Opened 2 years ago

Closed 2 years ago

#9270 closed defect (not a bug)

300 dpi

Reported by: wolf6689@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Dear ChimeraX team,
I am not able to save images at resolution 300 dpi or higher.  I would greatly appreciate your help to render high-resolution images.

Kind regards,
Martha Guevara


Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/IBD BR VARIANTS/IBDBR - PDB
> analysis CXS/XIAP T470I analysis.cxs"

Log from Tue Jun 27 00:13:41 2023 Startup Messages  
---  
warning | Custom presets folder '/Users/mguevarab/ChimeraX' does not exist  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mguevarab/Downloads/CS-
> ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif

CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif title:  
? [more info...]  
  
Chain information for CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1  
---  
Chain | Description  
A | 1  
  
Non-standard residues in CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1  
---  
15P — polyethylene glycol (N=34)  
1AQ — (3S,7R,8aR)-2-{(2S)-2-(4,4-difluorocyclohexyl)-2-[(N-methyl-L-
alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]-7-ethoxyoctahydropyrrolo[1,2-a]pyrazine-3-carboxamide  
NA — sodium ion  
X22 —
(3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide  
X23 —
(3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(aminomethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide  
ZN — zinc ion  
  

> select :15P,1AQ,NA,X22,X23

432 atoms, 465 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "/Users/mguevarab/OneDrive/University of Oxford/MSc Integrated
> Immunology/Term 3 - Trinity Term/MSc Project/Project protocol/Structure
> predictions/XIAP predictions/IBD BR VARIANTS/IBDBR - Best models
> AlphaFill/XIAP T470I.pdb" relModel #1

> SELECET :470

Unknown command: SELECET :470  

> select :470

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

> view sel

> view

> open "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/Normal XIAP PDB files/RING
> dimer 4ic2.pdb"

RING dimer 4ic2.pdb title:  
Crystal structure of the xiap ring domain [more info...]  
  
Chain information for RING dimer 4ic2.pdb #2  
---  
Chain | Description | UniProt  
A B | E3 ubiquitin-protein ligase xiap | XIAP_HUMAN 429-497  
  
Non-standard residues in RING dimer 4ic2.pdb #2  
---  
NI — nickel (II) ion  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!1 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 RING dimer 4ic2.pdb, chain B (#2) with CS-
ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif, chain A (#1), sequence alignment
score = 337.5  
RMSD between 56 pruned atom pairs is 0.752 angstroms; (across all 64 pairs:
1.822)  
  

> select #1 :470

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

> color sel red

> view sel

> show sel atoms

> ui mousemode right select

> select #2/B:470

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

> color sel blue

> show sel atoms

> select #2/B:1001@ZN

1 atom, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false ignoreHiddenModels true select true color
> #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    4 contacts
                   atom1                                atom2                 overlap  distance
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 453 SG   0.012    2.358
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 450 SG   -0.006    2.376
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 471 SG   -0.048    2.418
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 474 SG   -0.076    2.446
    

  
4 contacts  

> color sel purple

> select #2

1054 atoms, 1018 bonds, 21 pseudobonds, 174 residues, 3 models selected  

> hide sel cartoons

> hide (#!2 & sel) target a

> select #2 @Zn

4 atoms, 4 residues, 1 model selected  

> show sel atoms

> select #2/B:1001@ZN

1 atom, 1 residue, 1 model selected  

> ui mousemode right select

> select #2/B:1001@ZN

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #0000ff showDist true intraModel false relax false intraMol
> false intraRes false reveal true log true
    
    
    Finding intermodel H-bonds
    Using precise constraint criteria
    Models used:
    	1 CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif
    	2 RING dimer 4ic2.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> ui tool show Contacts

> contacts sel intraModel false intraMol false ignoreHiddenModels true select
> true color #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    4 contacts
                   atom1                                              atom2                               overlap  distance
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG   0.210    2.160
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG   0.147    2.223
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG   -0.058    2.428
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG   -0.347    2.717
    

  
4 contacts  

> color sel purple

> ui mousemode right select

> select subtract #2/B:1001@ZN

4 atoms, 4 residues, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false ignoreHiddenModels true select true color
> #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    22 contacts
                                 atom1                                                            atom2                                overlap  distance
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 470 CA    0.224    3.426
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 CB    0.201    3.449
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 CB    0.045    3.605
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ARG 456 NE    0.021    2.989
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 CB    0.004    3.646
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 470 CB    -0.074    3.724
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ASP 455 CB    -0.115    3.765
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 452 CB    -0.147    3.797
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ASP 455 CA    -0.176    3.826
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 N     -0.193    3.203
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ASP 455 N     -0.211    3.221
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ARG 456 CZ    -0.215    3.595
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 CB    -0.237    3.887
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG    -0.263    3.403
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 452 CG2   -0.265    3.915
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ARG 456 N     -0.266    3.276
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 452 CB    -0.291    3.941
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 N     -0.297    3.307
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 452 N     -0.307    3.317
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 452 CA    -0.317    3.967
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ARG 456 NH2   -0.318    3.328
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ARG 456 CB    -0.353    4.003
    

  
22 contacts  

> ui mousemode right select

> select #1/A:470

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

> ui tool show H-Bonds

> hbonds sel color #0000ff showDist true interModel false relax false intraRes
> false reveal true log true
    
    
    Finding intramodel H-bonds
    Using precise constraint criteria
    Models used:
    	1 CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ALA 459 N  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A ILE 470 O  no hydrogen  3.058  N/A
    

  
1 hydrogen bonds found  

> select #1/A:459

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel orange

> select #1/A:470

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

> ui mousemode right label

> label #1/A:470

> label #1/A:459

> ui mousemode right "move label"

> ui tool show "Model Panel"

> hide #1.4 models

> show #1.4 models

> hide #1.3.1 models

> save "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/IBD BR VARIANTS/IBDBR -
> Figures 3D map/3DMAP_T470I variant contacts.png" width 1188 height 1080
> supersample 3 transparentBackground true

> hide #!1 models

> select #2

1054 atoms, 1018 bonds, 21 pseudobonds, 174 residues, 3 models selected  

> show sel cartoons

> ui mousemode right select

> select #2/B:470

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

> show sel atoms

> ui tool show H-Bonds

> hbonds sel color #0000ff showDist true interModel false relax false intraRes
> false reveal true log true
    
    
    Finding intramodel H-bonds
    Using precise constraint criteria
    Models used:
    	2 RING dimer 4ic2.pdb
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    RING dimer 4ic2.pdb #2/B ALA 459 N  RING dimer 4ic2.pdb #2/B THR 470 O   no hydrogen  2.997  N/A
    RING dimer 4ic2.pdb #2/B THR 470 N  RING dimer 4ic2.pdb #2/B HOH 1102 O  no hydrogen  3.022  N/A
    

  
2 hydrogen bonds found  

> hide #2.3.1 models

> select #2/B:1102@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #2/B:459

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel orange

> ui mousemode right label

> label #2/B:459

> label #2/B:470

> ui mousemode right "move label"

> ui mousemode right select

> select #2/B:1001@ZN

1 atom, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false ignoreHiddenModels true select true color
> #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    4 contacts
                   atom1                                atom2                 overlap  distance
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 453 SG   0.012    2.358
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 450 SG   -0.006    2.376
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 471 SG   -0.048    2.418
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 474 SG   -0.076    2.446
    

  
4 contacts  

> select add #2

1054 atoms, 1018 bonds, 23 pseudobonds, 174 residues, 6 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "move label"

> save "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/IBD BR VARIANTS/IBDBR -
> Figures 3D map/3DMAP_T470I normal contacts.png" width 1188 height 1080
> supersample 3 transparentBackground true

> hide #!2 models

> show #!1 models

> select #2 @Zn

4 atoms, 4 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> show #!2 models

> select #2

1054 atoms, 1018 bonds, 23 pseudobonds, 174 residues, 6 models selected  

> hide sel cartoons

> select #2

1054 atoms, 1018 bonds, 23 pseudobonds, 174 residues, 6 models selected  

> hide sel atoms

> select #2 @Zn

4 atoms, 4 residues, 1 model selected  

> show sel atoms

> ui tool show Contacts

> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true color #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    16 contacts
                   atom1                                atom2                  overlap  distance
    RING dimer 4ic2.pdb #2/A ZN 1001 ZN  RING dimer 4ic2.pdb #2/A CYS 474 SG    0.112    2.258
    RING dimer 4ic2.pdb #2/B ZN 1002 ZN  RING dimer 4ic2.pdb #2/B HIS 467 ND1   0.112    2.128
    RING dimer 4ic2.pdb #2/A ZN 1002 ZN  RING dimer 4ic2.pdb #2/A CYS 465 SG    0.068    2.302
    RING dimer 4ic2.pdb #2/A ZN 1002 ZN  RING dimer 4ic2.pdb #2/A HIS 467 ND1   0.058    2.182
    RING dimer 4ic2.pdb #2/B ZN 1002 ZN  RING dimer 4ic2.pdb #2/B CYS 481 SG    0.051    2.319
    RING dimer 4ic2.pdb #2/A ZN 1001 ZN  RING dimer 4ic2.pdb #2/A CYS 471 SG    0.043    2.327
    RING dimer 4ic2.pdb #2/A ZN 1002 ZN  RING dimer 4ic2.pdb #2/A CYS 481 SG    0.033    2.337
    RING dimer 4ic2.pdb #2/B ZN 1002 ZN  RING dimer 4ic2.pdb #2/B CYS 484 SG    0.024    2.346
    RING dimer 4ic2.pdb #2/A ZN 1001 ZN  RING dimer 4ic2.pdb #2/A CYS 453 SG    0.017    2.353
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 453 SG    0.012    2.358
    RING dimer 4ic2.pdb #2/B ZN 1002 ZN  RING dimer 4ic2.pdb #2/B CYS 465 SG    0.009    2.361
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 450 SG    -0.006    2.376
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 471 SG    -0.048    2.418
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  RING dimer 4ic2.pdb #2/B CYS 474 SG    -0.076    2.446
    RING dimer 4ic2.pdb #2/A ZN 1001 ZN  RING dimer 4ic2.pdb #2/A CYS 450 SG    -0.096    2.466
    RING dimer 4ic2.pdb #2/A ZN 1002 ZN  RING dimer 4ic2.pdb #2/A CYS 484 SG    -0.112    2.482
    

  
16 contacts  

> undo

> select #2 @Zn

4 atoms, 4 residues, 1 model selected  

> select #2

1054 atoms, 1018 bonds, 35 pseudobonds, 174 residues, 6 models selected  

> hide sel atoms

> select #2 @Zn

4 atoms, 4 residues, 1 model selected  

> show sel atoms

> ui mousemode right select

> select #1/A:470

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

> show sel atoms

> select #2/B:1001@ZN

1 atom, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross intraModel false intraMol false
> ignoreHiddenModels true select true color #8f43c5 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    4 contacts
                   atom1                                              atom2                               overlap  distance
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 474 SG   0.210    2.160
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 471 SG   0.147    2.223
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 453 SG   -0.058    2.428
    RING dimer 4ic2.pdb #2/B ZN 1001 ZN  CS-ed148bdba8fe24f6c0a26ca1beb261961d35a5c2.cif #1/A CYS 450 SG   -0.347    2.717
    

  
4 contacts  

> ui mousemode right "move label"

> color sel purple

> ui mousemode right label

> label #1/A:450

> ui mousemode right select

> select #1/A:470

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

> select #1/A:470

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

> ui mousemode right "move label"

> save "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/IBD BR VARIANTS/IBDBR -
> Figures 3D map/3DMAP_T470I variant contacts 2.png" width 1188 height 1080
> supersample 3 transparentBackground true

> save "/Users/mguevarab/Library/CloudStorage/OneDrive-Personal/University of
> Oxford/MSc Integrated Immunology/Term 3 - Trinity Term/MSc Project/Project
> protocol/Structure predictions/XIAP predictions/IBD BR VARIANTS/IBDBR - PDB
> analysis CXS/XIAP T470I analysis.cxs"

——— End of log from Tue Jun 27 00:13:41 2023 ———

opened ChimeraX session  

> save "/Users/mguevarab/Desktop/XIAP 470I.jpg" width 936 height 683
> supersample 4

> save "/Users/mguevarab/Desktop/POSTER/XIAP T470I variant.png" width 2741
> height 2000 supersample 4 transparentBackground true

> save /Users/mguevarab/Desktop/image1.png supersample 3

No map chosen to save  

> save /Users/mguevarab/Desktop/POSTER/test.bmp width 6852 height 5000
> supersample 4

> save /Users/mguevarab/Desktop/POSTER/test.gif width 1480 height 1080
> supersample 4

> save /Users/mguevarab/Desktop/POSTER/test.png 300dpi

Expected a keyword  

> save /Users/mguevarab/Desktop/POSTER/test.png resolution 300dpi
> transparentBackground true

Expected a keyword  

> save /Users/mguevarab/Desktop/POSTER/test.png res 300 transparentBackground
> true

Expected a keyword  

> save /Users/mguevarab/Desktop/POSTER/test.png res 300

Expected a keyword  

> help help:user

No help found for 'help:user resolution'  
No help found for 'help:user save'  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3LL/A
      Chip: Unknown
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 5 days, 14 hours, 56 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 300 dpi

Reported by Martha Guevara

comment:2 by Tom Goddard, 2 years ago

Resolution: → not a bug
Status: assigned → closed

This mailing list discussion talks about how to save an image to get a specific dpi

​https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/7GOZM4NIZZUMJE5BCJS5B33LBOSFWMXR/

Basically you specify the width in pixels you want for the image using the width option

save myimage.png width 2000

ChimeraX does not know how many inches you want your image to be, so just multiply the number of inches wide you want for your image times 300 to get 300 dpi.

Here's the save image documentation

​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#image

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