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Opened 3 years ago
Last modified 3 years ago
#7707 assigned enhancement
Make "wait" command with no arguments work with mseries command
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Scenes/Animation | Version: | |
| Keywords: | Cc: | Elaine Meng, pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Tried playing mseries of 25 frames for 180 kD protein. it plays ok . this error occurred when it was playing; the proram apparently inactive showed the end frame; the mseries had run thru but just no visible output;
crbug/1173575, non-JS module files deprecated.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep30c.cxs
Log from Fri Sep 30 13:52:24 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\boardmeeting-CXS-files\sep30a.cxs format
> session
Log from Fri Sep 30 11:59:06 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29g.cxs
Log from Thu Sep 29 16:56:26 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29d.cxs
Log from Thu Sep 29 10:48:18 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\boardmeeting-CXS-files\sep29b.cxs format
> session
Log from Thu Sep 29 10:18:10 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep27.cxs
Log from Tue Sep 27 13:27:24 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "C:/Users/rkrishnan/Desktop/boardmeeting CXS files/sep26d.cxs"
Log from Mon Sep 26 17:18:53 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep26c.cxs format session
Log from Mon Sep 26 17:05:52 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep26b.cxs format session
Log from Mon Sep 26 15:27:14 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep26.cxs format session
Log from Mon Sep 26 13:32:05 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/sep23d.cxs
Log from Fri Sep 23 16:20:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep23c.cxs format session
Log from Fri Sep 23 16:01:24 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep23b.cxs format session
Log from Fri Sep 23 13:35:49 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/rkrishnan/Desktop/sep23.cxs
Log from Fri Sep 23 11:03:16 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/c5morph-
> sep22d-surf.cxs
Log from Thu Sep 22 10:55:26 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:\Users\rkrishnan\Desktop\sep21F.cxs format session
Log from Wed Sep 21 15:21:34 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21/nativeC5-C5b6.cxs
Log from Wed Sep 21 13:58:56 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a
> complement/morphing/4a5w-3cu7morph.cxs"
Log from Tue Sep 20 13:54:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a
> complement/morphing/3cu7native,randomcoil,16330.cxs"
Log from Mon Sep 19 13:56:36 2022
> cd "L:/Graphics/BCRX001/GraphicsBackup/C5a complement/morphing"
Current working directory is: L:\Graphics\BCRX001\GraphicsBackup\C5a
complement\morphing
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\3cu7-native.pdb
> format pdb
Summary of feedback from opening
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\3cu7-native.pdb
---
warning | Cannot find LINK/SSBOND residue CYS (669 )
Chain information for 3cu7-native.pdb #1
---
Chain | Description
A | No description available
B | No description available
> split
Split 3cu7-native.pdb (#1) into 2 models
Chain information for 3cu7-native.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 3cu7-native.pdb B #1.2
---
Chain | Description
B | No description available
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a complement/morphing/3prxsel-
> randomcoil.pdb" format zdock
Summary of feedback from opening L:/Graphics/BCRX001/GraphicsBackup/C5a
complement/morphing/3prxsel-randomcoil.pdb
---
warnings | Ignored bad PDB record found on line 11
Ignored bad PDB record found on line 701
Ignored bad PDB record found on line 703
Ignored bad PDB record found on line 705
Ignored bad PDB record found on line 707
4 messages similar to the above omitted
Chain information for 3prxsel-randomcoil.pdb #2
---
Chain | Description
A | No description available
> mmaker #2 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native.pdb A, chain A (#1.1) with 3prxsel-randomcoil.pdb,
chain A (#2), sequence alignment score = 322.5
RMSD between 45 pruned atom pairs is 0.805 angstroms; (across all 75 pairs:
3.421)
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a
> complement/morphing/6i2xsel.pdb"
Summary of feedback from opening L:/Graphics/BCRX001/GraphicsBackup/C5a
complement/morphing/6i2xsel.pdb
---
warnings | Ignored bad PDB record found on line 11
HELIX 1 1 LYS A 682 ALA A 688 1 Generated by MOE 7
Ignored bad PDB record found on line 12
HELIX 2 2 LYS A 696 TYR A 700 1 Generated by MOE 5
Ignored bad PDB record found on line 13
HELIX 3 3 PRO A 722 SER A 736 1 Generated by MOE 15
Ignored bad PDB record found on line 14
HELIX 4 4 GLN A 737 ARG A 739 5 Generated by MOE 3
Ignored bad PDB record found on line 15
HELIX 5 5 HIS A 744 HIS A 753 1 Generated by MOE 10
1 messages similar to the above omitted
Chain information for 6i2xsel.pdb #3
---
Chain | Description
A | No description available
> mmaker #3 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native.pdb A, chain A (#1.1) with 6i2xsel.pdb, chain A (#3),
sequence alignment score = 268.5
RMSD between 48 pruned atom pairs is 0.810 angstroms; (across all 75 pairs:
5.742)
> split ligands #3
Expected a keyword
> split ligands
Did not split 3cu7-native.pdb A, has only one piece
Did not split 3cu7-native.pdb B, has only one piece
Did not split 3prxsel-randomcoil.pdb, has only one piece
Split 6i2xsel.pdb (#3) into 2 models
Chain information for 6i2xsel.pdb #3.1
---
Chain | Description
A | No description available
> combine #3.2
> delete #3.2
> hide #4
> delete H
> delete pseudobonds
> delete NAG
Missing or invalid "atoms" argument: invalid atoms specifier
> show #1.2 models
> hide #1.2 models
> hide #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #4 models
> show #!3 models
> show #2 models
> show #4 models
> show #1.2 models
> hide #2 models
> hide #!3 models
> hide #4 models
> morph #2,3
Computed 51 frame morph #5
> coordset #5 1,51
> morph 100 #2,3
Missing or invalid "structures" argument: invalid structures specifier
> morph #2,3 100
Expected a keyword
> morph #2,3 frames 100
Computed 101 frame morph #6
> coordset #6 1,101
> select #6
623 atoms, 632 bonds, 80 residues, 1 model selected
> view
> view sel
> hide #1.2
> hide #1.2 cartoons
> hide #1 cartoons
> hide #5 models
> select clear
> show #2 models
> show #!3 models
> show #4 models
> rename #4 bcx16330
> hide #4 models
> show #4 models
> show #4
> delete #5
> save "L:/Graphics/BCRX001/GraphicsBackup/C5a complement/morphing/*.cxs.pdb"
Cannot save 'L:/Graphics/BCRX001/GraphicsBackup/C5a
complement/morphing/*.cxs.pdb': Unable to open file
'L:/Graphics/BCRX001/GraphicsBackup/C5a complement/morphing/*.cxs.pdb' for
writing
> save "L:/Graphics/BCRX001/GraphicsBackup/C5a
> complement/morphing/3cu7native,randomcoil,16330.cxs"
——— End of log from Mon Sep 19 13:56:36 2022 ———
opened ChimeraX session
> hide #6 models
> hide #4 models
> hide #!3 models
> hide #2 models
> hide #1.1 models
> hide #1.2 models
> show #1.1 models
> show #1.2 models
> 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
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
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #5
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #5
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> combine #1.1,1.2
No structures specified
> combine #1.1 #1.2
> rename combination native C5
Missing or invalid "models" argument: invalid models specifier
> rename #7 native C5
Expected a keyword
> rename #7 C5
> mmaker #5 to #7
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 C5, chain A (#7) with 4a5w, chain A (#5), sequence alignment score
= 3990.7
RMSD between 127 pruned atom pairs is 1.069 angstroms; (across all 919 pairs:
33.795)
> morph #5 #7
Computed 51 frame morph #8
> coordset #8 1,51
> split #5
Split 4a5w (#5) into 2 models
Chain information for 4a5w A #5.1
---
Chain | Description
A | No description available
Chain information for 4a5w B #5.2
---
Chain | Description
B | No description available
> show #!5.1 models
> hide #!5 models
> show #!5.2 models
> hide #!5.2 models
> delete pseudobonds bond
> delete pbonds bond
Expected a keyword
> delete pseudobonds
> hide #!5 models
> hide #!5.1 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!5.1 models
> hide #!8 models
> delete #8
> morph 100 #5.1 #7
Missing or invalid "structures" argument: invalid structures specifier
> morph 100 #5.1,7
Missing or invalid "structures" argument: invalid structures specifier
> morph #5.1,7
Require at least 2 structures for morph
> delete #5.2
> morph #5,7
models have different number of chains, 1 (Morph - 4a5w A #/A) and 2 (C5
#7/A,C5 #7/B)
> delete #5
[Repeated 1 time(s)]
> hide #5 models
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #8
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #8
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> delete #8/B
> hide #8.1 models
> show #8.1 models
> mmaker #8 to #7
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 C5, chain A (#7) with 4a5w, chain A (#8), sequence alignment score
= 3990.7
RMSD between 127 pruned atom pairs is 1.069 angstroms; (across all 919 pairs:
33.795)
> select ::name="NAG"
28 atoms, 28 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> mmaker #8 to #7
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 C5, chain A (#7) with 4a5w, chain A (#8), sequence alignment score
= 3990.7
RMSD between 127 pruned atom pairs is 1.069 angstroms; (across all 919 pairs:
33.795)
> morph #8,7
models have different number of chains, 1 (Morph - 4a5w #/A) and 2 (C5 #7/A,C5
#7/B)
> select add #8.2
5 pseudobonds, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8.2,1,0,0,0,0,1,0,0,0,0,1,0
[Repeated 1 time(s)]
> select #8
12111 atoms, 12386 bonds, 5 pseudobonds, 1528 residues, 2 models selected
> view matrix models
> #8,0.74415,-0.11534,-0.65797,189.17,-0.51766,0.52298,-0.67714,144.45,0.42221,0.84451,0.32947,125.52
> view matrix models
> #8,0.74415,-0.11534,-0.65797,172.76,-0.51766,0.52298,-0.67714,139.68,0.42221,0.84451,0.32947,126.58
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.49565,0.11429,-0.86097,165,-0.75377,0.54908,-0.36104,153.26,0.43148,0.82792,0.35829,127.75
> view matrix models
> #8,0.70226,0.288,-0.65107,178.22,-0.65989,0.60651,-0.44349,150.76,0.26716,0.74108,0.61598,137.54
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.70226,0.288,-0.65107,121.34,-0.65989,0.60651,-0.44349,133.68,0.26716,0.74108,0.61598,141.21
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.70226,0.288,-0.65107,116.93,-0.65989,0.60651,-0.44349,132.45,0.26716,0.74108,0.61598,141.58
> ui mousemode right rotate
> ui tool show Matchmaker
> select clear
Drag select of 785 residues
> matchmaker #2,4,6#1.2#3.1 & sel to #8 & sel
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 4a5w, chain A (#8) with 3cu7-native.pdb B, chain B (#1.2), sequence
alignment score = 1733.6
RMSD between 278 pruned atom pairs is 1.025 angstroms; (across all 369 pairs:
1.959)
> select clear
Drag select of 221 residues
Drag select of 508 residues
Drag select of 316 residues, 1 pseudobonds
> matchmaker #2,4,6#1.2#3.1 & sel to #8 & sel
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 4a5w, chain A (#8) with 3cu7-native.pdb B, chain B (#1.2), sequence
alignment score = 2071.3
RMSD between 326 pruned atom pairs is 0.952 angstroms; (across all 446 pairs:
2.671)
> select clear
> delete pseudobonds
> morph #7,8
models have different number of chains, 2 (Morph - C5 #/A,Morph - C5 #/B) and
1 (4a5w #8/A)
> split #8
Did not split 4a5w, has only one piece
Drag select of 1195 residues, 16 atoms, 12 bonds
Drag select of 800 residues
> matchmaker #2,4,6#1.2#3.1 & sel to #8 & sel
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 4a5w, chain A (#8) with 3cu7-native.pdb B, chain B (#1.2), sequence
alignment score = 2002.9
RMSD between 251 pruned atom pairs is 0.989 angstroms; (across all 459 pairs:
6.767)
> select clear
> splita #7
Unknown command: splita #7
> split #7
Split C5 (#7) into 2 models
Chain information for C5 A #7.1
---
Chain | Description
A | No description available
Chain information for C5 B #7.2
---
Chain | Description
B | No description available
> ui tool show "Show Sequence Viewer"
> hide #8.1 models
> hide #8.2 models
> hide #!8 models
> open 3cu7
3cu7 title:
Human Complement Component 5 [more info...]
Chain information for 3cu7 #9
---
Chain | Description | UniProt
A B | Complement C5 | CO5_HUMAN
Non-standard residues in 3cu7 #9
---
CD — cadmium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
3cu7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| software_defined_assembly
> open 3cu7split 9
'3cu7split' has no suffix
> split 9
Expected a structures specifier or a keyword
> split #9
Split 3cu7 (#9) into 4 models
Chain information for 3cu7 A #9.1
---
Chain | Description
A | No description available
Chain information for 3cu7 B #9.2
---
Chain | Description
B | No description available
> hide #!9.1 models
> hide #!9.2 models
> hide #9.3 models
> hide #9.4 models
> hide #!9 models
> hide #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #!7 models
> show #!9.1 models
> show #!9.2 models
> show #9.4 models
> 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
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
> view
> delete #9.4
> delete #9.3
> delete #9.2
> mmaker #9 to #8
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 4a5w, chain A (#8) with 3cu7 A, chain A (#9.1), sequence alignment
score = 6924.1
RMSD between 418 pruned atom pairs is 0.946 angstroms; (across all 1518 pairs:
28.603)
> view
> show #!8 models
> morph #9,8
Computed 51 frame morph #10
> coordset #10 1,51
Drag select of 1518 residues, 6 pseudobonds
> surface (#!10 & sel)
> select clear
> surface hidePatches #10#!9
> coordset slider #10
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
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
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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> 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
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
> coordset slider #10
> surface #10.1-2#!9-10
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> graphics silhouettes false
> movie record
> movie encode C:\Users\rkrishnan/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\rkrishnan/Desktop/movie.mp4
> movie record
> movie encode C:\Users\rkrishnan/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\rkrishnan/Desktop/movie.mp4
> surface hidePatches #10#!9
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> hide #1.2 models
> save "L:/Graphics/BCRX001/GraphicsBackup/C5a
> complement/morphing/4a5w-3cu7morph.cxs"
——— End of log from Tue Sep 20 13:54:40 2022 ———
opened ChimeraX session
> hide #!10 models
> show #1.1 models
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
No visible Surface models selected
> surface sel
> color surf red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color red surfaces
> show #1.2 models
> show #!8 models
> select 8:678-751
Expected an objects specifier or a keyword
> select #8:678-751
Nothing selected
> hide surfaces
> select #8:678-751
Nothing selected
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> select sticks
Expected an objects specifier or a keyword
> preset sticks sel
No preset name matches 'sticks sel'
> select ~sel
64136 atoms, 65570 bonds, 25 pseudobonds, 8101 residues, 19 models selected
> hide sel
> hide cartoons sel
Expected ',' or a keyword
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> show #5 models
> hide #5 models
> show #!10 models
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> surface (#!1.1 & sel)
> transparency (#!1.1 & sel) 30
> hide #!1.1 models
> hide #1.2 models
> show #!1.1 models
> hide #* target a
> show (#!1.1 & sel) target ab
> cartoon hide (#!1.1 & sel)
> select #1.1/A
7695 atoms, 7863 bonds, 971 residues, 1 model selected
> cartoon hide (#!1.1 & sel)
> show #1.2 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> cartoon (#!1.1 & sel)
> select clear
> select ~sel
64657 atoms, 66098 bonds, 25 pseudobonds, 8169 residues, 19 models selected
> surface (#1.2#!1.1 & sel)
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> color red sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color green surfaces
> select clear
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gray
> color sel orange red
> color sel red
> select clear
> show #5 models
> hide #!1 models
> show #5
> select add #5
1 model selected
> show #5
> show sel
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide #5 models
> show #!8 models
> select clear
> 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
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
> show #!9 models
> hide #!9 models
> rename #8 C5B
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #11
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #11
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> hide #!8 models
> mmaker #11 to #8
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 C5B, chain A (#8) with 4a5w, chain A (#11), sequence alignment
score = 7990.8
RMSD between 1528 pruned atom pairs is 0.000 angstroms; (across all 1528
pairs: 0.000)
> show #!8 models
> select #1
12861 atoms, 13150 bonds, 1625 residues, 3 models selected
> show sel
> 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
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
> hide #!1.1 models
> show #1.1
> show #1.1 models
> select clear
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> 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
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
> delete #5
> hide #5 target m
> rename #11 C5b6
> split #11
Split C5b6 (#11) into 2 models
Chain information for C5b6 A #11.1
---
Chain | Description
A | No description available
Chain information for C5b6 B #11.2
---
Chain | Description
B | No description available
> combine #11.2 B6
Expected a keyword
> combine #11.2
> rename #12 b6
> delete #11.2
> hide #!11.1 models
> delete #11
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> show sel surfaces
> select clear
> hide #11 models
> hide #!12 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!10 models
> mseries slider #10
> hide #!10 models
> show #!10 models
> hide #!1 models
> hide #!1.1 models
> hide #!10 models
> show #!10 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing
> for babu/morph-3cu7-4a5w.pdb"
Chain information for morph-3cu7-4a5w.pdb
---
Chain | Description
13.1/A 13.2/A 13.3/A 13.4/A 13.5/A 13.6/A 13.7/A 13.8/A 13.9/A 13.10/A 13.11/A
13.12/A 13.13/A 13.14/A 13.15/A 13.16/A 13.17/A 13.18/A 13.19/A 13.20/A
13.21/A 13.22/A 13.23/A 13.24/A 13.25/A 13.26/A 13.27/A 13.28/A 13.29/A
13.30/A 13.31/A 13.32/A 13.33/A 13.34/A 13.35/A 13.36/A 13.37/A 13.38/A
13.39/A 13.40/A 13.41/A 13.42/A 13.43/A 13.44/A 13.45/A 13.46/A 13.47/A
13.48/A 13.49/A 13.50/A 13.51/A | No description available
> hide #!13 models
> delete #13
> cd "L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing for
> babu"
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\morphing for babu
> open morph-3cu7-4a5w.pdb coordsets false
Chain information for morph-3cu7-4a5w.pdb
---
Chain | Description
14.1/A 14.2/A 14.3/A 14.4/A 14.5/A 14.6/A 14.7/A 14.8/A 14.9/A 14.10/A 14.11/A
14.12/A 14.13/A 14.14/A 14.15/A 14.16/A 14.17/A 14.18/A 14.19/A 14.20/A
14.21/A 14.22/A 14.23/A 14.24/A 14.25/A 14.26/A 14.27/A 14.28/A 14.29/A
14.30/A 14.31/A 14.32/A 14.33/A 14.34/A 14.35/A 14.36/A 14.37/A 14.38/A
14.39/A 14.40/A 14.41/A 14.42/A 14.43/A 14.44/A 14.45/A 14.46/A 14.47/A
14.48/A 14.49/A 14.50/A 14.51/A | No description available
> hide #!14 models
> mseries #14
> help help:user
> mseries slider #14
> show #!14 models
> color #14 green
> surface #14 grey
Expected a keyword
> surface #14 color grey
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> show #!1.1 models
> hide #!1.2 models
> select #1.2
5166 atoms, 5287 bonds, 654 residues, 1 model selected
> hide cartoons
> select subtract #1.2
1 model selected
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> turn y 2 90
> hide #!14 models
> show #!1.2 models
> select #1.1:678-751
521 atoms, 527 bonds, 68 residues, 1 model selected
> combine sel
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> select #15
7695 atoms, 7863 bonds, 971 residues, 1 model selected
> show sel surfaces
> delete #1
> delete #1
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
---
warnings | Ignored bad PDB record found on line 129
HELIX 1 1 GLU A 444 ASN A 446 5 Generated by MOE 3
Ignored bad PDB record found on line 130
HELIX 2 2 GLN A 532 MET A 534 5 Generated by MOE 3
Ignored bad PDB record found on line 131
HELIX 3 3 LEU A 620 PHE A 626 1 Generated by MOE 7
Ignored bad PDB record found on line 132
HELIX 4 4 ALA A 643 LEU A 648 1 Generated by MOE 6
Ignored bad PDB record found on line 133
HELIX 5 5 LYS A 681 GLU A 684 1 Generated by MOE 4
127 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (698 )
Cannot find LINK/SSBOND residue CYS (699 )
Cannot find LINK/SSBOND residue CYS (711 )
Chain information for 3cu7-native-c5a-c5b.pdb #16
---
Chain | Description
A | No description available
B | No description available
> split
Did not split 3prxsel-randomcoil.pdb, has only one piece
Did not split 6i2xsel.pdb, has only one piece
Did not split bcx16330, has only one piece
Did not split Morph - 3prxsel-randomcoil.pdb, has only one piece
Did not split C5B, has only one piece
Did not split C5 A, has only one piece
Did not split C5 B, has only one piece
Did not split 3cu7 A, has only one piece
Did not split Morph - 3cu7 A, has only one piece
Did not split b6, has only one piece
Did not split morph-3cu7-4a5w.pdb, has only one piece
[Repeated 50 time(s)]Did not split copy of 3cu7-native.pdb A, has only one
piece
Split 3cu7-native-c5a-c5b.pdb (#16) into 2 models
Chain information for 3cu7-native-c5a-c5b.pdb A #16.1
---
Chain | Description
A | No description available
Chain information for 3cu7-native-c5a-c5b.pdb B #16.2
---
Chain | Description
B | No description available
> hide #!16.2 models
> hide #!16.1 models
> show #!16.1 models
> mmaker #16 to #7.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker C5 B, chain B (#7.2) with 3cu7-native-c5a-c5b.pdb A, chain A
(#16.1), sequence alignment score = 3226.5
RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs:
0.000)
Matchmaker C5 B, chain B (#7.2) with 3cu7-native-c5a-c5b.pdb B, chain B
(#16.2), sequence alignment score = 8.1
RMSD between 5 pruned atom pairs is 1.052 angstroms; (across all 35 pairs:
12.892)
> show #!16.2 models
> hide #!16.2 models
> show #!16.2 models
> hide sel surfaces
> hide #!16.1 models
> show #!16.1 models
> hide #!16.1 models
> show #!16.1 models
> hide #!16.1 models
> show #13 models
> hide #13 models
> hide #!15 models
> close session
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
---
warnings | Ignored bad PDB record found on line 129
HELIX 1 1 GLU A 444 ASN A 446 5 Generated by MOE 3
Ignored bad PDB record found on line 130
HELIX 2 2 GLN A 532 MET A 534 5 Generated by MOE 3
Ignored bad PDB record found on line 131
HELIX 3 3 LEU A 620 PHE A 626 1 Generated by MOE 7
Ignored bad PDB record found on line 132
HELIX 4 4 ALA A 643 LEU A 648 1 Generated by MOE 6
Ignored bad PDB record found on line 133
HELIX 5 5 LYS A 681 GLU A 684 1 Generated by MOE 4
127 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (698 )
Cannot find LINK/SSBOND residue CYS (699 )
Cannot find LINK/SSBOND residue CYS (711 )
Chain information for 3cu7-native-c5a-c5b.pdb #1
---
Chain | Description
A | No description available
B | No description available
> split
Split 3cu7-native-c5a-c5b.pdb (#1) into 2 models
Chain information for 3cu7-native-c5a-c5b.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 3cu7-native-c5a-c5b.pdb B #1.2
---
Chain | Description
B | No description available
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #2
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #2
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> split #2
Split 4a5w (#2) into 2 models
Chain information for 4a5w A #2.1
---
Chain | Description
A | No description available
Chain information for 4a5w B #2.2
---
Chain | Description
B | No description available
> hide #!2.1 models
> show #!2.1 models
> combine #2.2 B6
Expected a keyword
> help help:user
> combine #2.2 close name B6
Invalid "close" argument: Expected true or false (or 1 or 0)
> combine #2.2 name B6 close true
> rename #2.1 C5B
> combine #2 #2.1
> delete #4
> close session
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
---
warnings | Ignored bad PDB record found on line 129
HELIX 1 1 GLU A 444 ASN A 446 5 Generated by MOE 3
Ignored bad PDB record found on line 130
HELIX 2 2 GLN A 532 MET A 534 5 Generated by MOE 3
Ignored bad PDB record found on line 131
HELIX 3 3 LEU A 620 PHE A 626 1 Generated by MOE 7
Ignored bad PDB record found on line 132
HELIX 4 4 ALA A 643 LEU A 648 1 Generated by MOE 6
Ignored bad PDB record found on line 133
HELIX 5 5 LYS A 681 GLU A 684 1 Generated by MOE 4
127 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (698 )
Cannot find LINK/SSBOND residue CYS (699 )
Cannot find LINK/SSBOND residue CYS (711 )
Chain information for 3cu7-native-c5a-c5b.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #2
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #2
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native-c5a-c5b.pdb, chain A (#1) with 4a5w, chain A (#2),
sequence alignment score = 7019.7
RMSD between 418 pruned atom pairs is 0.946 angstroms; (across all 1518 pairs:
28.603)
> hide #2/B
> split #2
Split 4a5w (#2) into 2 models
Chain information for 4a5w A #2.1
---
Chain | Description
A | No description available
Chain information for 4a5w B #2.2
---
Chain | Description
B | No description available
> hide #2.2
> select #2.2 cartoons
Expected a keyword
> select #2.2
6889 atoms, 7066 bonds, 4 pseudobonds, 878 residues, 3 models selected
> hide sel cartoons
> split #1
Split 3cu7-native-c5a-c5b.pdb (#1) into 2 models
Chain information for 3cu7-native-c5a-c5b.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 3cu7-native-c5a-c5b.pdb B #1.2
---
Chain | Description
B | No description available
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
Drag select of 963 residues
Drag select of 76 residues, 1 pseudobonds
> select up
19803 atoms, 20177 bonds, 5 pseudobonds, 1967 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!1.2#!2.1-2 & sel to #1.1 & sel
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 3cu7-native-c5a-c5b.pdb A, chain A (#1.1) with 4a5w A, chain A
(#2.1), sequence alignment score = 2486.3
RMSD between 381 pruned atom pairs is 0.971 angstroms; (across all 523 pairs:
3.572)
Matchmaker 3cu7-native-c5a-c5b.pdb A, chain A (#1.1) with 4a5w B, chain B
(#2.2), sequence alignment score = 33.3
RMSD between 7 pruned atom pairs is 0.974 angstroms; (across all 321 pairs:
34.681)
> morph #1.1, #2.1
Missing or invalid "structures" argument: only initial part "#1.1" of atom
specifier valid
> hide #!1.1 models
> show #!1.1 models
> select clear
> hide #!1.1 models
> show #!1.1 models
> hide #!2.2 models
> morph #1.1, 2.1
Require at least 2 structures for morph
> morph #1,2.1
Computed 51 frame morph #3
> coordset #3 1,51
> hide pseudobonds
> hide pseudobonds #3
Expected ',' or a keyword
> set bgColor black
> set bgColor transparent
> select #3/A:765
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> delete pseudobonds
> save morph-C5-c5b.pdb models #3 allCoordsets coords true
Invalid "allCoordsets" argument: Expected true or false (or 1 or 0)
> save morph-C5-c5b.pdb models #3 allCoordsets true
> help help:user
> show #!1.2 models
> hide #!1.2 models
> show #!2.2 models
> select #2.2
6889 atoms, 7066 bonds, 878 residues, 1 model selected
> show sel
> close session
> open 4a5w format mmcif fromDatabase pdb
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #1
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #1
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> split
Split 4a5w (#1) into 2 models
Chain information for 4a5w A #1.1
---
Chain | Description
A | No description available
Chain information for 4a5w B #1.2
---
Chain | Description
B | No description available
> color bychain
> close session
[Repeated 1 time(s)]
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3cu7-native-c5a-c5b.pdb
---
warnings | Ignored bad PDB record found on line 129
HELIX 1 1 GLU A 444 ASN A 446 5 Generated by MOE 3
Ignored bad PDB record found on line 130
HELIX 2 2 GLN A 532 MET A 534 5 Generated by MOE 3
Ignored bad PDB record found on line 131
HELIX 3 3 LEU A 620 PHE A 626 1 Generated by MOE 7
Ignored bad PDB record found on line 132
HELIX 4 4 ALA A 643 LEU A 648 1 Generated by MOE 6
Ignored bad PDB record found on line 133
HELIX 5 5 LYS A 681 GLU A 684 1 Generated by MOE 4
127 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (698 )
Cannot find LINK/SSBOND residue CYS (699 )
Cannot find LINK/SSBOND residue CYS (711 )
Chain information for 3cu7-native-c5a-c5b.pdb #1
---
Chain | Description
A | No description available
B | No description available
> 4a5w
Unknown command: 4a5w
> open 4a5w
4a5w title:
Crystal structure of C5b6 [more info...]
Chain information for 4a5w #2
---
Chain | Description | UniProt
A | complement C5 | CO5_HUMAN
B | complement component C6 | CO6_HUMAN
Non-standard residues in 4a5w #2
---
BMA — beta-D-mannopyranose
CA — calcium ion
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native-c5a-c5b.pdb, chain A (#1) with 4a5w, chain A (#2),
sequence alignment score = 7019.7
RMSD between 418 pruned atom pairs is 0.946 angstroms; (across all 1518 pairs:
28.603)
> color bychain
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21/nativeC5-C5b6.cxs
——— End of log from Wed Sep 21 13:58:56 2022 ———
opened ChimeraX session
> open morph-C5toC56.pdb coordsets false
No such file/path: morph-C5toC56.pdb
> cd L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep21
> open morph-C5toC56.pdb coordsets false
Chain information for morph-C5toC56.pdb
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A
3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.21/A 3.22/A 3.23/A
3.24/A 3.25/A 3.26/A 3.27/A 3.28/A 3.29/A 3.30/A 3.31/A 3.32/A 3.33/A 3.34/A
3.35/A 3.36/A 3.37/A 3.38/A 3.39/A 3.40/A 3.41/A 3.42/A 3.43/A 3.44/A 3.45/A
3.46/A 3.47/A 3.48/A 3.49/A 3.50/A 3.51/A | No description available
3.1/B 3.2/B 3.3/B 3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B 3.10/B 3.11/B 3.12/B
3.13/B 3.14/B 3.15/B 3.16/B 3.17/B 3.18/B 3.19/B 3.20/B 3.21/B 3.22/B 3.23/B
3.24/B 3.25/B 3.26/B 3.27/B 3.28/B 3.29/B 3.30/B 3.31/B 3.32/B 3.33/B 3.34/B
3.35/B 3.36/B 3.37/B 3.38/B 3.39/B 3.40/B 3.41/B 3.42/B 3.43/B 3.44/B 3.45/B
3.46/B 3.47/B 3.48/B 3.49/B 3.50/B 3.51/B | No description available
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21/sep21D.cxs
> hide #!3 models
> mseries slider #3
> hide #!1 models
> hide #!2 models
> show #!3 models
> select #3.1/B:734
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
77 atoms, 77 bonds, 12 residues, 1 model selected
> select up
113 atoms, 113 bonds, 18 residues, 1 model selected
> select up
131 atoms, 130 bonds, 21 residues, 1 model selected
> select up
284 atoms, 282 bonds, 48 residues, 1 model selected
> color sel red
> surface selllll
Expected an atoms specifier or a keyword
> surface sel
> select clear
> surface #3
> select add #3.1/B:685@CG
1 atom, 1 residue, 1 model selected
> select #3.1/B:685@O
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
48 atoms, 47 bonds, 8 residues, 2 models selected
> select up
141 atoms, 141 bonds, 25 residues, 2 models selected
> select up
153 atoms, 152 bonds, 27 residues, 2 models selected
> select up
284 atoms, 282 bonds, 48 residues, 2 models selected
> color (#!3.1 & sel) red
> select clear
> color surf #3 grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> delete pseudobonds
> surface #3 color grey
> select add #3.1/B:741@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
36 atoms, 34 bonds, 6 residues, 2 models selected
> select up
131 atoms, 130 bonds, 21 residues, 2 models selected
> select up
284 atoms, 282 bonds, 48 residues, 2 models selected
> color (#!3.1 & sel) red
> select clear
> select add #3.2/B:738@N
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
18 atoms, 17 bonds, 3 residues, 2 models selected
> select up
113 atoms, 113 bonds, 18 residues, 2 models selected
> select up
131 atoms, 130 bonds, 21 residues, 2 models selected
> select up
284 atoms, 282 bonds, 48 residues, 2 models selected
> select clear
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21/sep21E.cxs
> help help:user
> mseries #1 step 1
> select #3:679-751
14484 atoms, 14382 bonds, 2448 residues, 51 models selected
> ui tool show "Color Actions"
> color sel red target cs
> select clear
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep21/sep21F.cxs
——— End of log from Wed Sep 21 15:21:34 2022 ———
opened ChimeraX session
> help help:user
> morph #1,2 frames 25
Computed 26 frame morph #4
> coordset #4 1,26
> hide #!3 models
> hide #!4 models
> show #!1 models
> delete #3
[Repeated 1 time(s)]
> show #3 models
> hide #3 target m
> select #1/B:682
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
78 atoms, 77 bonds, 4 residues, 1 model selected
> select up
1007 atoms, 1014 bonds, 65 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> select add #4/B:733
1012 atoms, 1018 bonds, 66 residues, 2 models selected
> select up
1136 atoms, 1142 bonds, 80 residues, 2 models selected
> select up
1172 atoms, 1178 bonds, 86 residues, 2 models selected
> select up
1190 atoms, 1195 bonds, 89 residues, 2 models selected
> select up
1343 atoms, 1347 bonds, 116 residues, 2 models selected
> select up
38021 atoms, 38581 bonds, 3191 residues, 2 models selected
> select down
1343 atoms, 1347 bonds, 116 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> save L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/c5,morph-
> sep22.cxs
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/c5morph-
> sep22a.cxs
> save morph-25.pdb models #4 allCoordsets true
> save L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/*.pdb
Cannot save
'L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/*.pdb':
Unable to open file
'L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/*.pdb' for
writing
> open morph-25.pdb coordsets false
No such file/path: morph-25.pdb
> open
> L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep22\moroh-25.pdb
> coordsets false
No such file/path:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep22\moroh-25.pdb
> cd L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep22
> open
> L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep22\moroh-25.pdb
> coordsets false
No such file/path:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep22\moroh-25.pdb
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/moroh-25.pdb
> coordsets false
No such file/path:
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/moroh-25.pdb
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/morph-25.pdb
> coordsets false
Chain information for morph-25.pdb
---
Chain | Description
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A 5.21/A 5.22/A 5.23/A
5.24/A 5.25/A 5.26/A | No description available
5.1/B 5.2/B 5.3/B 5.4/B 5.5/B 5.6/B 5.7/B 5.8/B 5.9/B 5.10/B 5.11/B 5.12/B
5.13/B 5.14/B 5.15/B 5.16/B 5.17/B 5.18/B 5.19/B 5.20/B 5.21/B 5.22/B 5.23/B
5.24/B 5.25/B 5.26/B | No description available
> mseries slider #5
> hide #!4 models
> select #5:679-751
7384 atoms, 7353 bonds, 31 pseudobonds, 1248 residues, 52 models selected
> name frozen c5a sel
> color c5a red
> hide c5a
> hide c5a cartoons
> surface #5 color grey
> hide c5a surfaces
> delete pseudobonds
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/c5morph-
> sep22b-surf.cxs
> show c5a
> surface c5a
> color red
> surface c5a color red
> select clear
> hide c5a cartoons,surfaces
> hide c5a cartoons,surf,sticks
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> hide c5a cartoons,surfaces,atoms
> show c5a
> show c5a surfaces
> hide c5a cartoons,surfaces,atoms
> split #2
Split 4a5w (#2) into 2 models
Chain information for 4a5w A #2.1
---
Chain | Description
A | No description available
Chain information for 4a5w B #2.2
---
Chain | Description
B | No description available
> show #2.2 models
> surface #2.2 color yellow
> view name c5b6
> hide #!2.2 models
> show c5a surfaces
> view name c5a-b
> hide c5a cartoons,surfaces,atoms
> view name c5b
> hide #!2 models
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/c5morph-
> sep22c-surf.cxs
> view name c5b6
> show #!2.2 models
> view name c5b6
> hide #!2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> show #!2.2 models
> hide #!5 models
> hide #2.1 models
> hide #!2.2 models
> show #2.1 models
> show #!2.2 models
> surface #2.1 color grey
> select ::name="BMA"
33 atoms, 33 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="NAG"
56 atoms, 56 bonds, 4 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select ::name="FUC"
10 atoms, 10 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> view name c5b6
> view name c5
> view name c5a-b
> view c5a-b
> hide #!2 models
> show #!1 models
> split #1
Split 3cu7-native-c5a-c5b.pdb (#1) into 2 models
Chain information for 3cu7-native-c5a-c5b.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 3cu7-native-c5a-c5b.pdb B #1.2
---
Chain | Description
B | No description available
> surface #1 gray
Expected a keyword
> surface #1 color gray
> color #1.2 red
> view name p1
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> show #!2 models
> show #!1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> view name p2
> view p1
> show #!1.1 models
> show #!1.2 models
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!5 models
> show #!2 models
> show #!2.1 models
> show #!2.2 models
> hide #!2.1 models
> hide #!2.2 models
> show #!1 models
> show #!1.2 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!5 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> open
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/test.html
Opened test.html
> mseries slider #5
> show #!1.2 models
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep22/c5morph-
> sep22d-surf.cxs
——— End of log from Thu Sep 22 10:55:26 2022 ———
opened ChimeraX session
> open L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/6i2xsel.pdb
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3prxsel-
> randomcoil.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/6i2xsel.pdb
---
warnings | Ignored bad PDB record found on line 11
HELIX 1 1 LYS A 682 ALA A 688 1 Generated by MOE 7
Ignored bad PDB record found on line 12
HELIX 2 2 LYS A 696 TYR A 700 1 Generated by MOE 5
Ignored bad PDB record found on line 13
HELIX 3 3 PRO A 722 SER A 736 1 Generated by MOE 15
Ignored bad PDB record found on line 14
HELIX 4 4 GLN A 737 ARG A 739 5 Generated by MOE 3
Ignored bad PDB record found on line 15
HELIX 5 5 HIS A 744 HIS A 753 1 Generated by MOE 10
1 messages similar to the above omitted
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/3prxsel-
randomcoil.pdb
---
warnings | Ignored bad PDB record found on line 11
HELIX 1 1 LYS A 681 LYS A 689 1 Generated by MOE 9
Ignored bad PDB record found on line 12
HELIX 2 2 CYS A 698 ASP A 701 1 Generated by MOE 4
Ignored bad PDB record found on line 13
HELIX 3 3 CYS A 711 ALA A 715 1 Generated by MOE 5
Ignored bad PDB record found on line 14
HELIX 4 4 PRO A 722 LEU A 738 1 Generated by MOE 17
Ignored bad PDB record found on line 15
HELIX 5 5 ARG A 739 ASN A 741 5 Generated by MOE 3
Chain information for 6i2xsel.pdb #6
---
Chain | Description
A | No description available
Chain information for 3prxsel-randomcoil.pdb #7
---
Chain | Description
A | No description available
> hide #!1.2 models
> show #!1.2 models
> mm#6 to #1.2
Unknown command: mm#6 to #1.2
> mmaker #6 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native-c5a-c5b.pdb B, chain B (#1.2) with 6i2xsel.pdb, chain A
(#6), sequence alignment score = 262.6
RMSD between 48 pruned atom pairs is 0.810 angstroms; (across all 68 pairs:
4.871)
> mmaker #7 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native-c5a-c5b.pdb B, chain B (#1.2) with 3prxsel-
randomcoil.pdb, chain A (#7), sequence alignment score = 292
RMSD between 45 pruned atom pairs is 0.805 angstroms; (across all 68 pairs:
3.014)
> hide #!1.2 models
> hide #6 models
> hide #7 models
> hide surfaces
> show #!1.2 models
> shoe #1.2 cartoon
Unknown command: shoe #1.2 cartoon
> hide #!2 models
> show #!2 models
> show #1.2 cartoons
> show #7 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #7 cartoons
> color red #7
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red #7 cartoon
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red #7
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red #7 cartoon
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color cartoon red #7
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color red #7
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red #7 cartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #7 #ff0516 transparency 0
> show #6 models
> morph #7,6
Computed 51 frame morph #8
> coordset #8 1,51
> split #6
Split 6i2xsel.pdb (#6) into 2 models
Chain information for 6i2xsel.pdb A #6.1
---
Chain | Description
A | No description available
> show #6.2 models
> hide #6.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #8 models
> show #7 models
QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"
> open C:/Users/rkrishnan/Desktop/morph-sep20a.html
Opened morph-sep20a.html
> view
> roll y 2
> coulombic #1
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES
surface #1.1.1: minimum, -23.12, mean -1.20, maximum 33.63
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.91, mean 3.64, maximum 20.39
> hide surfaces
> rainbow
> stop
> view
> color #1.1 grey
> color #7 red
> rename #7 c5a-randomcoil
[Repeated 1 time(s)]
> show #!5 models
> hide #!5 models
> combine #6.2 bcx61330
Expected a keyword
> combine #6.2
> hide #9 models
> rename #9 BCXinh
> show #9 models
> hide #9 models
> rename #5 c5surface-mseries
> rename #8 RC-AlphaH
> cd L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep23
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\C5a-complement\morphing\sep23
> save
> L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep23/c5sep222a.cxs
> clear log
Unknown command: clear log
> help help:user
> save C:/Users/rkrishnan/sep23.cxs
——— End of log from Fri Sep 23 11:03:16 2022 ———
opened ChimeraX session
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #7 models
> show #7 models
> hide #7 models
> color #1 grey
> show #3 models
> show #!4 models
> show #!5 models
> show #9 models
> show #8 models
> show #7 models
> hide #5
> hide #5 all
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5 All
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5 cartoons
> hide #2 cartoons
> hide #4 cartoons
> hide #5 cartoons
> hide #6 cartoons
> hide #9 atoms
> hide #8 cartoons
> hide #7 cartoons
> save C:/Users/rkrishnan/Desktop/sep23a.cxs
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> color #1.1 magenta
> color #1.1 khaki
> color #1.2 red
> roll y 2
> stop
> undo
[Repeated 1 time(s)]
> color #1.2 red
> color #1.1 khaki
> name view p1
"p1": invalid atom specifier
> view name p1
> save C:/Users/rkrishnan/Desktop/sep23b.cxs
——— End of log from Fri Sep 23 13:35:49 2022 ———
opened ChimeraX session
> color #2.2 yellow
> surface #2.2
> show #2.2 surfaces
> show #!2.2 models
> hide #2.2 surfaces
> hide atoms
> show #2.2 surfaces
> hide atoms
> hide #2.2 surfaces
> show #8 cartoons
> select #8:742-758
196 atoms, 197 bonds, 17 residues, 1 model selected
> color sel cornflower blue
> hide #7 models
> hide #9 models
> select #8:679-741
484 atoms, 491 bonds, 63 residues, 1 model selected
> color sel orange
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> select clear
> hide #8
> hide #8 models
> color #2.2 yellow transparency 0
> show #!1.2 models
> show #8 models
> hide #8 models
> save C:/Users/rkrishnan/Desktop/sep23c.cxs
——— End of log from Fri Sep 23 16:01:24 2022 ———
opened ChimeraX session
> show #5
> hide atoms
> hide #!1 models
> show #5
> color #5 gray
> show #5 cartoons
> mseries slider #5
> select #5:679-758
7384 atoms, 7353 bonds, 1248 residues, 26 models selected
> select #5:679-758
7384 atoms, 7353 bonds, 1248 residues, 26 models selected
> delete sel
> hide #5 atoms
> delete pseudobonds
> show #!1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1 models
> surface #5
> hide #5 models
> show #!1 models
> save C:/Users/rkrishnan/Desktop/sep23d.cxs
——— End of log from Fri Sep 23 16:20:32 2022 ———
opened ChimeraX session
> view
> camera stereo
> view
> show #1 models
> hide #2-9 models
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> crossfade 100
> hide #1 models
> hide #2.2 models
> crossfade 300
> surface #2.2 color cornflower blue
> show #2.2 models
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> show #1 models
> hide #2-9 models
> color #1.1 #6 khaki
> color #1.2 red
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> stop
> view p1
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> view
> zoom 1.5 frames 20
> roll y 1
> stop
> view p1
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> crossfade 100
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 400
> show #2.2 models
> zoom 0.75 frames 20
[Repeated 1 time(s)]
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> crossfade 100
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 400
> show #2.2 models
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> surface #1 transparency 0
> color #1.1 gray
> color #1.2 red
> show #1 models
> hide #2-9 models
> view p1
> view
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> crossfade 100
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 600
> show #2.2 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 700
> crossfade 100
> show #2.2 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 800
> crossfade 100
> show #2.2 models
> show #1 models
> hide #2-9 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 800
> crossfade 100
> show #2.2 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 800
> crossfade 100
> show #2.2 models
> show #1 models
> hide #2-9 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 800
> crossfade 100
> show #2.2 models
> show #1 models
> hide #2-9 models
> crossfade 300
> hide #1.2 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> crossfade 300
> hide #1.2 models
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> crossfade 300
> hide #1.2 models
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> crossfade 300
> hide #1.2 models
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> color preset cartoons/nucleotides ribbons/slabs
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> hide surfaces
> rainbow
> show #1 models
> hide #2-9 models
> show #1 models
> hide #2-9 models
> stop
> view p1
> stop
> view p1
> show #1 models
> hide #2-9 models
> view
> show #1 models
> hide #2-9 models
> hide #1.1 models
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> color #6:742-758 cornflower blue
> color #6:679-741 orange
> view p2
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 12 atom styles
> view p2
> fly p2 p3
fly: Unknown position name "p3"
> help help:user
> view p1
> view p2
> view p3
Expected an objects specifier or a view name or a keyword
> camera mono
> open C:/Users/rkrishnan/Desktop/morph-sep25.html
Opened morph-sep25.html
> hide #8 models
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #9 models
> color #9 forest green
> style #9 ball
Changed 62 atom styles
> color #9 byhetero
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 62 atom styles
> color #9 byhetero
> view p3
Expected an objects specifier or a view name or a keyword
> view p2
> coordset slider #8
> show #8.1 models
> view
> show #9
> hide #8:751
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 12 atom styles
> hide #8:751
> delete H #9
Expected a keyword
> delete H
> view name p3
> select clear
> select #9/B:1701@N19
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.5383,-0.25556,0.80307,62.609,-0.69421,-0.40581,-0.59447,-87.756,0.47782,-0.8775,0.04103,19.115
> view matrix models
> #9,-0.5383,-0.25556,0.80307,70.135,-0.69421,-0.40581,-0.59447,-97.661,0.47782,-0.8775,0.04103,21.015
> view matrix models
> #9,-0.5383,-0.25556,0.80307,74.921,-0.69421,-0.40581,-0.59447,-103.18,0.47782,-0.8775,0.04103,21.675
> view name p2
> fly p3 p2
> fly p2 p3
> select clear
> clear sel
Unknown command: clear sel
> select clear
> fly p2 p3
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> view list
Named views: c5, c5a-b, c5b, c5b6, p1, p2, p3
> show #1 models
> hide #2-9 models
> view
> stop
> view p1
> show #1 models
> hide #2-9 models
> show #1 models
> hide #2-9 models
> stop
> view p1
> color #1.1 #6 khaki
> color #1.2 red
> show #1 models
> hide #2-9 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> rainbow
> hide surfaces
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> hide #1.1-7 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> hide #5 models
> open C:/Users/rkrishnan/Desktop/morph-sep25.html
Opened morph-sep25.html
> crossfade 200
> hide #1.1,2,3,4,5,6,7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> hide #1.1
> hide #5 models
> hide #4-6 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> view list
Named views: c5, c5a-b, c5b, c5b6, p1, p2, p3
> hide #2.2 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> view p2
> fly p2 p3
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> view p2
> fly p2 p3
> view p2
> fly p2 p3
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> crossfade 200
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> show #1.2
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> show #1.2
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 300
> hide #1.2 models
> crossfade 200
> show #1.2 models
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> show #1.2 models
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> crossfade 200
> show #1.2 models
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 300
> hide #1.2 models
> crossfade 200
> show #1.2 models
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> show #1.2 surfaces
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> show #1.2 surfaces
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> view p2
> show #9
> fly p2 p3
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> view p2
> show #9
> fly p2 p3
> view p2
> show #9
> fly p2 p3
> crossfade 200
> show #1.2 surfaces
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> view p2
> show #9
> fly p2 p3
> list view
Unknown command: list view
> help help:user
> List view
Unknown command: List view
> list views
Unknown command: list views
> view list
Named views: c5, c5a-b, c5b, c5b6, p1, p2, p3
> color #6:742-758 cornflower blue
> color #6:679-741 orange
> color #6:742-758 cornflower blue
> color #6:679-741 orange
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> crossfade 200
> show #1.2 surfaces
> hide #1.1
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> surface #8 transparency 80 color ghost white
> hide #1 models
> view
> zoom 1.5 frames 20
> view p3
> crossfade 300
> view p3
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> view list
Named views: c5, c5a-b, c5b, c5b6, p1, p2, p3
> save C:/Users/rkrishnan/Desktop/sep26.cxs
——— End of log from Mon Sep 26 13:32:05 2022 ———
opened ChimeraX session
> open C:/Users/rkrishnan/Desktop/morph-sep26.html
Opened morph-sep26.html
> help help:user
> 2dlabels text "C5 morph to C5b-C6 complex" color light sea green size 26
> xpos .03 ypos .92
> crossfade 300
> hide #1.2 models
> mseries #5 step 1 loop 5
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 1050
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> rainbow
> hide surfaces
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
993 hydrogen bonds
Adding 'H' to 3cu7-native-c5a-c5b.pdb A #1.1/A LEU 752
Adding 'H' to 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882
Adding 'H' to 3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
Adding 'H' to 3cu7-native-c5a-c5b.pdb B #1.2/B LEU 749
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
12830 hydrogens added
> coulombic #1
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES
surface #1.1.1: minimum, -25.41, mean -1.48, maximum 27.00
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.99, mean 3.55, maximum 19.05
> hide surfaces
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 10
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #1.1 models
> view
> crossfade 200
> show #1.2 surfaces
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> surface #8
> transparency 95
> color ghost white
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> coordset slider #8
> show #8.1 models
> crossfade 200
> hide#1.2 model; hide #1.1 model; hide #2.2 model; hide #4-7 target m; show
> #8 models; color #8:742-758 cornflower blue;color #8:679-741 orange;surf #8;
> transparency 95; color ghost white;
Unknown command: hide#1.2 model; hide #1.1 model; hide #2.2 model; hide #4-7
target m; show #8 models; color #8:742-758 cornflower blue;color #8:679-741
orange;surf #8; transparency 95; color ghost white;
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> surface #8
> transparency 95
> color ghost white
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> hide surfaces #8;
Expected ',' or a keyword
> hide surfaces #8
Expected ',' or a keyword
> hide surfaces
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> show #8.1 models
> show surfaces
> transparency 95
> help help:user
> ccordset#1-51 transparency 90
Unknown command: ccordset#1-51 transparency 90
> coordset#1-51 transparency 90
Unknown command: coordset#1-51 transparency 90
> surface coordset#1-51
Expected an atoms specifier or a keyword
> surface coordset #1-51
Expected an atoms specifier or a keyword
> coordset #8 1-51 transparency 95
Expected a keyword
> coordset #8 transparency 95
Expected a keyword
> coordset #8 surf transparency 95
Expected a keyword
> surface #8 transparency 95
[Repeated 1 time(s)]
> stop
> morph #8
Require at least 2 structures for morph
> coordset #8
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> coordset slider #8
> show #8.1 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> crossfade 300
> hide #1.2 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #1.1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> coordset slider #8
> show #8.1 models
> transparency #8-10#!1 90
> coordset slider #8
> show #8.1 models
> transparency #8-10#!1 90
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8
> show #8.1 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> hide #1.1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> coordset slider #8
> show #8.1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8
> fly p2 p3
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdsteady;
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdsteady;
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdSteady @Ca;
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdSteady surface
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdSteady surface
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 holdSteady
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency #8-10#!1-51 90
> coordset slider #8 1-51 transparency 95
Expected a keyword
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency 95
> coordset slider #8
> show #8.1 models
> movie record
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency 95
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency 95
> coordset slider #8
> show #8.1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> transparency 95
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> save C:/Users/rkrishnan/Desktop/sep26b.cxs
——— End of log from Mon Sep 26 15:27:14 2022 ———
opened ChimeraX session
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> transparency 95
> coordset slider #8
> show #8.1 models
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> coordset slider #8
[Repeated 1 time(s)]
> surface transparency 90
> delete #8.1
> delete #8.1
> close #8.1
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> save C:/Users/rkrishnan/Desktop/sep26c.cxs
——— End of log from Mon Sep 26 17:05:52 2022 ———
opened ChimeraX session
> roll y 1
> rainbow
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> crossfade 300
> hide #1.2 models
> crossfade 100
> hide #1 models
> wait 100
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> surface #8 transparency 80 color ghost white
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> select add #8.1
623 atoms, 80 residues, 1 model selected
> transparency (#!8 & sel) 90
> select clear
> coordset slider #8
> close #8.1
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> close #8.1
> crossfade 200
> hide #1.1 models
> show #8 models
> surface #8 transparency 80 color ghost white
> hide #1 models
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> save C:/Users/rkrishnan/Desktop/sep26d.cxs
——— End of log from Mon Sep 26 17:18:53 2022 ———
opened ChimeraX session
> color #10.1 white models transparency 0
> help help:user
> 2dlabels #10.1 bold true
> color #10.1 blue
> color #10.1 gold
> open C:/Users/rkrishnan/Desktop/commands-html-chimerax/morph-sep26.html
Opened morph-sep26.html
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> view
> stop
> view p1
> zoom 1.5 frames 20
> zoom 0.75 frames 20
> view p1
> color #1.1 #6 khaki
> color #1.2 red
> hide surfaces
> color #1.1 #6 khaki
> color #1.2 red
> stop
> view p1
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> color preset cartoons/nucleotides ribbons/slabs #1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> prset cartoons #1
Unknown command: prset cartoons #1
> preset cartoons #1
No preset name in category 'Cartoons/Nucleotides' matches '#1'
> preset #1 cartoons
No preset name matches '#1 cartoons'
> hide surfaces
[Repeated 1 time(s)]
> hide atoms
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> rainbow
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> stop
> view p1
[Repeated 1 time(s)]
> color #1.1 #6 khaki
> color #1.2 red
> color preset cartoons/nucleotides ribbons/slabs #1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> roll y 1
> stop
> view p1
> stop
> view p1
[Repeated 1 time(s)]
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> color #1.1 #6 khaki
> color #1.2 red
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> rainbow
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> color #1.1 #6 khaki
> color #1.2 red
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> mseries #5 step 1 loop 5
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 1050
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> mseries #5 step 1 loop 5
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 1050
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 100
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 100
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1 models
> wait 100
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> crossfade 100
> hide #1 models
> wait 100
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> crossfade
> hide #1 models
> wait 30
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> view
> crossfade
> hide #1 models
> wait 30
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> view
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> surface #2.2 color cornflower blue
> wait 850
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 300
> hide #1.2 models
> surface #2.2 color cornflower blue
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 3
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> wait 850
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #1.1 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #1.1 models
> view
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> fly p2 p3
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> fly p3 p2
> show #9
> fly p3 p2
> hide #9 models
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> view c25a
Expected an objects specifier or a view name or a keyword
> view c5a
No displayed objects specified.
> view list
Named views: c5, c5a-b, c5b, c5b6, p1, p2, p3
> select #1.1
24635 atoms, 24918 bonds, 1557 residues, 1 model selected
> select #1.2
1056 atoms, 1062 bonds, 68 residues, 1 model selected
> select view
Expected an objects specifier or a keyword
> view 31.2
Expected an objects specifier or a view name or a keyword
> view #1.2
> hide #1.1 models
> view
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> clear sel
Unknown command: clear sel
> select clear
> hide #1.1 models
> view #1.2
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> view #1.2
> hide #1.1 models
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> transparency 95
> coordset slider #8
> show #8 models
> surface #8 transparency 80 color ghost white
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> fly p2 p3
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> fly p2 p3
[Repeated 1 time(s)]
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.2 models
> hide #1.1 models
> hide #2.2 models
> hide #4-7 target m
> show #8 models
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> coordset slider #8
> fly p2 p3
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> crossfade 200
> hide #1.1 models
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.1 models
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.1 models
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> view #1.2
> hide #1.1 models
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> view #1.2
> hide #1.1 models
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.1 models
> crossfade 200
> view #1.2
> crossfade 200
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> crossfade 200
> hide #1.1 models
> wait 50
> view #1.2
> crossfade 200
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 200
> hide #1.1 models
> wait 50
> view #1.2
> crossfade 200
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> crossfade 100
> hide #1.1 models
> wait 70
> view #1.2
> crossfade 200
> show #8 models
> close #8.1
> surface #8 transparency 80 color ghost white
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> coordset slider #8
> view p2
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9 models
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10
> show #10
> help help:user
> 2dlabels text "Morphing movie" color white bold true size 26 xpos .03 ypos
> .89
> 2dlabels text "dummy text" color white bold true size 26 xpos .03 ypos .85
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> ui tool show "Color Actions"
> rainbow #!1.1-2
> view name p4
> open C:/Users/rkrishnan/Desktop/commands-html-chimerax/morph-sep27a.html
Opened morph-sep27a.html
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> view p4
> stop
> view p1
> show #1 models
> hide #2-9 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10
> view
> save C:/Users/rkrishnan/Desktop/commands-html-chimerax/sep27.cxs
——— End of log from Tue Sep 27 13:27:24 2022 ———
opened ChimeraX session
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
[Repeated 1 time(s)]
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
[Repeated 1 time(s)]
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p8; coordset #8 1,51 computeSs true loop 1;
Expected an objects specifier or a view name or a keyword
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p8; coordset #8 1,51 computeSs true loop 1;
Expected an objects specifier or a view name or a keyword
> view p8
Expected an objects specifier or a view name or a keyword
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> hide #7 models
> view name p8
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p8
> coordset #8 1,51 computeSs true loop 1
> save C:/Users/rkrishnan/Desktop/sep29b.cxs
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p8
> coordset #8 1,51 computeSs true loop 1
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p8
> coordset #8 1,51 computeSs true loop 1
> view p8
> view p2
> view p3
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 1
> view p3
> view p2
> view p3
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p4
> show #10
> view p1
> hide #10
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> zoom 0.75 frames 20
[Repeated 3 time(s)]
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing
> for babu/5i5k-chainA-X-Y-eculizumab.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing for
babu/5i5k-chainA-X-Y-eculizumab.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 88
LEU A 92 1 5
Start residue of secondary structure not found: HELIX 2 2 ASP A 302 LYS A 308
1 7
Start residue of secondary structure not found: HELIX 3 3 SER A 314 ASN A 319
1 6
Start residue of secondary structure not found: HELIX 4 4 THR A 531 VAL A 535
1 5
Start residue of secondary structure not found: HELIX 5 5 ALA A 608 GLY A 611
1 4
136 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 1 1 THR A 22 PRO A 28 0
Start residue of secondary structure not found: SHEET 2 2 1 PHE A 31 ARG A 32
0
Start residue of secondary structure not found: SHEET 3 3 1 SER A 36 TYR A 44
0
Start residue of secondary structure not found: SHEET 4 4 1 PHE A 50 SER A 58
0
Start residue of secondary structure not found: SHEET 6 6 1 GLN A 80 THR A 86
0
Start residue of secondary structure not found: SHEET 7 7 1 TYR A 101 SER A
108 0
82 messages similar to the above omitted
Chain information for 5i5k-chainA-X-Y-eculizumab.pdb
---
Chain | Description
11.1/A | No description available
11.2/A | No description available
11.3/A | No description available
> combine #11.1-end
Remapping chain ID 'A' in 5i5k-chainA-X-Y-eculizumab.pdb #11.2 to 'B'
Remapping chain ID 'A' in 5i5k-chainA-X-Y-eculizumab.pdb #11.3 to 'C'
> rename #12 5i5k-eculiFAb-C5
> mmaker #12 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3cu7-native-c5a-c5b.pdb A, chain A (#1.1) with 5i5k-eculiFAb-C5,
chain A (#12), sequence alignment score = 7156.3
RMSD between 849 pruned atom pairs is 1.304 angstroms; (across all 1549 pairs:
15.643)
> close #11
> split #12
Split 5i5k-eculiFAb-C5 (#12) into 3 models
Chain information for 5i5k-eculiFAb-C5 A #12.1
---
Chain | Description
A | No description available
Chain information for 5i5k-eculiFAb-C5 B #12.2
---
Chain | Description
B | No description available
Chain information for 5i5k-eculiFAb-C5 C #12.3
---
Chain | Description
C | No description available
> close #12.1
> surface #12.2
> combine #12.2 #12.3
[Repeated 1 time(s)]
> reanme #13 5i5k-eculi-FAb
Unknown command: reanme #13 5i5k-eculi-FAb
> rename #13 5i5k-eculi-FAb
> surface #13
> close #12
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29b.cxs
——— End of log from Thu Sep 29 10:18:10 2022 ———
opened ChimeraX session
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> zoom 0.75 frames 20
> view p1
> view p4
> show #10
> view p1
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 1
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> color #8:742-758 cornflower blue
> color #8:679-741 orange
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> select #9/B:1701@C21
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> nucleotides sel fill
> style sel ringFill thin
Changed 1 residue ring style
> select clear
> select #9/B:1701@N19
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> select clear
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> view p2
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 surfaces
> hide #7 models
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p4
> show #10
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> roll y 1
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> view p4
> show #10
> roll y 1
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p1
> view p4
> show #10
> color #1.1 #6 khaki
> color #1.2 red
> stop
> view p1
> show #1 models
> hide #2-10 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> color #1.1 #6 khaki
> view p4
> show #10
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> view p4
> show #10
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p1
> view p4
> show #10
> delete #10
> close #10
> 2dlabels text "Structural Biology of C5" size 26 xpos 0.03 ypos 0.92 bold
> true color white
> 2dlabels text "• C5 is a critical protein the terminal pathway of complement
> system" color white size 17 xpos 0.03 ypos 0.73
> 2dlabels text "• C5 is cleaved by the convertase enzyme into two parts – C5a
> and C5b" color white size 17 xpos 0.03 ypos 0.82
> 2dlabels text "• C5b initiates the formation of the membrane attack complex
> (MAC) that lyses cells" size 17 color white xpos 0.03 ypos 0.77
> 2dlabels text "• Alexion’s antibody, Soliris, targets C5 and blocks the
> breakup of C5 into C5a and C5b" size 17 color white xpos 0.03 ypos 0.73
> 2dlabels text "•Soliris has been approved as an injectable therapy for
> several complement-mediated diseases" size 17 color white xpos 0.03 ypos
> 0.69
> 2dlabels text "• BioCryst Discovery group is attempting to design an oral
> small molecule that mimics the action of Alexion’s antibody." size 17 color
> white xpos 0.03 ypos 0.65
> 2dlabels text "• Unlike all other targets in BioCryst’s pipeline, C5 is not
> an enzyme." size 15 color white xpos 0.07 ypos 0.61
> 2dlabels text "• C5 small molecule inhibitor aims to block protein protein
> interactions." size 17 color white xpos 0.03 ypos 0.57
> 2dlabels text "• Discovery group has made very good progress identifying
> potent C5 small molecule inhibitors." size 17 color white xpos 0.03 ypos
> 0.50
> 2dlabels text "• Optimizing bioavailability and other physical properities."
> size 15 color white xpos 0.07 ypos 0.47
> ui mousemode right "move label"
> 2dlabels #10.5 xpos 0.021 ypos 0.713
> 2dlabels #10.3 xpos 0.003 ypos 0.865
> 2dlabels #10.4 xpos 0.003 ypos 0.823
> 2dlabels #10.2 xpos 0.005 ypos 0.784
> 2dlabels #10.5 xpos 0.006 ypos 0.745
> 2dlabels #10.6 xpos 0.004 ypos 0.701
> 2dlabels #10.7 xpos 0.005 ypos 0.667
> 2dlabels #10.8 xpos 0.032 ypos 0.633
> 2dlabels #10.9 xpos 0.007 ypos 0.596
> 2dlabels #10.10 xpos 0.007 ypos 0.535
> 2dlabels #10.11 xpos 0.040 ypos 0.489
> 2dlabels text "• A first for BioCryst." size 15 color white xpos 0.07 ypos
> 0.54
> 2dlabels #10.10 xpos 0.003 ypos 0.509
> 2dlabels #10.12 xpos 0.057 ypos 0.562
> 2dlabels #10.10 xpos 0.002 ypos 0.530
> 2dlabels #10.11 xpos 0.029 ypos 0.491
> 2dlabels #10.12 xpos 0.037 ypos 0.559
> color #10.1 yellow
> ui tool show "Color Actions"
> color #10.2-end ivory
> color #10.2-end lemonchiffon
> color #10.2-end lemon chiffon
> color #10.2-end gold
> color #10.2-end light goldenrod yellow
> color #10.2-end light blue
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29c.cxs
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29d.cxs
——— End of log from Thu Sep 29 10:48:18 2022 ———
opened ChimeraX session
> 2dlabels #10.2-end size 14
> 2dlabels #10.2-end size 13
[Repeated 1 time(s)]
> 2dlabels #10.2-end size 13 color white
> 2dlabels #10.2-end size 13 bold true
> ui mousemode right "move label"
> 2dlabels #10.11 xpos 0.006 ypos 0.087
> 2dlabels #10.10 xpos 0.008 ypos 0.154
> 2dlabels #10.11 xpos 0.033 ypos 0.125
> 2dlabels #10.12 xpos 0.043 ypos 0.185
[Repeated 1 time(s)]
> 2dlabels #10.12 xpos 0.050 ypos 0.208
> 2dlabels #10.9 xpos 0.012 ypos 0.241
> 2dlabels #10.8 xpos 0.014 ypos 0.338
> 2dlabels #10.7 xpos 0.007 ypos 0.378
> 2dlabels #10.6 xpos 0.010 ypos 0.498
> 2dlabels #10.5 xpos 0.003 ypos 0.584
> 2dlabels #10.2 xpos 0.014 ypos 0.659
> 2dlabels #10.4 xpos 0.007 ypos 0.732
> 2dlabels #10.2 xpos 0.007 ypos 0.655
> 2dlabels #10.3 xpos 0.003 ypos 0.803
> 2dlabels #10.3 xpos -0.006 ypos 0.639
> 2dlabels #10.2 xpos 0.011 ypos 0.840
> 2dlabels #10.3 xpos 0.008 ypos 0.653
> 2dlabels #10.5 xpos 0.011 ypos 0.589
> 2dlabels #10.7 xpos 0.009 ypos 0.405
> 2dlabels #10.8 xpos 0.038 ypos 0.366
> 2dlabels #10.9 xpos 0.012 ypos 0.280
> 2dlabels #10.12 xpos 0.065 ypos 0.246
> open C:/Users/rkrishnan/Desktop/commands-html-chimerax/morph-sep29-fina.html
Opened morph-sep29-fina.html
> 2dlabels #10.1 xpos 0.079 ypos 0.916
> 2dlabels #10.5 xpos 0.010 ypos 0.577
> 2dlabels #10.4 xpos 0.010 ypos 0.757
> 2dlabels #10.3 xpos 0.014 ypos 0.682
> 2dlabels #10.5 xpos 0.013 ypos 0.599
> cd C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files
Current working directory is: C:\Users\rkrishnan\Desktop\boardmeeting-CXS-
files
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29e.cxs
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p4
> show #10
> view
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> open "L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing
> for babu/3pvm-Ac5-B-cvf.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/morphing for
babu/3pvm-Ac5-B-cvf.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 302
TYR A 312 1 11
Start residue of secondary structure not found: HELIX 2 2 LEU A 315 ASN A 319
1 5
Start residue of secondary structure not found: HELIX 3 3 THR A 531 VAL A 535
1 5
Start residue of secondary structure not found: HELIX 4 4 ALA A 608 GLN A 613
1 6
Start residue of secondary structure not found: HELIX 5 5 ARG A 622 LEU A 627
1 6
107 messages similar to the above omitted
Chain information for 3pvm-Ac5-B-cvf.pdb
---
Chain | Description
12.1/A | No description available
12.2/B | No description available
> hide #!12.1 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> hide #13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #12.2 models
> surface #12.2 color yellow
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29f.cxs
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> crossfade 30
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> crossfade 30
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> style #8-9#!6 ringFill off
Changed 81 residue ring styles
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p4
> show #10
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep29g.cxs
——— End of log from Thu Sep 29 16:56:26 2022 ———
opened ChimeraX session
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> roll y 1
> camera stereo
> roll y 1
> view
> camera a mono
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> camera a mono
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> camera mono
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 300
> hide #1.2 models
> surface #2.2 color cornflower blue
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 7
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> wait 1600
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 300
> hide #1.2 models
> surface #2.2 color cornflower blue
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 7
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> wait 1800
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> zoom 0.75
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> stop
> view p1
> show #1 models
> hide #2-10 models
> hide #13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #12.2 models
> surface #12.2 color yellow
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> crossfade 200
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> crossfade 200
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> wait 200
> crossfade 200
> view
> crossfade 200
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> crossfade 200
> view
> hide #1.2 models
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> crossfade 200
> view
> hide #1.2 models
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> crossfade 200
> view
> hide #1.2 models
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 30
> crossfade 200
> view
> hide #1.2 models
> wait 30
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 30
> crossfade 200
> view
> hide #1.2 models
> wait 30
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 100
> crossfade 200
> view
> hide #1.2 models
> wait 100
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 100
> crossfade 200
> view
> hide #1.2 models
> wait 100
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 200
> crossfade 200
> view
> hide #1.2 models
> wait 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 200
> crossfade 200
> view
> hide #1.2 models
> wait 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> crossfade 200
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1 models
> crossfade 200
> view
> wait 200
> crossfade 200
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view
> wait 300
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view
> wait 300
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view #1.2 model; wait 300; hide #1.2 model; crossfade 200; coulombic #6.1;
> show #6.1 models;turn x 140;
Expected an integer >= 1 or a keyword
> crossfade 200
> hide #1.1 models
> view #1.2 model; wait 300; hide #1.2 model; crossfade 200; coulombic #6.1;
> show #6.1 models;turn x 140;
Expected an integer >= 1 or a keyword
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view #1.2 model; wait 300; hide #1.2 model; crossfade 200; coulombic #6.1;
> show #6.1 models;turn x 140;
Expected an integer >= 1 or a keyword
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> view
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> hide #1.1
> hide #1.1 models
> crossfade 200
> hide #1.1 models
> crossfade 200
> hide #1.1 models
> view
> crossfade 200
> hide #1.1 models
> wait 250
> view
> undo
[Repeated 3 time(s)]
> crossfade 200
> hide #1.1 models
> wait 250
> view
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 300
> hide #1.2 models
> wait 250
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> wait 250
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> wait 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> wait 150
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> wait 100
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> help help:user
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 50
> cturn x 140 100;
Unknown command: cturn x 140 100;
> turn x 140 100
> turn x 140 10
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 50
> cturn x 140 100;
Unknown command: cturn x 140 100;
> turn x 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 50
> turn x 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 50
> turn x 140
> turn x 140 100
> undo
> turn x 140 1
> turn x 140 10
> turn x 140 -1
Missing or invalid "frames" argument: Must be greater than or equal to 1
> help help:user
> turn x 140
[Repeated 2 time(s)]
> turn x 140 frames 10
> turn x 140 frames 360
> turn x 140
[Repeated 4 time(s)]
> turn x 140 rock 1
> turn x 140
> turn x 140 cycle 10
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140 cycle 100
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140 cycle 1
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140
> turn x 140 cycle 136
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140 cycle 0
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140 cycle 1
Expected 'forever' or an integer >= 1 or a keyword
> turn x 140 rock 2
> turn x 140
> turn x 140 rock 10
> stop
> turn x 140 rock 1
> turn x 140 rock 2
> turn x 140 rock 3
> turn x 140 rock 3stop
Invalid "rock" argument: Expected an integer
> stop
> turn x 140 wobble 1
> turn x 140 wobble 5
> stop
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\rkrishnan\Desktop\movie1.mp4
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> turn x 140
> wait 140
> turn x 2 140
> turn x 1 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 50
> hide #8 models
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 50
> hide #8 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 170
> hide #8 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 170
> hide #8 models
> show #6.1 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 170
> hide #8 models
> crossfade 100
> show #6.1 models
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> crossfade 150
> show #1.1 models
> wait 100
> view
> turn x 1 -140
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -140
[Repeated 1 time(s)]
> turn x 1 -140;
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 -140
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 2 -140
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 2 140
> undo
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> crossfade 150
> show #1.1 models
> wait 100
> view
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> turn z 1 30
> undo
> turn z 1 -30
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn z -30
> turn y 1 180
> turn z1 180
Expected an axis vector or a keyword
> turn z 1 180
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> turn z 150
> undo
[Repeated 2 time(s)]
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 300
> hide #1.2 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 300
> fly p2 p3
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> turn z 1 150
> turn y 1 180
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> turn z 1 150
> turn y 1 180
> wait 50
> transparency 70
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> wait 30
> turn z 1 150
> wait 30
> turn y 1 180
> wait 30
> transparency 90
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> wait 30
> turn z 1 150
> wait 150
> turn y 1 180
> wait 150
> transparency #6.1 90
> transparency #6.1 10
> transparency #6.1 30
> transparency #6.1 40
> view #9 model
Expected an integer >= 1 or a keyword
> view #9
> hide atoms
[Repeated 1 time(s)]
> show #9 style sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #9 models
> show #9 models atoms
Expected ',' or a keyword
> show #9 models atoms;
Expected ',' or a keyword
> select clear
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> wait 30
> turn z 1 150
> wait 150
> turn y 1 180
> wait 150
> hide #6.1 target a
> transparency #6.1 40
> view #9
> hide #6.1 target ac
> view #9
> transparency #6.1 80
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> wait 30
> turn z 1 150
> wait 150
> turn y 1 180
> wait 150
> transparency #6.1 80
> view #9
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> crossfade 200
> hide #1.1 models
> wait 250
> crossfade 200
> view
> crossfade 200
> wait 250
> hide #1.2 models
> crossfade 200
> coulombic #6.1
Coulombic values for 6i2xsel.pdb A_A SES surface #6.1.1: minimum, -9.07, mean
2.73, maximum 14.92
> show #6.1 models
> wait 140
> turn x 1 140
> crossfade 30
> hide #1.2 models
> hide #6.1 models
> show #7 models
> surface #7
> rainbow #!7
> hide #7 atoms
> turn x 140
> transparency #7 70
> view p2
> show #9 models
> wait 200
> fly p2 p3
> hide #7 models
> coordset #8 1 computeSs false
> show #8 models
> close #8.1
> surface #8 transparency 80
> hide #1 models
> show #8:751
> color #8:751 byhetero
> style #8:751 ball
Changed 11 atom styles
> wait 100
> show #9 models
> color #9 forest green
> style #9 ball
Changed 31 atom styles
> color #9 byhetero
> show #9
> view p3
> coordset #8 1,51 computeSs true loop 3
> wait 180
> hide #8 models
> crossfade 200
> show #6.1 models
> wait 200
> crossfade 150
> show #1.1 models
> wait 100
> crossfade 100
> view
> wait 30
> turn z 1 150
> wait 150
> turn y 1 180
> wait 150
> transparency #6.1 80
> transparency #1.1 transparency 40
Missing or invalid "percent" argument: Expected a number
> transparency #1.1 70
> transparency #1.1 45
> select #6.1/A:737@CA
1 atom, 1 residue, 1 model selected
> transparency #1.1 0
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
55 atoms, 54 bonds, 7 residues, 2 models selected
> transparency #6.1 0
> select clear
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> hide #13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #12.2 models
> surface #12.2 color yellow
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> stop
> view p1
> show #1 models
> hide #2-10 models
> hide #13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #12.2 models
> surface #12.2 color yellow
> stop
> view p1
> show #1 models
> hide #2-12 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> show #13-end models
> surface #13 color magenta
> view p4
> show #10
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10 models
> view p4
> show #10
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 3cu7-native-c5a-c5b.pdb A (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A GLU 20
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
A #1.1/A LEU 752, 3cu7-native-c5a-c5b.pdb A #1.1/A LYS 882,
3cu7-native-c5a-c5b.pdb A #1.1/A TYR 1399
Chain-final residues that are actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A CYS 1676
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb A
#1.1/A LEU 673, 3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871,
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386
923 hydrogen bonds
3cu7-native-c5a-c5b.pdb A #1.1/A LEU 673 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A PRO 871 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb A #1.1/A ILE 1386 is not terminus, removing H atom
from 'C'
No usable SEQRES records for 3cu7-native-c5a-c5b.pdb B (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B LEU 679
Chain-initial residues that are not actual N termini: 3cu7-native-c5a-c5b.pdb
B #1.2/B LEU 749
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 3cu7-native-c5a-c5b.pdb B
#1.2/B ARG 751, 3cu7-native-c5a-c5b.pdb B #1.2/B SER 743
36 hydrogen bonds
3cu7-native-c5a-c5b.pdb B #1.2/B ARG 751 is not terminus, removing H atom from
'C'
3cu7-native-c5a-c5b.pdb B #1.2/B SER 743 is not terminus, removing H atom from
'C'
0 hydrogens added
> coulombic #1
Coulombic values for 3cu7-native-c5a-c5b.pdb A_A SES surface #1.1.1: minimum,
-24.18, mean -1.42, maximum 26.53
Coulombic values for 3cu7-native-c5a-c5b.pdb B_B SES surface #1.2.1: minimum,
-8.98, mean 3.58, maximum 18.82
> roll y 1
> 2dlabels #10.2-end size 14
> 2dlabels #10.2-end size 15
> ui mousemode right "move label"
> 2dlabels #10.2-end xpos 0.01
> 2dlabels #10.8 xpos 0.039 ypos 0.366
> 2dlabels #10.12 xpos 0.044 ypos 0.242
> 2dlabels #10.11 xpos 0.043 ypos 0.122
> 2dlabels #10.2-end size 17
> view p4
> show #10
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep30a.cxs
——— End of log from Fri Sep 30 11:59:06 2022 ———
opened ChimeraX session
> 2dlabels #10 .1 end size 14
Expected a keyword
> 2dlabels #10 .1-end size 14
Expected a keyword
> 2dlabels #10.2-end size 13
> open C:/Users/rkrishnan/Desktop/commands-html-chimerax/morph-sep30a.html
Opened morph-sep30a.html
> 2dlabels #10.7 text " Discovery group is designing an oral SME that mimics
> the action of Alexion’s antibody"
> 2dlabels #10.7 text "• Discovery group is designing an oral SME that mimics
> the action of Alexion’s antibody"
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep30b.cxs
> 2dlabels text "Structural Biology of C5" size 26 xpos 0.43 ypos 0.92 bold
> true color white
> save C:/Users/rkrishnan/Desktop/boardmeeting-CXS-files/sep30c.cxs
——— End of log from Fri Sep 30 13:52:24 2022 ———
opened ChimeraX session
> open C:/Users/rkrishnan/Desktop/commands-html-chimerax/morph-
> sep30-final.html
Opened morph-sep30-final.html
> view p1
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10
> show #10.1
> crossfade 300
> hide #1.2 models
> surface #2.2 color cornflower blue
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 7
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> wait 1800
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> zoom 0.75
> roll y 1
> stop
crbug/1173575, non-JS module files deprecated.
> open L:/Graphics/BCRX001/GraphicsBackup/C5a-complement/morphing/sep30/morph-
> sep30-final.html
Opened morph-sep30-final.html
> color #1.1 #6 khaki
> stop
> view p1
> show #1 models
> hide #2-13 models
> surface #1
> transparency 0
> color #1.1 gray
> color #1.2 red
> hide #10
> show #10.1
> crossfade 300
> hide #1.2 models
> surface #2.2 color cornflower blue
> crossfade
> hide #1 models
> wait
wait requires a frame count argument unless motion is in progress
> mseries #5 step 1 loop 7
> surface #5 color gray
> show #5.1 models
> hide #1 models
> hide #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 200
> wait
wait requires a frame count argument unless motion is in progress
> wait 1800
> crossfade 200
> show #2.2 models
> wait
wait requires a frame count argument unless motion is in progress
> view
OpenGL version: 3.3.0 NVIDIA 461.55
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Pro for Workstations (Build 19044)
Memory: 34,016,542,720
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (7)
comment:1 by , 3 years ago
| Component: | Unassigned → Scenes/Animation |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mseries: wait requires a frame count argument unless motion is in progress |
comment:2 by , 3 years ago
| Cc: | added |
|---|---|
| Summary: | mseries: wait requires a frame count argument unless motion is in progress → Make "wait" command with no arguments work with mseries command |
| Type: | defect → enhancement |
The ChimeraX "wait" command with no numeric frame count only works for motion commands like turn, roll, move and certain other commands. The ChimeraX documentation for wait explains this
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/wait.html
although it strangely says to look at Chimera documentation the list of commands where it says
"Wait without arguments will automatically wait for the following multi-frame commands to finish: move, turn, rock, roll, scale, clip, thickness, section, reset, fly, 2dlabels visibility changes."
The mseries command shows and hides models and is not a "motion" command and so the wait command needs a frame count to work with it, e.g "wait 100".
It would be nice if wait without a frame count worked for mseries and other commands that change the scene over several frames. I'll reclassify this bug report as an enahancement ticket requesting that improvement.
follow-up: 3 comment:3 by , 3 years ago
It says that because at some point you (I think it was you) told me the set of commands for which wait without arguments works is the same as in Chimera. But maybe you're saying I should just put a list in the ChimeraX docs directly? I would do that, if if you could tell me which ones it really works for in ChimeraX. I just wasn't confident enough to fabricate the list myself. Or I could just remove the parenthetical statement completely and not even try to make a list. If you have an opinion on which is better, let me know.
follow-up: 4 comment:4 by , 3 years ago
Here are all the ChimeraX commands that wait without argument works with: move, turn, rock, roll, zoom, bondrot, label2d, view, fly.
follow-up: 5 comment:5 by , 3 years ago
Hi Tom, regarding that list of commands, there is no "bondrot" command -- there is a "torsion" command but it does not have a frames argument... am I missing something? Thanks!
comment:6 by , 3 years ago
We dropped "bondrot" in favor of a simpler "torsion" command, but the code for bondrot is still in the module but commented out (and likely wouldn't work without changes). Tom likely grepped the source for "frames" arguments and that included the commented-out bondrot.
comment:7 by , 3 years ago
| Cc: | added |
|---|
You are right there is no bondrot command. There is code for such a command but the code that registers the bondrot command is commented out, stuff Eric wrote. And the torsion command which is in the same file does not have a frames option. So drop bondrot from my list of commands that wait with no arguments works on.
Note:
See TracTickets
for help on using tickets.
Also in the log: "crbug/1173575, non-JS module files deprecated." which is apparently a reference to Chromimum bug 1173575