Opened 2 years ago

Closed 2 years ago

#9580 closed defect (fixed)

HTTP Error 500 fetching palette info

Reported by: rkrishnan@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.dev202307052255 (2023-07-05 22:55:15 UTC)
Description
tried to color coulombic surface using palette options

Log:
UCSF ChimeraX version: 1.7.dev202307052255 (2023-07-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "L:\Graphics\BCRX001\GraphicsBackup\babu company
> meeting\pnp-1ula,1ulb.cxs" format session

Log from Mon Aug 14 15:46:36 2023UCSF ChimeraX version: 1.7.dev202307052255
(2023-07-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-1ula,1ulb.cxs"

Log from Mon Aug 14 13:45:03 2023UCSF ChimeraX version: 1.7.dev202307220101
(2023-07-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "L:\Graphics\BCRX001\GraphicsBackup\babu company
> meeting\morph-1pf7-immucillin,1pbn-nat.cxs" format session

Log from Fri Aug 11 14:22:16 2023UCSF ChimeraX version: 1.7.dev202307052255
(2023-07-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "L:\Graphics\BCRX001\GraphicsBackup\babu company
> meeting\pnp-2djf,1pbn,1pf7.cxs" format session

Log from Fri Aug 11 13:00:42 2023UCSF ChimeraX version: 1.7.dev202307052255
(2023-07-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "L:\Graphics\BCRX001\GraphicsBackup\babu company
> meeting\pnp-2djf,1pbn.cxs" format session

Log from Fri Aug 11 12:13:59 2023You can double click a model's Name or ID in
the model panel to edit those fields  
UCSF ChimeraX version: 1.7.dev202307052255 (2023-07-05)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3djx

Summary of feedback from opening 3djx fetched from pdb  
---  
notes | Fetching compressed mmCIF 3djx from
http://files.rcsb.org/download/3djx.cif  
Fetching CCD C5P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/C5P/C5P.cif  
  
3djx title:  
Bovine Seminal Ribonuclease- cytidine 5' phosphate complex [more info...]  
  
Chain information for 3djx #1  
---  
Chain | Description | UniProt  
A B | Seminal ribonuclease | RNS_BOVIN 1-124  
  
Non-standard residues in 3djx #1  
---  
C5P — cytidine-5'-monophosphate  
  

> close session

> open 3djf

Summary of feedback from opening 3djf fetched from pdb  
---  
notes | Fetching compressed mmCIF 3djf from
http://files.rcsb.org/download/3djf.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
Fetching CCD BC3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/BC3/BC3.cif  
  
3djf title:  
Crystal Structure of Schistosoma mansoni Purine Nucleoside Phosphorylase in a
complex with BCX-34 [more info...]  
  
Chain information for 3djf #1  
---  
Chain | Description | UniProt  
A B C | Purine-nucleoside phosphorylase | Q9BMI9_SCHMA 1-287  
  
Non-standard residues in 3djf #1  
---  
BC3 —
2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
(peldesine,BCX-34)  
DMS — dimethyl sulfoxide  
SO4 — sulfate ion  
  

> open 1pbn

Summary of feedback from opening 1pbn fetched from pdb  
---  
note | Fetching compressed mmCIF 1pbn from
http://files.rcsb.org/download/1pbn.cif  
  
1pbn title:  
Purine nucleoside phosphorylase [more info...]  
  
Chain information for 1pbn #2  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_BOVIN 1-289  
  
1pbn mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3djf, chain B (#1) with 1pbn, chain A (#2), sequence alignment
score = 876.6  
RMSD between 243 pruned atom pairs is 0.884 angstroms; (across all 266 pairs:
1.908)  
  

> split #1

Split 3djf (#1) into 3 models  
Chain information for 3djf A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3djf B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 3djf C #1.3  
---  
Chain | Description  
C | No description available  
  

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #1.3 models

> close #1.1

> close #1.3

> view

> morph #2 #1.2

Computed 51 frame morph #3  

> coordset #3 1,51

> show #2 models

> hide #2 models

> show #2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> hide #2 models

> hide #!1 models

> morph #1.2 #2

Computed 51 frame morph #4  

> coordset #4 1,51

> hide #!3 models

> show #!1 models

> show #!1.2 models

> hide #!1 models

> hide #!1.2 models

> show #2 models

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-2djf,1pbn.cxs"

——— End of log from Fri Aug 11 12:13:59 2023 ———

opened ChimeraX session  

> hide #2 models

> open 1pf7

Summary of feedback from opening 1pf7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 1pf7 from
http://files.rcsb.org/download/1pf7.cif  
Fetching CCD IMH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/IMH/IMH.cif  
  
1pf7 title:  
Crystal structure of human PNP complexed with immucillin H [more info...]  
  
Chain information for 1pf7 #5  
---  
Chain | Description | UniProt  
E | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1pf7 #5  
---  
IMH — 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol (Forodesine;
Immucillin H)  
SO4 — sulfate ion  
  
1pf7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!3 to #5

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 1pf7, chain E (#5) with Morph - 1pbn, chain A (#3), sequence
alignment score = 1298.4  
RMSD between 241 pruned atom pairs is 0.898 angstroms; (across all 268 pairs:
1.433)  
  

> matchmaker #!4 to #5

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 1pf7, chain E (#5) with Morph - 3djf B, chain B (#4), sequence
alignment score = 824.7  
RMSD between 250 pruned atom pairs is 0.715 angstroms; (across all 268 pairs:
2.599)  
  

> matchmaker #5 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 3djf B, chain B (#1.2) with 1pf7, chain E (#5), sequence alignment
score = 803.1  
RMSD between 236 pruned atom pairs is 1.003 angstroms; (across all 268 pairs:
2.835)  
  

> matchmaker #5 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1pbn, chain A (#2) with 1pf7, chain E (#5), sequence alignment
score = 1321.8  
RMSD between 260 pruned atom pairs is 0.706 angstroms; (across all 288 pairs:
1.824)  
  

> hide #!4 models

> hide #!3 models

> show #2 models

> morph #1 #5

Computed 51 frame morph #6  

> coordset #6 1,51

> morph #1 #5

Computed 51 frame morph #7  

> coordset #7 1,51

> hide #2 models

> hide #!6 models

> morph #2 #5

Computed 51 frame morph #8  

> coordset #8 1,51

> hide #!7 models

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-2djf,1pbn,1pf7.cxs"

——— End of log from Fri Aug 11 13:00:42 2023 ———

opened ChimeraX session  

> split 1pf7

Expected a structures specifier or a keyword  

> split #5

Did not split 1pf7, has only one piece  

> split ligands #5

Expected a keyword  

> split #5 ligands

Split 1pf7 (#5) into 5 models  
Chain information for 1pf7 #5.1  
---  
Chain | Description  
E | No description available  
  

> show #5.2 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

19 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel :< 5

737 atoms, 701 bonds, 106 residues, 8 models selected  

> select sel :< 5

3075 atoms, 3022 bonds, 467 residues, 9 models selected  

> show (#8#5.2 & sel) target ab

Drag select of 1 residues, 1 bonds  

> color #8 springgreen

> color #5.2 yellow

> select add #5.2

31 atoms, 22 bonds, 2 residues, 2 models selected  

> style sel ball

Changed 31 atom styles  

> select clear

> select add #8/A:88@CD1

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> select add #8

2160 atoms, 2204 bonds, 288 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select add #8

2160 atoms, 2204 bonds, 288 residues, 1 model selected  

> color sel byhetero

> select clear

> select add #5.2/E:290@N3

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Output directory does not exist: C:\Users\RKrishnan/Desktop  

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Output directory does not exist: C:\Users\RKrishnan/Desktop  

> help help:user

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Output directory does not exist: C:\Users\RKrishnan/Desktop  

> help help:user/preferences.html#startup

> movie encode C:\Users\RKrishnan\Desktop\movie.mp4 framerate 25.0

Output directory does not exist: C:\Users\RKrishnan\Desktop  

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/morph-1pf7-immucillin,1pbn-nat.cxs"

——— End of log from Fri Aug 11 14:22:16 2023 ———

opened ChimeraX session  

> surface #8#5.2#!5

> hide #!8 models

> show #5.1 models

> show #5.1-2 surfaces

> show #2 models

> show #2#5.2#!5.1 surfaces

> hide #!5.1 models

> hide #!5 models

> show #!5 models

> hide #5.2 models

> show #5.2 models

> hide #!2 models

> show #!5.1 models

> split 3djf ligand

Expected a structures specifier or a keyword  

> split #1 ligands

Split 3djf B (#1.2) into 3 models  
Chain information for 3djf B #1.2.1  
---  
Chain | Description  
B | No description available  
  

> hide #!1.2 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #1.2.2 models

> hide #5.2 models

> hide #1.2.2 models

> show #!1.2.1 models

> show #!5.1#!1.2.1 surfaces

> hide #!5 models

> hide #!5.1 models

> show #1.2.2 models

> hide #!1.2.1 models

> show #!5.1 models

> show #!2 models

> hide #!5.1 models

> hide #1.2.2#!2 surfaces

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

18 atoms, 20 bonds, 1 residue, 1 model selected  

> select sel @< 5

348 atoms, 279 bonds, 92 residues, 9 models selected  

> select sel @< 5

9172 atoms, 1309 bonds, 1250 residues, 10 models selected  

> show (#1.2.2#!2 & sel) target ab

> select clear

> show #!5.1 models

> hide #1.2.2#!2#!5.1 surfaces

> select add #5.1/E:200

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show (#!5.1 & sel) target ab

> view sel

> select add #2/A:200@CB

12 atoms, 11 bonds, 2 residues, 3 models selected  

> select #2/A:200@CB

1 atom, 1 residue, 1 model selected  

> select #5.1/E:200@CB

1 atom, 1 residue, 1 model selected  

> select subtract #5.1/E:200@CB

1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select add #5.1/E:200@CD1

3 atoms, 1 bond, 1 residue, 2 models selected  

> select up

11 atoms, 11 bonds, 1 residue, 2 models selected  

> swapaa sel ALA

Using Dunbrack library  
Swapping 1pf7 #5.1/E PHE 200 to ALA  

> select add #2/A:200@CB

5 atoms, 3 bonds, 2 residues, 3 models selected  

> select up

16 atoms, 15 bonds, 2 residues, 4 models selected  

> swapaa sel ALA

Using Dunbrack library  
Swapping 1pbn #2/A PHE 200 to ALA  
Swapping 1pf7 #5.1/E ALA 200 to ALA  

> select clear

> hide #!2 models

> show #!2 models

> hide #!5.1 models

> show #!5.1 models

> morph #2 #5.1

Computed 51 frame morph #9  

> coordset #9 1,51

> show #9#1.2.2 surfaces

> ui tool show "Side View"

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\RKrishnan/Desktop/movie.mp4  
  

> morph #2 #5.1 frames 200

Computed 201 frame morph #10  

> coordset #10 1,201

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> morph #2 #5.1

Computed 51 frame morph #11  

> coordset #11 1,51

> help help:user

> morph #2,5 coreFraction 0.1 frames 75 wrap true

models have different number of chains, 1 (Morph - 1pbn #/A) and 0 ()  

> morph #2,5.1 coreFraction 0.1 frames 75 wrap true

Require at least 2 structures for morph  

> morph #2,5 coreFraction 0.1 frames 75 wrap true

models have different number of chains, 1 (Morph - 1pbn #/A) and 0 ()  

> open 1pf7

Summary of feedback from opening 1pf7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 1pf7 from
http://files.rcsb.org/download/1pf7.cif  
Fetching CCD IMH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/IMH/IMH.cif  
  
1pf7 title:  
Crystal structure of human PNP complexed with immucillin H [more info...]  
  
Chain information for 1pf7 #12  
---  
Chain | Description | UniProt  
E | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1pf7 #12  
---  
IMH — 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol (Forodesine;
Immucillin H)  
SO4 — sulfate ion  
  
1pf7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #5

> morph #2,12 coreFraction 0.1 frames 75 wrap true

Computed 151 frame morph #5  

> coordset #5 1,151

> close session

> open 1pf7 format mmcif fromDatabase pdb

1pf7 title:  
Crystal structure of human PNP complexed with immucillin H [more info...]  
  
Chain information for 1pf7 #1  
---  
Chain | Description | UniProt  
E | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1pf7 #1  
---  
IMH — 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol (Forodesine;
Immucillin H)  
SO4 — sulfate ion  
  
1pf7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1pbn

Summary of feedback from opening 1pbn fetched from pdb  
---  
note | Fetching compressed mmCIF 1pbn from
http://files.rcsb.org/download/1pbn.cif  
  
1pbn title:  
Purine nucleoside phosphorylase [more info...]  
  
Chain information for 1pbn #2  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_BOVIN 1-289  
  
1pbn mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 6djf

Summary of feedback from opening 6djf fetched from pdb  
---  
notes | Fetching compressed mmCIF 6djf from
http://files.rcsb.org/download/6djf.cif  
Fetching CCD GNV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/GNV/GNV.cif  
  
6djf title:  
Crystal structure of Tdp1 catalytic domain in complex with compound XZ502
[more info...]  
  
Chain information for 6djf #3  
---  
Chain | Description | UniProt  
A B | Tyrosyl-DNA phosphodiesterase 1 | TYDP1_HUMAN 148-608  
  
Non-standard residues in 6djf #3  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GNV — 4-hydroxyquinoline-3,8-dicarboxylic acid  
  
6djf mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #2#!3 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 1pf7, chain E (#1) with 1pbn, chain A (#2), sequence alignment
score = 1321.8  
RMSD between 260 pruned atom pairs is 0.706 angstroms; (across all 288 pairs:
1.824)  
  
Matchmaker 1pf7, chain E (#1) with 6djf, chain B (#3), sequence alignment
score = 27.1  
RMSD between 5 pruned atom pairs is 1.201 angstroms; (across all 202 pairs:
22.064)  
  

> matchmaker #!3 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 1pf7, chain E (#1) with 6djf, chain B (#3), sequence alignment
score = 27.1  
RMSD between 5 pruned atom pairs is 1.201 angstroms; (across all 202 pairs:
22.064)  
  
Drag select of 75 atoms, 298 residues, 68 bonds  

> select up

2419 atoms, 2487 bonds, 305 residues, 1 model selected  

> select up

3004 atoms, 3094 bonds, 378 residues, 1 model selected  

> select up

3529 atoms, 3640 bonds, 445 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #3

> open 3djf

Summary of feedback from opening 3djf fetched from pdb  
---  
notes | Fetching compressed mmCIF 3djf from
http://files.rcsb.org/download/3djf.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
Fetching CCD BC3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/BC3/BC3.cif  
  
3djf title:  
Crystal Structure of Schistosoma mansoni Purine Nucleoside Phosphorylase in a
complex with BCX-34 [more info...]  
  
Chain information for 3djf #3  
---  
Chain | Description | UniProt  
A B C | Purine-nucleoside phosphorylase | Q9BMI9_SCHMA 1-287  
  
Non-standard residues in 3djf #3  
---  
BC3 —
2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
(peldesine,BCX-34)  
DMS — dimethyl sulfoxide  
SO4 — sulfate ion  
  

> ui tool show Matchmaker

> matchmaker #!3 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 1pf7, chain E (#1) with 3djf, chain C (#3), sequence alignment
score = 882.8  
RMSD between 242 pruned atom pairs is 1.025 angstroms; (across all 282 pairs:
1.655)  
  

> select ligand

110 atoms, 110 bonds, 12 residues, 2 models selected  

> morph #2,1 coreFraction 0.1 frames 75 wrap true

Computed 151 frame morph #4  

> coordset #4 1,151

> morph #2,1 coreFraction 0.1 frames 200 wrap true

Computed 401 frame morph #5  

> coordset #5 1,401

> split #3 ligands

Split 3djf (#3) into 9 models  
Chain information for 3djf #3.1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #3.9 models

> hide #3.8 models

> hide #3.7 models

> hide #3.6 models

> hide #3.5 models

> hide #3.4 models

> show #3.4 models

> hide #3.3 models

> hide #3.2 models

> hide #!3.1 models

> show #4-5#3.4 surfaces

> hide #!3 models

> hide #!4 models

> show #!3.1 models

> hide #!3.1 models

> show #!4 models

> hide #!5 models

> close #5

> close #4

> show #2 models

> select add #3.4/C:290@C02

35 atoms, 33 bonds, 5 residues, 2 models selected  

> select up

36 atoms, 34 bonds, 5 residues, 2 models selected  

> select up

52 atoms, 53 bonds, 5 residues, 2 models selected  

> select sel @< 5

472 atoms, 375 bonds, 140 residues, 5 models selected  

> show (#2#3.4 & sel) target ab

> select sel :< 5

2396 atoms, 2307 bonds, 386 residues, 6 models selected  

> select sel :< 5

5317 atoms, 5205 bonds, 832 residues, 7 models selected  

> show (#2#3.4 & sel) target ab

> select clear

> select add #2/A:200@CG

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 1 model selected  

> swapaa sel #ala

Using Dunbrack library  
1pbn #2/A PHE 200: phi -88.2, psi 158.2 trans  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\swap_res\cmd.py", line 40, in swap_aa  
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\swap_res\swap_res.py", line 42, in swap_aa  
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\swap_res\swap_res.py", line 236, in get_rotamers  
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\dunbrack_rotamer_lib\lib.py", line 67, in rotamer_params  
return self._get_params(res_name, file_name, cache, archive)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\rotamers\rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
^^^^^^^^^^^^^^^^^  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\rotamers\rot_lib.py", line 186, in _get_params  
"%s library does not support residue type '%s'" % (self.display_name,
base_name))  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> swapaa sel ala

Using Dunbrack library  
Swapping 1pbn #2/A PHE 200 to ALA  

> show #1 models

> hide #2 models

> delete #1 ligand

Expected a keyword  

> delete #1:ligandddd

> select add #1/E:290@C2'

5 atoms, 3 bonds, 2 residues, 2 models selected  

> select up

24 atoms, 25 bonds, 2 residues, 2 models selected  

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> select add #3.4/C:290@N01

6 atoms, 4 bonds, 2 residues, 2 models selected  

> select up

23 atoms, 24 bonds, 2 residues, 2 models selected  

> select sel :< 5

457 atoms, 427 bonds, 74 residues, 5 models selected  

> show (#1#3.4 & sel) target ab

> select clear

> select add #1/E:200@CB

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 1 model selected  

> swapaa sel ala

Using Dunbrack library  
Swapping 1pf7 #1/E PHE 200 to ALA  

> select clear

> morph #2,1 coreFraction 0.1 frames 75 wrap true

Computed 151 frame morph #4  

> coordset #4 1,151

> hide #3.4 models

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> show #!3.1 models

> hide #!3.1 models

> show #3.4 models

> hide #3.2 models

> show #4#3.4 surfaces

> ui tool show "Color Actions"

> color cornflower blue target s

> color goldenrod target a

> color byhetero target a

> select add #3.4/C:290@C04

1 atom, 1 residue, 1 model selected  

> select up

18 atoms, 20 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 18 atom styles  

> select clear

[Repeated 1 time(s)]

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\RKrishnan/Desktop/movie.mp4  
  

> morph #2,1 coreFraction 0.1 frames 75

Computed 76 frame morph #5  

> coordset #5 1,76

> hide #!4 models

> show #5#3.4 surfaces

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> close #4

> morph #2,1 coreFraction 0.1 frames 100

Computed 101 frame morph #4  

> coordset #4 1,101

> hide #4 models

> hide #!5 models

> show #4 models

> show #4#3.4 surfaces

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\RKrishnan/Desktop/movie.mp4  
  

> show #2 models

> hide #!4 models

> hide #3.4 models

> show #2 surfaces

> show #3.4 models

> close #1-2#3.2-9#3-5#3.1

> open 1m73

Summary of feedback from opening 1m73 fetched from pdb  
---  
note | Fetching compressed mmCIF 1m73 from
http://files.rcsb.org/download/1m73.cif  
  
1m73 title:  
Crystal structure of human PNP At 2.3A resolution [more info...]  
  
Chain information for 1m73 #1  
---  
Chain | Description | UniProt  
E | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 2-289  
  
Non-standard residues in 1m73 #1  
---  
SO4 — sulfate ion  
  
1m73 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1pf7

1pf7 title:  
Crystal structure of human PNP complexed with immucillin H [more info...]  
  
Chain information for 1pf7 #2  
---  
Chain | Description | UniProt  
E | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1pf7 #2  
---  
IMH — 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol (Forodesine;
Immucillin H)  
SO4 — sulfate ion  
  
1pf7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1m73, chain E (#1) with 1pf7, chain E (#2), sequence alignment
score = 1452.3  
RMSD between 270 pruned atom pairs is 0.402 angstroms; (across all 288 pairs:
1.172)  
  

> morph #2,1 coreFraction 0.1 frames 75

Computed 76 frame morph #3  

> coordset #3 1,76

> show #3 surfaces

> morph #2,1 coreFraction 0.1 frames 100

Computed 101 frame morph #4  

> coordset #4 1,101

> hide #!3 models

> select ligand

49 atoms, 45 bonds, 7 residues, 2 models selected  

> hide #* target a

> show #4 target ab

> show #2 models

> hide #2 models

> hide #4 atoms

> split #2

Did not split 1pf7, has only one piece  

> split #2 ligands

Split 1pf7 (#2) into 5 models  
Chain information for 1pf7 #2.1  
---  
Chain | Description  
E | No description available  
  

> show #2.2 models

> select add #2.2

34 atoms, 33 bonds, 4 residues, 2 models selected  

> show (#2.2 & sel) target ab

> select clear

> hide #!2 models

> show #!2 models

> select clear

> show #4#2.2 surfaces

> color #4#2.2#!2 cornflower blue

> select add #2.2/E:290@C2'

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 21 bonds, 1 residue, 1 model selected  

> 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  
  

> open 1ula

Summary of feedback from opening 1ula fetched from pdb  
---  
note | Fetching compressed mmCIF 1ula from
http://files.rcsb.org/download/1ula.cif  
  
1ula title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ula #5  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ula #5  
---  
SO4 — sulfate ion  
  
1ula mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1ulb

Summary of feedback from opening 1ulb fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ulb from
http://files.rcsb.org/download/1ulb.cif  
Fetching CCD GUN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/GUN/GUN.cif  
  
1ulb title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ulb #6  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ulb #6  
---  
GUN — guanine  
SO4 — sulfate ion  
  
1ulb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #5 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 1m73, chain E (#1) with 1ula, chain A (#5), sequence alignment
score = 1396.5  
RMSD between 278 pruned atom pairs is 0.551 angstroms; (across all 288 pairs:
0.895)  
  

> matchmaker #6 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 1m73, chain E (#1) with 1ulb, chain A (#6), sequence alignment
score = 1383.9  
RMSD between 259 pruned atom pairs is 0.518 angstroms; (across all 288 pairs:
1.560)  
  

> hide #!4 models

> hide #5 models

> hide #2.2 models

> hide #!2 models

> morph #5,6 coreFraction 0.1 frames 100

Computed 101 frame morph #7  

> coordset #7 1,101

> show #7 surfaces

> color sel indian red target s

> color sel cornflower blue target s

> color #7 magenta

> color #7 #5500ffff

> color #7 #4c91ffff

> split #6 ligands

Split 1ulb (#6) into 4 models  
Chain information for 1ulb #6.1  
---  
Chain | Description  
A | No description available  
  

> show #6.2 models

> show #7#6.2#!6 target ab

> select add #7/A:200@CE2

20 atoms, 21 bonds, 2 residues, 2 models selected  

> select up

30 atoms, 32 bonds, 2 residues, 3 models selected  

> select up

63 atoms, 66 bonds, 7 residues, 3 models selected  

> swapaa sel ala

Command cancelled by user  

> select clear

> select #7/A:200@CE2

1 atom, 1 residue, 1 model selected  

> swapaa sel ala

Using Dunbrack library  
Swapping Morph - 1ula #7/A PHE 200 to ALA  

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\RKrishnan/Desktop/movie.mp4  
  
Compositor returned null texture  

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Movie saved to C:\Users\RKrishnan/Desktop/movie.mp4  
  

> select add #6.2/A:290@C5

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel surfaces

> color (#!6.2 & sel) byhetero

> select clear

> ui tool show "Color Actions"

> color goldenrod target s

> undo

> select clear

> select add #6.2/A:290@C5

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 12 bonds, 1 residue, 2 models selected  

> close #1-2#3-4

> merge #6.2

Unknown command: merge #6.2  

> combine #6.2

> hide sel surfaces

> help help:user

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-1ula,1ulb.cxs"

——— End of log from Mon Aug 14 13:45:03 2023 ———

opened ChimeraX session  

> save morph.pdb models #7 allCoordsets true

> open morph.pdb coordsets false

Chain information for morph.pdb  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.21/A 2.22/A 2.23/A
2.24/A 2.25/A 2.26/A 2.27/A 2.28/A 2.29/A 2.30/A 2.31/A 2.32/A 2.33/A 2.34/A
2.35/A 2.36/A 2.37/A 2.38/A 2.39/A 2.40/A 2.41/A 2.42/A 2.43/A 2.44/A 2.45/A
2.46/A 2.47/A 2.48/A 2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A
2.57/A 2.58/A 2.59/A 2.60/A 2.61/A 2.62/A 2.63/A 2.64/A 2.65/A 2.66/A 2.67/A
2.68/A 2.69/A 2.70/A 2.71/A 2.72/A 2.73/A 2.74/A 2.75/A 2.76/A 2.77/A 2.78/A
2.79/A 2.80/A 2.81/A 2.82/A 2.83/A 2.84/A 2.85/A 2.86/A 2.87/A 2.88/A 2.89/A
2.90/A 2.91/A 2.92/A 2.93/A 2.94/A 2.95/A 2.96/A 2.97/A 2.98/A 2.99/A 2.100/A
2.101/A | No description available  
  

> select #2.1/A:1-289

2252 atoms, 2303 bonds, 289 residues, 1 model selected  

> select #2.2/A:1-289

2252 atoms, 2303 bonds, 289 residues, 1 model selected  

> select #2.101/A:1-289

2252 atoms, 2303 bonds, 289 residues, 1 model selected  

> hide #!7.1 models

> hide #!7 models

> hide #!6.2 models

> hide #!6 models

> hide #!2 models

> show #!2 models

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for morph.pdb_A SES surface #2.101.1: minimum, -18.22, mean
-1.31, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

[Repeated 1 time(s)]

> hide #2.1 models

> hide #2.2 models

> hide #2.4 models

> hide #2.3 models

> show #2.2 models

> show #2.1 models

> show #2.3 models

> show #2.4 models

> hide #1 models

> show #1 models

> help help:user

[Repeated 2 time(s)]

> hide #1#2.1-100#!2.101 cartoons

> mseries #2.1-101 pauseFrames 5 step 3

> show #1#2.100 cartoons

> mseries #2.1-101

[Repeated 1 time(s)]

> mseries #2.1-60

> mseries #2.1-101

> show #1#2.43 surfaces

> mlp #1#!2.101

Map values for surface "morph.pdb_A SES surface": minimum -28.4, mean -5.688,
maximum 21.46  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #2

227452 atoms, 232603 bonds, 29189 residues, 102 models selected  

> coulombic sel & #!2.101

Coulombic values for morph.pdb_A SES surface #2.101.1: minimum, -18.22, mean
-1.31, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mseries #2.1-101

> show #2.1 models

> hide #!2 models

> show #!2 models

> show #2.100 models

> coulombic sel & #2.100#!2.101

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for morph.pdb_A SES surface #2.100.1: minimum, -17.58, mean
-1.31, maximum 14.72  
Coulombic values for morph.pdb_A SES surface #2.101.1: minimum, -18.22, mean
-1.31, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> show #2.99 models

> coulombic sel & #2.99#!2.100-101

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for morph.pdb_A SES surface #2.99.1: minimum, -19.07, mean
-1.31, maximum 14.42  
Coulombic values for morph.pdb_A SES surface #2.100.1: minimum, -17.58, mean
-1.31, maximum 14.72  
Coulombic values for morph.pdb_A SES surface #2.101.1: minimum, -18.22, mean
-1.31, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> show #2.98 models

> show #2.97 models

> show #2.96 models

> show #2.95 models

> show #2.94 models

> show #2.93 models

> show #2.92 models

> show #2.91 models

> show #2.90 models

> show #2.89 models

> show #2.88 models

> show #2.87 models

> show #2.86 models

> show #2.85 models

> show #2.84 models

> show #2.83 models

> show #2.82 models

> show #2.81 models

> show #2.80 models

> show #2.79 models

> show #2.78 models

> show #2.77 models

> show #2.76 models

> show #2.75 models

> show #2.74 models

> show #2.73 models

> show #2.72 models

> show #2.71 models

> show #2.70 models

> show #2.69 models

> show #2.68 models

> show #2.67 models

> show #2.59 models

> show #2.60 models

> show #2.61 models

> show #2.62 models

> show #2.63 models

> show #2.64 models

> show #2.65 models

> show #2.66 models

> coulombic sel & #2.59-98#!2.99-101

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 39 time(s)]Coulombic values for morph.pdb_A SES surface #2.59.1:
minimum, -14.91, mean -1.20, maximum 12.45  
Coulombic values for morph.pdb_A SES surface #2.60.1: minimum, -19.13, mean
-1.19, maximum 12.38  
Coulombic values for morph.pdb_A SES surface #2.61.1: minimum, -21.24, mean
-1.22, maximum 13.18  
Coulombic values for morph.pdb_A SES surface #2.62.1: minimum, -21.05, mean
-1.21, maximum 13.22  
Coulombic values for morph.pdb_A SES surface #2.63.1: minimum, -21.49, mean
-1.21, maximum 13.17  
Coulombic values for morph.pdb_A SES surface #2.64.1: minimum, -19.88, mean
-1.23, maximum 13.13  
Coulombic values for morph.pdb_A SES surface #2.65.1: minimum, -19.56, mean
-1.22, maximum 13.09  
Coulombic values for morph.pdb_A SES surface #2.66.1: minimum, -13.64, mean
-1.22, maximum 13.04  
Coulombic values for morph.pdb_A SES surface #2.67.1: minimum, -13.50, mean
-1.22, maximum 13.03  
Coulombic values for morph.pdb_A SES surface #2.68.1: minimum, -13.86, mean
-1.23, maximum 13.01  
Coulombic values for morph.pdb_A SES surface #2.69.1: minimum, -13.75, mean
-1.22, maximum 13.20  
Coulombic values for morph.pdb_A SES surface #2.70.1: minimum, -13.86, mean
-1.20, maximum 13.20  
Coulombic values for morph.pdb_A SES surface #2.71.1: minimum, -13.39, mean
-1.20, maximum 13.18  
Coulombic values for morph.pdb_A SES surface #2.72.1: minimum, -13.42, mean
-1.21, maximum 13.22  
Coulombic values for morph.pdb_A SES surface #2.73.1: minimum, -13.47, mean
-1.22, maximum 13.26  
Coulombic values for morph.pdb_A SES surface #2.74.1: minimum, -13.52, mean
-1.21, maximum 13.30  
Coulombic values for morph.pdb_A SES surface #2.75.1: minimum, -17.60, mean
-1.21, maximum 13.41  
Coulombic values for morph.pdb_A SES surface #2.76.1: minimum, -13.63, mean
-1.22, maximum 13.36  
Coulombic values for morph.pdb_A SES surface #2.77.1: minimum, -16.89, mean
-1.22, maximum 14.49  
Coulombic values for morph.pdb_A SES surface #2.78.1: minimum, -15.64, mean
-1.22, maximum 14.14  
Coulombic values for morph.pdb_A SES surface #2.79.1: minimum, -13.60, mean
-1.22, maximum 13.69  
Coulombic values for morph.pdb_A SES surface #2.80.1: minimum, -14.44, mean
-1.21, maximum 13.77  
Coulombic values for morph.pdb_A SES surface #2.81.1: minimum, -21.84, mean
-1.22, maximum 13.82  
Coulombic values for morph.pdb_A SES surface #2.82.1: minimum, -14.41, mean
-1.24, maximum 13.97  
Coulombic values for morph.pdb_A SES surface #2.83.1: minimum, -15.71, mean
-1.24, maximum 14.14  
Coulombic values for morph.pdb_A SES surface #2.84.1: minimum, -23.43, mean
-1.24, maximum 14.25  
Coulombic values for morph.pdb_A SES surface #2.85.1: minimum, -23.93, mean
-1.24, maximum 14.14  
Coulombic values for morph.pdb_A SES surface #2.86.1: minimum, -25.92, mean
-1.22, maximum 13.94  
Coulombic values for morph.pdb_A SES surface #2.87.1: minimum, -32.41, mean
-1.23, maximum 13.98  
Coulombic values for morph.pdb_A SES surface #2.88.1: minimum, -18.58, mean
-1.23, maximum 14.25  
Coulombic values for morph.pdb_A SES surface #2.89.1: minimum, -23.96, mean
-1.25, maximum 14.21  
Coulombic values for morph.pdb_A SES surface #2.90.1: minimum, -23.18, mean
-1.24, maximum 14.24  
Coulombic values for morph.pdb_A SES surface #2.91.1: minimum, -23.97, mean
-1.27, maximum 14.32  
Coulombic values for morph.pdb_A SES surface #2.92.1: minimum, -22.76, mean
-1.27, maximum 14.49  
Coulombic values for morph.pdb_A SES surface #2.93.1: minimum, -17.12, mean
-1.26, maximum 14.29  
Coulombic values for morph.pdb_A SES surface #2.94.1: minimum, -15.16, mean
-1.28, maximum 14.35  
Coulombic values for morph.pdb_A SES surface #2.95.1: minimum, -25.38, mean
-1.30, maximum 14.69  
Coulombic values for morph.pdb_A SES surface #2.96.1: minimum, -22.02, mean
-1.29, maximum 14.31  
Coulombic values for morph.pdb_A SES surface #2.97.1: minimum, -24.07, mean
-1.29, maximum 14.46  
Coulombic values for morph.pdb_A SES surface #2.98.1: minimum, -20.61, mean
-1.31, maximum 14.30  
Coulombic values for morph.pdb_A SES surface #2.99.1: minimum, -19.07, mean
-1.31, maximum 14.42  
Coulombic values for morph.pdb_A SES surface #2.100.1: minimum, -17.58, mean
-1.31, maximum 14.72  
Coulombic values for morph.pdb_A SES surface #2.101.1: minimum, -18.22, mean
-1.31, maximum 14.74  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mseries #2.1-101

> hide #!2 models

> show #!2 models

> show sel & #2.31 surfaces

> close #2

> morph #5,6 frames 30

models have different number of chains, 1 (Morph - 1ula #/A) and 0 ()  

> open 1ulb

Summary of feedback from opening 1ulb fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ulb from
http://files.rcsb.org/download/1ulb.cif  
Fetching CCD GUN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/GUN/GUN.cif  
  
1ulb title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ulb #2  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ulb #2  
---  
GUN — guanine  
SO4 — sulfate ion  
  
1ulb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> morph #5,2 frames 30

Computed 31 frame morph #3  

> coordset #3 1,31

> ui tool show Matchmaker

> matchmaker #3#6.1,3-4#!7#!6.2 to #5

No matrix compatible with both reference structure and all match structures  

> matchmaker #2 to #5

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 1ula, chain A (#5) with 1ulb, chain A (#2), sequence alignment
score = 1364  
RMSD between 264 pruned atom pairs is 0.481 angstroms; (across all 289 pairs:
1.411)  
  

> close session

> open 1ulb format mmcif fromDatabase pdb

1ulb title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ulb #1  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ulb #1  
---  
GUN — guanine  
SO4 — sulfate ion  
  
1ulb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1ula

Summary of feedback from opening 1ula fetched from pdb  
---  
note | Fetching compressed mmCIF 1ula from
http://files.rcsb.org/download/1ula.cif  
  
1ula title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ula #2  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ula #2  
---  
SO4 — sulfate ion  
  
1ula mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close session

> open 1ula format mmcif fromDatabase pdb

1ula title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ula #1  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ula #1  
---  
SO4 — sulfate ion  
  
1ula mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1ulb

1ulb title:  
Application of crystallographic and modeling methods In the design of purine
nucleoside phosphorylase inhibitors [more info...]  
  
Chain information for 1ulb #2  
---  
Chain | Description | UniProt  
A | PURINE NUCLEOSIDE PHOSPHORYLASE | PNPH_HUMAN 1-289  
  
Non-standard residues in 1ulb #2  
---  
GUN — guanine  
SO4 — sulfate ion  
  
1ulb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> reanme #1 native pnp

Unknown command: reanme #1 native pnp  

> reanme #1 native-pnp

Unknown command: reanme #1 native-pnp  

> reanme #1 native-pnp

Unknown command: reanme #1 native-pnp  

> renumber #1 native-pnp

Expected a keyword  

> rename #1 native-pnp

> rename #2 guanine-pnp

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker native-pnp, chain A (#1) with guanine-pnp, chain A (#2), sequence
alignment score = 1364  
RMSD between 264 pruned atom pairs is 0.481 angstroms; (across all 289 pairs:
1.411)  
  

> select ::name="SO4"

20 atoms, 16 bonds, 4 residues, 2 models selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

11 atoms, 12 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> ui tool show "Side View"

> morph #,2 frames 50

Missing or invalid "structures" argument: invalid structures specifier  

> morph #1,2 frames 50

Computed 51 frame morph #3  

> coordset #3 1,51

> copy #1

Unknown command: copy #1  

> combine #2 complex

Expected a keyword  

> combine #2

> split #4 ligands

Split copy of guanine-pnp (#4) into 2 models  
Chain information for copy of guanine-pnp #4.1  
---  
Chain | Description  
A | No description available  
  

> hide #4.1 models

> save morph.pdb models #3 allCoordsets true

> open "L:/Graphics/BCRX001/GraphicsBackup/babu company meeting/morph.pdb"
> format swissdock

Summary of feedback from opening L:/Graphics/BCRX001/GraphicsBackup/babu
company meeting/morph.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
  
  
Ignored bad PDB record found on line 4  
  
  
Ignored bad PDB record found on line 6  
  
  
Ignored bad PDB record found on line 8  
  
  
Ignored bad PDB record found on line 10  
  
  
140 messages similar to the above omitted  
  
Chain information for morph.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 5.27/A 5.28/A 5.29/A 5.30/A 5.31/A 5.32/A 5.33/A 5.34/A
5.35/A 5.36/A 5.37/A 5.38/A 5.39/A 5.40/A 5.41/A 5.42/A 5.43/A 5.44/A 5.45/A
5.46/A 5.47/A 5.48/A 5.49/A 5.50/A 5.51/A | No description available  
  

> hide #!4 models

> hide #4.2 models

> select add #5

115158 atoms, 117810 bonds, 14739 residues, 52 models selected  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
morph.pdb #5.1/A SER 289 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 50 time(s)]Coulombic values for morph.pdb_A SES surface #5.1.1:
minimum, -15.27, mean -1.31, maximum 14.19  
Coulombic values for morph.pdb_A SES surface #5.2.1: minimum, -15.09, mean
-1.17, maximum 14.38  
Coulombic values for morph.pdb_A SES surface #5.3.1: minimum, -15.70, mean
-1.18, maximum 13.92  
Coulombic values for morph.pdb_A SES surface #5.4.1: minimum, -15.95, mean
-1.17, maximum 13.81  
Coulombic values for morph.pdb_A SES surface #5.5.1: minimum, -15.89, mean
-1.18, maximum 13.56  
Coulombic values for morph.pdb_A SES surface #5.6.1: minimum, -16.13, mean
-1.20, maximum 13.74  
Coulombic values for morph.pdb_A SES surface #5.7.1: minimum, -16.60, mean
-1.20, maximum 13.34  
Coulombic values for morph.pdb_A SES surface #5.8.1: minimum, -16.39, mean
-1.19, maximum 12.92  
Coulombic values for morph.pdb_A SES surface #5.9.1: minimum, -16.03, mean
-1.20, maximum 12.56  
Coulombic values for morph.pdb_A SES surface #5.10.1: minimum, -16.37, mean
-1.22, maximum 12.50  
Coulombic values for morph.pdb_A SES surface #5.11.1: minimum, -16.71, mean
-1.22, maximum 12.28  
Coulombic values for morph.pdb_A SES surface #5.12.1: minimum, -17.03, mean
-1.20, maximum 12.39  
Coulombic values for morph.pdb_A SES surface #5.13.1: minimum, -17.14, mean
-1.20, maximum 12.69  
Coulombic values for morph.pdb_A SES surface #5.14.1: minimum, -16.94, mean
-1.20, maximum 12.42  
Coulombic values for morph.pdb_A SES surface #5.15.1: minimum, -18.38, mean
-1.21, maximum 12.27  
Coulombic values for morph.pdb_A SES surface #5.16.1: minimum, -17.27, mean
-1.23, maximum 12.09  
Coulombic values for morph.pdb_A SES surface #5.17.1: minimum, -16.29, mean
-1.20, maximum 23.85  
Coulombic values for morph.pdb_A SES surface #5.18.1: minimum, -16.33, mean
-1.21, maximum 12.26  
Coulombic values for morph.pdb_A SES surface #5.19.1: minimum, -16.47, mean
-1.22, maximum 12.56  
Coulombic values for morph.pdb_A SES surface #5.20.1: minimum, -16.38, mean
-1.19, maximum 12.19  
Coulombic values for morph.pdb_A SES surface #5.21.1: minimum, -17.41, mean
-1.18, maximum 11.79  
Coulombic values for morph.pdb_A SES surface #5.22.1: minimum, -15.77, mean
-1.17, maximum 13.46  
Coulombic values for morph.pdb_A SES surface #5.23.1: minimum, -18.53, mean
-1.17, maximum 16.92  
Coulombic values for morph.pdb_A SES surface #5.24.1: minimum, -24.40, mean
-1.17, maximum 13.94  
Coulombic values for morph.pdb_A SES surface #5.25.1: minimum, -18.16, mean
-1.20, maximum 12.07  
Coulombic values for morph.pdb_A SES surface #5.26.1: minimum, -21.88, mean
-1.18, maximum 12.19  
Coulombic values for morph.pdb_A SES surface #5.27.1: minimum, -25.29, mean
-1.16, maximum 12.38  
Coulombic values for morph.pdb_A SES surface #5.28.1: minimum, -27.91, mean
-1.19, maximum 12.46  
Coulombic values for morph.pdb_A SES surface #5.29.1: minimum, -15.76, mean
-1.22, maximum 12.57  
Coulombic values for morph.pdb_A SES surface #5.30.1: minimum, -23.77, mean
-1.20, maximum 12.93  
Coulombic values for morph.pdb_A SES surface #5.31.1: minimum, -15.87, mean
-1.23, maximum 13.16  
Coulombic values for morph.pdb_A SES surface #5.32.1: minimum, -18.85, mean
-1.21, maximum 15.04  
Coulombic values for morph.pdb_A SES surface #5.33.1: minimum, -13.58, mean
-1.23, maximum 13.79  
Coulombic values for morph.pdb_A SES surface #5.34.1: minimum, -25.86, mean
-1.24, maximum 13.30  
Coulombic values for morph.pdb_A SES surface #5.35.1: minimum, -13.60, mean
-1.26, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.36.1: minimum, -24.42, mean
-1.25, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.37.1: minimum, -14.02, mean
-1.24, maximum 13.75  
Coulombic values for morph.pdb_A SES surface #5.38.1: minimum, -14.12, mean
-1.23, maximum 13.30  
Coulombic values for morph.pdb_A SES surface #5.39.1: minimum, -13.84, mean
-1.24, maximum 13.51  
Coulombic values for morph.pdb_A SES surface #5.40.1: minimum, -13.51, mean
-1.24, maximum 14.60  
Coulombic values for morph.pdb_A SES surface #5.41.1: minimum, -17.24, mean
-1.25, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.42.1: minimum, -13.46, mean
-1.26, maximum 13.98  
Coulombic values for morph.pdb_A SES surface #5.43.1: minimum, -13.31, mean
-1.25, maximum 14.24  
Coulombic values for morph.pdb_A SES surface #5.44.1: minimum, -15.28, mean
-1.26, maximum 14.44  
Coulombic values for morph.pdb_A SES surface #5.45.1: minimum, -21.15, mean
-1.28, maximum 14.20  
Coulombic values for morph.pdb_A SES surface #5.46.1: minimum, -14.08, mean
-1.28, maximum 14.26  
Coulombic values for morph.pdb_A SES surface #5.47.1: minimum, -14.82, mean
-1.27, maximum 14.60  
Coulombic values for morph.pdb_A SES surface #5.48.1: minimum, -19.29, mean
-1.31, maximum 14.54  
Coulombic values for morph.pdb_A SES surface #5.49.1: minimum, -17.10, mean
-1.32, maximum 14.37  
Coulombic values for morph.pdb_A SES surface #5.50.1: minimum, -19.07, mean
-1.31, maximum 14.70  
Coulombic values for morph.pdb_A SES surface #5.51.1: minimum, -19.84, mean
-1.33, maximum 14.60  
To also show corresponding color key, enter the above coulombic command and
add key true  

> ui tool show "Side View"

> hide sel surfaces

> show #4.2 models

> show sel surfaces

> hide #!5 models

> hide #3 models

> mseries slider #5.1-50

> show #!5 models

> mseries slider #5.1-49

> mseries slider #5.-49

Missing or invalid "models" argument: only initial part "#5" of atom specifier
valid  

> mseries slider #5.1-49

> mseries slider #5.1-49 pauseFrames 3

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> hide #4.2 models

> hide #!5 models

> show #!5 models

> select subtract #5

51 models selected  

> select add #5

115158 atoms, 117810 bonds, 14739 residues, 52 models selected  

> hide #!5.51 models

> show #4.2 models

> select add #4.2

115169 atoms, 117822 bonds, 14740 residues, 104 models selected  

> close #5

> show #1 models

> show #2 models

> select add #2/A:199

17 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #2/A:198

24 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #1/A:199

30 atoms, 29 bonds, 4 residues, 3 models selected  

> select clear

> select add #2/A:290@C5

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 12 bonds, 1 residue, 1 model selected  

> select sel :< 5

374 atoms, 358 bonds, 52 residues, 5 models selected  

> show (#1-2#4.2 & sel) target ab

> select clear

> select add #1/A:200@CG

1 atom, 1 residue, 1 model selected  

> select add #2/A:200@CD1

2 atoms, 2 residues, 2 models selected  

> select add #1/A:200@CD1

3 atoms, 2 residues, 2 models selected  

> select add #1/A:200@CD2

4 atoms, 2 residues, 2 models selected  

> select up

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

> swapaa sel ala

Using Dunbrack library  
Swapping native-pnp #1/A PHE 200 to ALA  
Swapping guanine-pnp #2/A PHE 200 to ALA  

> select clear

> close #3

> morph #1,2 frames 50

Computed 51 frame morph #3  

> coordset #3 1,51

> show #3#4.2 surfaces

> save morph.pdb models #3 allCoordsets true

[Repeated 1 time(s)]

> open "L:/Graphics/BCRX001/GraphicsBackup/babu company meeting/morph.pdb"

Chain information for morph.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 5.27/A 5.28/A 5.29/A 5.30/A 5.31/A 5.32/A 5.33/A 5.34/A
5.35/A 5.36/A 5.37/A 5.38/A 5.39/A 5.40/A 5.41/A 5.42/A 5.43/A 5.44/A 5.45/A
5.46/A 5.47/A 5.48/A 5.49/A 5.50/A 5.51/A | No description available  
  

> hide #!3 models

> coulombic #4.2#5.1-51

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
morph.pdb #5.1/A SER 289 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 51 time(s)]Assigning partial charges to residue GUN (net charge +0)
with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX1/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\RKRISH~1\AppData\Local\Temp\tmpjqc5obj8\ante.in.mol2 -fi mol2 -o
C:\Users\RKRISH~1\AppData\Local\Temp\tmpjqc5obj8\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(GUN) ``  
(GUN) `Welcome to antechamber 20.0: molecular input file processor.`  
(GUN) ``  
(GUN) `Info: Finished reading file
(C:\Users\RKRISH~1\AppData\Local\Temp\tmpjqc5obj8\ante.in.mol2); atoms read
(16), bonds read (17).`  
(GUN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GUN) `Running: "C:/Program Files/ChimeraX1/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GUN) `bash.exe: warning: could not find /tmp, please create!`  
(GUN) ``  
(GUN) ``  
(GUN) `Running: "C:/Program Files/ChimeraX1/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GUN) `bash.exe: warning: could not find /tmp, please create!`  
(GUN) `Info: Total number of electrons: 78; net charge: 0`  
(GUN) ``  
(GUN) `Running: "C:/Program Files/ChimeraX1/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(GUN) `bash.exe: warning: could not find /tmp, please create!`  
(GUN) ``  
(GUN) `Running: "C:/Program Files/ChimeraX1/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX1/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(GUN) `bash.exe: warning: could not find /tmp, please create!`  
(GUN) ``  
(GUN) `Running: "C:/Program Files/ChimeraX1/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GUN) `bash.exe: warning: could not find /tmp, please create!`  
(GUN) ``  
Charges for residue GUN determined  
Coulombic values for copy of guanine-pnp GUN_A SES surface #4.2.1: minimum,
-4.20, mean 0.08, maximum 2.00  
Coulombic values for morph.pdb_A SES surface #5.1.1: minimum, -15.26, mean
-1.32, maximum 14.19  
Coulombic values for morph.pdb_A SES surface #5.2.1: minimum, -15.08, mean
-1.18, maximum 14.38  
Coulombic values for morph.pdb_A SES surface #5.3.1: minimum, -15.69, mean
-1.18, maximum 13.92  
Coulombic values for morph.pdb_A SES surface #5.4.1: minimum, -15.94, mean
-1.18, maximum 13.81  
Coulombic values for morph.pdb_A SES surface #5.5.1: minimum, -15.87, mean
-1.19, maximum 13.56  
Coulombic values for morph.pdb_A SES surface #5.6.1: minimum, -16.11, mean
-1.21, maximum 13.74  
Coulombic values for morph.pdb_A SES surface #5.7.1: minimum, -16.58, mean
-1.21, maximum 13.34  
Coulombic values for morph.pdb_A SES surface #5.8.1: minimum, -16.37, mean
-1.20, maximum 12.92  
Coulombic values for morph.pdb_A SES surface #5.9.1: minimum, -16.01, mean
-1.21, maximum 12.56  
Coulombic values for morph.pdb_A SES surface #5.10.1: minimum, -16.35, mean
-1.23, maximum 12.50  
Coulombic values for morph.pdb_A SES surface #5.11.1: minimum, -16.70, mean
-1.22, maximum 12.28  
Coulombic values for morph.pdb_A SES surface #5.12.1: minimum, -17.01, mean
-1.20, maximum 12.39  
Coulombic values for morph.pdb_A SES surface #5.13.1: minimum, -17.12, mean
-1.20, maximum 12.69  
Coulombic values for morph.pdb_A SES surface #5.14.1: minimum, -16.92, mean
-1.20, maximum 12.42  
Coulombic values for morph.pdb_A SES surface #5.15.1: minimum, -18.38, mean
-1.21, maximum 12.27  
Coulombic values for morph.pdb_A SES surface #5.16.1: minimum, -17.27, mean
-1.23, maximum 12.09  
Coulombic values for morph.pdb_A SES surface #5.17.1: minimum, -16.27, mean
-1.21, maximum 23.85  
Coulombic values for morph.pdb_A SES surface #5.18.1: minimum, -16.31, mean
-1.22, maximum 12.26  
Coulombic values for morph.pdb_A SES surface #5.19.1: minimum, -16.45, mean
-1.22, maximum 12.56  
Coulombic values for morph.pdb_A SES surface #5.20.1: minimum, -16.36, mean
-1.20, maximum 12.19  
Coulombic values for morph.pdb_A SES surface #5.21.1: minimum, -17.41, mean
-1.18, maximum 11.79  
Coulombic values for morph.pdb_A SES surface #5.22.1: minimum, -15.75, mean
-1.17, maximum 13.46  
Coulombic values for morph.pdb_A SES surface #5.23.1: minimum, -18.53, mean
-1.17, maximum 16.92  
Coulombic values for morph.pdb_A SES surface #5.24.1: minimum, -24.40, mean
-1.16, maximum 13.94  
Coulombic values for morph.pdb_A SES surface #5.25.1: minimum, -18.14, mean
-1.19, maximum 12.07  
Coulombic values for morph.pdb_A SES surface #5.26.1: minimum, -21.86, mean
-1.18, maximum 12.19  
Coulombic values for morph.pdb_A SES surface #5.27.1: minimum, -25.28, mean
-1.15, maximum 12.38  
Coulombic values for morph.pdb_A SES surface #5.28.1: minimum, -27.89, mean
-1.18, maximum 12.46  
Coulombic values for morph.pdb_A SES surface #5.29.1: minimum, -15.74, mean
-1.21, maximum 12.57  
Coulombic values for morph.pdb_A SES surface #5.30.1: minimum, -23.76, mean
-1.20, maximum 12.94  
Coulombic values for morph.pdb_A SES surface #5.31.1: minimum, -15.87, mean
-1.22, maximum 13.16  
Coulombic values for morph.pdb_A SES surface #5.32.1: minimum, -14.50, mean
-1.20, maximum 15.04  
Coulombic values for morph.pdb_A SES surface #5.33.1: minimum, -13.58, mean
-1.22, maximum 13.79  
Coulombic values for morph.pdb_A SES surface #5.34.1: minimum, -25.86, mean
-1.23, maximum 13.30  
Coulombic values for morph.pdb_A SES surface #5.35.1: minimum, -13.60, mean
-1.26, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.36.1: minimum, -24.42, mean
-1.24, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.37.1: minimum, -14.02, mean
-1.23, maximum 13.75  
Coulombic values for morph.pdb_A SES surface #5.38.1: minimum, -14.12, mean
-1.23, maximum 13.30  
Coulombic values for morph.pdb_A SES surface #5.39.1: minimum, -13.84, mean
-1.23, maximum 13.51  
Coulombic values for morph.pdb_A SES surface #5.40.1: minimum, -13.51, mean
-1.24, maximum 14.60  
Coulombic values for morph.pdb_A SES surface #5.41.1: minimum, -17.24, mean
-1.24, maximum 13.83  
Coulombic values for morph.pdb_A SES surface #5.42.1: minimum, -13.46, mean
-1.25, maximum 13.98  
Coulombic values for morph.pdb_A SES surface #5.43.1: minimum, -13.31, mean
-1.24, maximum 14.24  
Coulombic values for morph.pdb_A SES surface #5.44.1: minimum, -15.28, mean
-1.25, maximum 14.44  
Coulombic values for morph.pdb_A SES surface #5.45.1: minimum, -21.15, mean
-1.27, maximum 14.21  
Coulombic values for morph.pdb_A SES surface #5.46.1: minimum, -14.08, mean
-1.28, maximum 14.26  
Coulombic values for morph.pdb_A SES surface #5.47.1: minimum, -14.82, mean
-1.27, maximum 14.60  
Coulombic values for morph.pdb_A SES surface #5.48.1: minimum, -19.29, mean
-1.30, maximum 14.54  
Coulombic values for morph.pdb_A SES surface #5.49.1: minimum, -17.10, mean
-1.31, maximum 14.37  
Coulombic values for morph.pdb_A SES surface #5.50.1: minimum, -19.07, mean
-1.31, maximum 14.70  
Coulombic values for morph.pdb_A SES surface #5.51.1: minimum, -19.84, mean
-1.32, maximum 14.60  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mseries slider #5.1-51

> hide #!5 models

> mseries slider #5.1-51

> show #!5 models

> select add #4.2

11 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select clear

> style #!4.2#!5.25 sphere

Changed 2263 atom styles  

> style #!4.2#!5.25 ball

Changed 2263 atom styles  

> movie record

> movie encode C:\Users\RKrishnan/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Output directory does not exist: C:\Users\RKrishnan/Desktop  

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-1ula,1ulb.cxs"

> select add #4.2

11 atoms, 12 bonds, 1 residue, 1 model selected  

> color (#!4.2 & sel) magenta

> save "L:/Graphics/BCRX001/GraphicsBackup/babu company
> meeting/pnp-1ula,1ulb.cxs"

——— End of log from Mon Aug 14 15:46:36 2023 ———

opened ChimeraX session  

> hide #!5 models

> show #1 models

Fetching url http://www.colourlovers.com/api/palettes?keywords=red-orange-
blue&format=json&numResults=100 failed:  
HTTP Error 500: Internal Server Error  




OpenGL version: 3.3.0 - Build 31.0.101.4255
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 21BR00FFUS
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 34,009,374,720
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i7-1270P
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307052255
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.30.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.40.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.4
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 years ago

Cc: pett added
Component: Unassigned → Command Line
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → HTTP Error 500 fetching palette info

Hi,

I think this was a temporary server error contacting the colourlovers.com web site for information about the palette. If you try again it likely will work. It's working for me now.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

A coloring command with palette named red-orange-blue tried to look up that palette name at the ColourLovers web site and failed because that web site no longer works with http. It requires https. I changed the ChimeraX code to use https.

There is no palette named red-orange-blue built into ChimeraX and so it tries to fetch a palette by that name from the web site. No palette by that name exists. If your intent was to just use those 3 colors you can specify them in a ChimeraX command such as

rainbow palette red:orange:blue

This makes a palette with those 3 named colors.

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