id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9270 300 dpi wolf6689@… Tom Goddard "{{{ 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 }}} " defect closed normal Input/Output not a bug all ChimeraX