QWindowsWindow::setGeometry: Unable to set geometry 349x641+1026+394 (frame:
367x688+1017+356) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 347x633+1027+401 (frame:
365x680+1018+363) margins: 9, 38, 9, 9 minimum size: 279x371 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=367, y=511)))  

> ui mousemode right label

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube

> show cartoons

> color byattribute bfactor palette rainbow target r

1104 residues, atom bfactor range 28.9 to 98.8  

> key showTool true

> ui mousemode right "color key"

> focus #1:140-270

Unknown command: focus #1:140-270  

QWindowsWindow::setGeometry: Unable to set geometry 349x641+1026+394 (frame:
367x688+1017+356) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 347x633+1027+401 (frame:
365x680+1018+363) margins: 9, 38, 9, 9 minimum size: 279x371 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=367, y=511)))  

> close session

> ui mousemode right label

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> close session

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube

> show cartoons

> color byattribute bfactor palette rainbow target r

1104 residues, atom bfactor range 28.9 to 98.8  

> key showTool true

> ui mousemode right "color key"

> focus #1:/140-270

Unknown command: focus #1:/140-270  

QWindowsWindow::setGeometry: Unable to set geometry 349x641+1026+394 (frame:
367x688+1017+356) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 347x633+1027+401 (frame:
365x680+1018+363) margins: 9, 38, 9, 9 minimum size: 279x371 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=367, y=511)))  

> close session

> ui mousemode right label

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler  
s._changes_cb(*args)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb  
if self.structure == None:  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
Error processing trigger "changes":  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 750x599+825+415 (frame:
768x646+816+377) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x591+826+422 (frame: 766x638+817+384)
margins: 9, 38, 9, 9 minimum size: 600x325 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=453)))  

> open Z:/Aorta/Anne/Experiments/AlphaFold/Script.cxc

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #1  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  
Computing secondary structure  

> select #1

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #2  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #2

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:147 glu

Using Dunbrack library  
BGN_WT.pdb #1/A LYS 147: phi 54.9, psi 58.7 trans  
BGN_WT.pdb #2/A LYS 147: phi 54.9, psi 58.7 trans  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #1/A GLU
147  
Applying GLU rotamer (chi angles: -60.9 -175.5 -10.2) to BGN_WT.pdb #2/A GLU
147  

> open BGN_WT.pdb

BGN_WT.pdb title:  
Alphafold monomer V2.0 prediction for biglycan (P21810) [more info...]  
  
Chain information for BGN_WT.pdb #3  
---  
Chain | Description | UniProt  
A | biglycan | PGS1_HUMAN 1-368  
  

> select #3

2933 atoms, 3002 bonds, 368 residues, 1 model selected  

> swapaa /A:259 val

Using Dunbrack library  
BGN_WT.pdb #1/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #2/A GLY 259: phi -95.4, psi 111.1 trans  
BGN_WT.pdb #3/A GLY 259: phi -95.4, psi 111.1 trans  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #1/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #2/A VAL 259  
Applying VAL rotamer (chi angles: 179.3) to BGN_WT.pdb #3/A VAL 259  

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#2), sequence
alignment score = 1843.7  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> matchmaker #3 to #1

Computing secondary structure  
[Repeated 2 time(s)]  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 BGN_WT.pdb, chain A (#1) with BGN_WT.pdb, chain A (#3), sequence
alignment score = 1840.9  
RMSD between 368 pruned atom pairs is 0.000 angstroms; (across all 368 pairs:
0.000)  
  

> select all

8808 atoms, 9015 bonds, 1104 residues, 3 models selected  

> hide atoms

> cartoon style modeHelix tube

> show cartoons

> color byattribute bfactor palette rainbow target r

1104 residues, atom bfactor range 28.9 to 98.8  

> key showTool true

> ui mousemode right "color key"

> select #1:/140-270

Expected an objects specifier or a keyword  

QWindowsWindow::setGeometry: Unable to set geometry 349x641+1026+394 (frame:
367x688+1017+356) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 347x633+1027+401 (frame:
365x680+1018+363) margins: 9, 38, 9, 9 minimum size: 279x371 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=367, y=511)))  




OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.44 30.0.13044.0
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 21A4
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 14,846,324,736
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 months ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Cannot instantiate sseq.structure

comment:2 by Eric Pettersen, 5 months ago

Resolution:	→ can't reproduce
Status:	accepted → closed

I have no idea how "ui mousemode right label" could try to instantiate sseq.structure right after a "close session".

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