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Opened 6 years ago
Last modified 6 years ago
#2902 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | 0.9 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-06) Description When saving snapshot in ChimeraX, the output png image only shows bottom right quarter of the whole window. But typing "windowsize" shows the right image size. I wonder if this is a render problem of MacOS, because I found the windowsize can't use the complete resolution of the screen of MacBook Pro, which has a 2880*1800 screen. I only can save images with XXXX*682 size, which is very low resolution. Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/Enc_DyP_background_transparency3.cxs opened ChimeraX session > view orient cofr false > lighting simple > toolshed show "Side View" > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting full > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-2_C2_manualC2.pdb #2 --- Chain | Description A B C D E F G H I J K L | No description available > hide #!2 models > lighting simple > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > select #2 29124 atoms, 29880 bonds, 48 pseudobonds, 1 model selected > style selAtoms stick Changed 29124 atom styles > show selAtoms ribbons > hide selAtoms > select clear > lighting soft > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/Enc_DyP_background_transparency3.cxs opened ChimeraX session > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb --- warnings | Ignored bad PDB record found on line 242 ALLOWED : 3.80 % Ignored bad PDB record found on line 243 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 244 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 245 FAVORED : 95.44 % Ignored bad PDB record found on line 246 OUTLIERS : 0.76 % 16 messages similar to the above omitted Chain information for Enc_final_I1.pdb --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A 1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A 1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A 1.57/A 1.58/A 1.59/A 1.60/A | No description available > lighting simple > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure2/shell_outside_cartoon.cxs opened ChimeraX session > lighting simple > select #1.41 2025 atoms, 2067 bonds, 1 model selected > select clear > lighting simple > lighting simple > view orient cofr false > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-2_C2_manualC2.pdb #2 --- Chain | Description A B C D E F G H I J K L | No description available > style selAtoms stick Changed 150624 atom styles > select #2 29124 atoms, 29880 bonds, 48 pseudobonds, 1 model selected > show selAtoms ribbons > hide selAtoms > close #2 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-3_C2expand.pdb --- Chain | Description 2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C 2.1/D 2.2/D 2.1/E 2.2/E 2.1/F 2.2/F | No description available > style selAtoms stick Changed 150624 atom styles > show selAtoms > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure2/shell_outside_cartoon.cxs opened ChimeraX session > view orient cofr false > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-3_C2expand.pdb --- Chain | Description 2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C 2.1/D 2.2/D 2.1/E 2.2/E 2.1/F 2.2/F | No description available > lighting simple > select #1.41 2025 atoms, 2067 bonds, 1 model selected > select clear > select clear > select #2 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected > show selAtoms ribbons > style selAtoms stick Changed 29124 atom styles > hide selAtoms > hide selAtoms > show selAtoms ribbons > hide selAtoms surfaces > select clear > toolshed show "Side View" > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > select #1 121500 atoms, 124020 bonds, 1 model selected > hide selAtoms ribbons > show selAtoms surfaces > select clear > select #1 121500 atoms, 124020 bonds, 45 models selected > hide selAtoms surfaces > show selAtoms ribbons > select clear > select #2 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected > preset cartoons/nucleotides cylinders/stubs Changed 0 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; cartoon style protein modeh tube rad 2 sides 24 thick 0.6; cartoon style nucleic x round width 1.6 thick 1.6; nucleotides stubs > select clear > lighting simple > lighting simple > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-2_C2_manualC2.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-2_C2_manualC2.pdb #3 --- Chain | Description A B C D E F G H I J K L | No description available > view orient cofr false > close #3 > lighting soft > lighting full > lighting simple > lighting soft > lighting full > lighting simple > set silhouettes true > set silhouettes false > lighting shadows true > lighting simple > lighting shadows true > lighting full > lighting simple > lighting simple > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > view orient cofr false > lighting simple > lighting simple > lighting simple > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-0_manualC2.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-0_manualC2.pdb --- warnings | Ignored bad PDB record found on line 156 ALLOWED : 4.23 % Ignored bad PDB record found on line 157 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 158 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 159 FAVORED : 95.77 % Ignored bad PDB record found on line 160 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-0_manualC2.pdb #3 --- Chain | Description A B C D E F G H I J K L | No description available > close #3 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined- coot-1.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined- coot-1.pdb --- warnings | Ignored bad PDB record found on line 32 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 33 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 34 BOND : 0.007 0.050 29904 Ignored bad PDB record found on line 35 ANGLE : 0.851 10.479 40908 Ignored bad PDB record found on line 36 CHIRALITY : 0.051 0.241 4392 16 messages similar to the above omitted Chain information for RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined- coot-1.pdb #3 --- Chain | Description A B C D E F G H I J K L | No description available > select #3 29102 atoms, 29859 bonds, 48 pseudobonds, 1 model selected > style selAtoms stick Changed 29102 atom styles > show selAtoms ribbons > hide selAtoms > select clear > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure3/Enc-DyP_map.cxs opened ChimeraX session > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_1.cxs opened ChimeraX session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb --- warnings | Ignored bad PDB record found on line 242 ALLOWED : 3.80 % Ignored bad PDB record found on line 243 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 244 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 245 FAVORED : 95.44 % Ignored bad PDB record found on line 246 OUTLIERS : 0.76 % 16 messages similar to the above omitted Chain information for Enc_final_I1.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 | No description available > lighting simple > view orient cofr false > view orient cofr false > view orient cofr false > hide #!1.1 models > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb Summary of feedback from opening /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final- coot-3_C2expand.pdb --- warnings | Ignored bad PDB record found on line 150 ALLOWED : 4.56 % Ignored bad PDB record found on line 151 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 152 CIS-GENERAL : 0.0 Ignored bad PDB record found on line 153 FAVORED : 95.44 % Ignored bad PDB record found on line 154 OUTLIERS : 0.00 % 16 messages similar to the above omitted Chain information for DyP_final-coot-3_C2expand.pdb --- Chain | Description 3.1/A 3.2/A 3.1/B 3.2/B 3.1/C 3.2/C 3.1/D 3.2/D 3.1/E 3.2/E 3.1/F 3.2/F | No description available > hide #!3.2 models > show #!1.1 models > hide #!1.1 models > select #1.1 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected > show selAtoms ribbons > hide selAtoms ribbons > show selAtoms > hide selAtoms surfaces > style selAtoms sphere Changed 14562 atom styles > hide #!3 models > show #!3 models > hide #!3 models > select #1.1 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected > select #1.1 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected > show #!1.1 models > show #!3 models > hide #!3 models > select clear > hide #!2 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.2 models > show #!3.1 models > hide #!3.2 models > show #!3.2 models > hide #!1.1 models > show #!1.1 models > hide #!1.2 models > color #3.2/D #371e72 > show #!1.2 models > hide #!1.2 models > color #3.2/C #1b5689 > show #!1.2 models > hide #!1.2 models > color #3.2/F #c6495c > show #!1.2 models > hide #!1.2 models > color #3.2/B #fffd90 > show #!1.2 models > hide #!1.2 models > color #3.2/A #49e177 > show #!1.2 models > hide #!1.2 models > color #3.2/E #6d8a16 > hide #!1 models > show #!1 models > close #1 > show #!2 models > hide #!2 models > show #!2 models > show #!2 models > view orient cofr false > view cofr false > view cofr false > view orient cofr false > view orient cofr false > view cofr false > select #2 121500 atoms, 124020 bonds, 1 model selected > preset cartoons/nucleotides cylinders/stubs Changed 28608 atom styles Preset expands to these ChimeraX commands: surf hide; style (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x rect; cartoon style protein modeh tube rad 2 sides 24 thick 0.6; cartoon style nucleic x round width 1.6 thick 1.6; nucleotides stubs > select clear > select #3 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected > hide selAtoms > hide selAtoms > hide selAtoms surfaces > select #2 121500 atoms, 124020 bonds, 1 model selected > hide selAtoms surfaces > hide selAtoms > select #3 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected > toolshed show "Side View" > view orient cofr false > view cofr false > view orient cofr false > select clear > lighting shadows true > lighting full > lighting soft > lighting full > lighting soft > lighting simple > lighting simple > lighting simple > lighting simple > set silhouettes true > set silhouettes false > set silhouettes true > set silhouettes false > lighting simple > lighting flat > lighting flat > lighting simple > lighting simple > lighting simple > set silhouettes false > lighting simple > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false Unknown command: scale 1.1 > windowsize window size 864 682 > windowsize 1080 1080 > windowsize window size 1080 682 > windowsize 864 682 > windowsize 864 682 > windowsize window size 864 682 > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting shadows true > lighting shadows false > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting shadows true > lighting shadows false > lighting flat > lighting flat > lighting simple > lighting flat > lighting simple > lighting simple > set silhouettes false > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting simple > lighting shadows true > lighting shadows false > set silhouettes true > set silhouettes false > lighting simple > lighting simple > windowsize window size 864 682 > save session /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.cxs > save /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.png transparentBackground true supersample 3 > close session > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.cxs opened ChimeraX session > save /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.png transparentBackground true supersample 3 > windowsize window size 864 682 > close session OpenGL version: 4.1 ATI-3.5.5 OpenGL renderer: AMD Radeon R9 M370X OpenGL Engine OpenGL vendor: ATI Technologies Inc.
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