The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Surface->Mesh not working through GUI
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/rorygordon/Desktop/P450Cam-Comparison.pdb
P450Cam-Comparison.pdb title:
Crystal structure of the electron transfer complex of cytochrome P450CAM with
putidaredoxin [more info...]
Chain information for P450Cam-Comparison.pdb
---
Chain | Description
1.1/A | camphor 5-monooxygenase
1.1/B | PDX
1.2/E | No description available
1.2/G | No description available
> select #1.1/A
3266 atoms, 3317 bonds, 7 pseudobonds, 3 models selected
> delete atoms (#!1.1 & sel)
> delete bonds (#!1.1 & sel)
> select #1.1/B
812 atoms, 813 bonds, 4 pseudobonds, 2 models selected
> delete atoms (#!1.1 & sel)
> delete bonds (#!1.1 & sel)
> select /G
1682 atoms, 1577 bonds, 4 pseudobonds, 2 models selected
> color (#!1.2 & sel) cyan
> color sel byhetero
> color sel byhetero
> select /E
6947 atoms, 6610 bonds, 11 pseudobonds, 2 models selected
> color (#!1.2 & sel) light gray
> color sel byhetero
> select clear
> set bgColor white
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting full
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting full
> lighting full
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select /G
1682 atoms, 1577 bonds, 4 pseudobonds, 2 models selected
> color (#!1.2 & sel) light sea green
> color (#!1.2 & sel) cyan
> color sel byhetero
> select /E
6947 atoms, 6610 bonds, 11 pseudobonds, 2 models selected
> color (#!1.2 & sel) dark gray
> color (#!1.2 & sel) light gray
> color sel byhetero
> select ::name="HEM"
73 atoms, 76 bonds, 4 pseudobonds, 2 models selected
> color (#!1.2 & sel) byelement
> color (#!1.2 & sel) #f9ffeaff
> color (#!1.2 & sel) #f8ffeaff
> color (#!1.2 & sel) #fbffe9ff
> color (#!1.2 & sel) #fff7deff
> color (#!1.2 & sel) #ffeed6ff
> color (#!1.2 & sel) #ffdcc3ff
> color (#!1.2 & sel) #fecdb0ff
> color (#!1.2 & sel) #fec7a4ff
> color (#!1.2 & sel) #fec29cff
> color (#!1.2 & sel) #fec099ff
> color (#!1.2 & sel) #febf97ff
> color (#!1.2 & sel) #febd96ff
> color (#!1.2 & sel) #feb78dff
> color (#!1.2 & sel) #feb386ff
> color (#!1.2 & sel) #feb185ff
> color (#!1.2 & sel) #feb183ff
> color (#!1.2 & sel) #feab78ff
> color (#!1.2 & sel) #fea96fff
> color (#!1.2 & sel) #fea76aff
> color (#!1.2 & sel) #fea669ff
> color (#!1.2 & sel) #fea466ff
> color (#!1.2 & sel) #fe9f60ff
> color (#!1.2 & sel) #fea162ff
> color (#!1.2 & sel) #fea261ff
> color (#!1.2 & sel) #fea459ff
> color (#!1.2 & sel) #fea654ff
> color (#!1.2 & sel) #fea755ff
> color (#!1.2 & sel) #feb45fff
> color (#!1.2 & sel) #fec974ff
> color (#!1.2 & sel) #feca76ff
> color (#!1.2 & sel) #fecc77ff
> color (#!1.2 & sel) #fecb75ff
> color (#!1.2 & sel) #fec46dff
> color (#!1.2 & sel) #febf6aff
> color (#!1.2 & sel) #feb764ff
> color (#!1.2 & sel) #feb563ff
> color (#!1.2 & sel) #feb05eff
> color (#!1.2 & sel) #feae5dff
> color (#!1.2 & sel) #fead5cff
> color (#!1.2 & sel) #fea657ff
> color (#!1.2 & sel) #fea354ff
> color (#!1.2 & sel) #fe9d50ff
> color (#!1.2 & sel) #fd9b4eff
> color (#!1.2 & sel) #fd9449ff
> color (#!1.2 & sel) #fd823cff
> color (#!1.2 & sel) #fd7f3aff
> color (#!1.2 & sel) #fd7b37ff
> color (#!1.2 & sel) #fd7c37ff
> color (#!1.2 & sel) #fd7a2eff
> color (#!1.2 & sel) #fd7c2bff
> color (#!1.2 & sel) #fd7d2bff
> color (#!1.2 & sel) #fd7e2aff
> color (#!1.2 & sel) #fd8128ff
> color (#!1.2 & sel) #fd8427ff
> color (#!1.2 & sel) #fd8528ff
> color (#!1.2 & sel) #fd8729ff
> color (#!1.2 & sel) #fd8828ff
> color (#!1.2 & sel) #fd8927ff
> color (#!1.2 & sel) #fd8b26ff
> color (#!1.2 & sel) #fd8d25ff
> color (#!1.2 & sel) #fd8e26ff
> color (#!1.2 & sel) #fd9128ff
> color (#!1.2 & sel) #fd952cff
> color (#!1.2 & sel) #fe9d32ff
> color (#!1.2 & sel) #fe9e33ff
> color (#!1.2 & sel) #fea134ff
> color (#!1.2 & sel) #fea035ff
> color (#!1.2 & sel) #fd973fff
> color (#!1.2 & sel) #fd9645ff
> color (#!1.2 & sel) #fd964aff
> color (#!1.2 & sel) #fd9750ff
> color (#!1.2 & sel) #fd9955ff
> color (#!1.2 & sel) #fd9856ff
> color (#!1.2 & sel) #fd9957ff
> color (#!1.2 & sel) #fd9959ff
> color (#!1.2 & sel) #fd9b5cff
> color (#!1.2 & sel) #fd9b5eff
> color (#!1.2 & sel) #fd9c61ff
> color (#!1.2 & sel) #fea069ff
> color (#!1.2 & sel) #fea66eff
> color (#!1.2 & sel) #feaa74ff
> color (#!1.2 & sel) #feae7cff
> color (#!1.2 & sel) #feb98aff
> color (#!1.2 & sel) #feb98cff
> color (#!1.2 & sel) #fec098ff
> color (#!1.2 & sel) #fecaa6ff
> color (#!1.2 & sel) #ffd3b0ff
> color (#!1.2 & sel) #ffd4b2ff
> color (#!1.2 & sel) #ffd6b3ff
> color (#!1.2 & sel) #ffdcb9ff
> color (#!1.2 & sel) #ffe1bfff
> color (#!1.2 & sel) #ffdfbdff
> color (#!1.2 & sel) #ffd9bdff
> color (#!1.2 & sel) #ffd8bcff
> color (#!1.2 & sel) #ffd6baff
> color (#!1.2 & sel) #fecab3ff
> color (#!1.2 & sel) #feb5a5ff
> color (#!1.2 & sel) #feb4a3ff
> color (#!1.2 & sel) #fea69bff
> color (#!1.2 & sel) #fea89bff
> color (#!1.2 & sel) #feac9aff
> color (#!1.2 & sel) #feb099ff
> color (#!1.2 & sel) #feb298ff
> color (#!1.2 & sel) #feb197ff
> color (#!1.2 & sel) #feb496ff
> color (#!1.2 & sel) #febb92ff
> color (#!1.2 & sel) #febc8fff
> color (#!1.2 & sel) #feb78cff
> color (#!1.2 & sel) #feb68aff
> color (#!1.2 & sel) #feaf87ff
> color (#!1.2 & sel) #feae86ff
> color (#!1.2 & sel) #feac85ff
> color (#!1.2 & sel) #feab83ff
> color (#!1.2 & sel) #fea780ff
> color (#!1.2 & sel) #fd9d7aff
> color (#!1.2 & sel) #fd9b79ff
> color (#!1.2 & sel) #fd9976ff
> color (#!1.2 & sel) #feac81ff
> color (#!1.2 & sel) #feae82ff
> color (#!1.2 & sel) #feae84ff
> color (#!1.2 & sel) #feaf87ff
> color (#!1.2 & sel) #feae8aff
> color (#!1.2 & sel) #fead8eff
> color (#!1.2 & sel) #feac8fff
> color (#!1.2 & sel) #feaa93ff
> color (#!1.2 & sel) #fea894ff
> color (#!1.2 & sel) #fea696ff
> color (#!1.2 & sel) #fea496ff
> color (#!1.2 & sel) #fea397ff
> color (#!1.2 & sel) #fea398ff
> color (#!1.2 & sel) #fea298ff
> color (#!1.2 & sel) #fea199ff
> color (#!1.2 & sel) #fd9a99ff
> color sel byhetero
> select clear
> select ::name="HOH"
538 atoms, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/rorygordon/Desktop/image1.png supersample 3
> select ::name="CAM"
27 atoms, 28 bonds, 1 model selected
> color sel magenta
> color sel byhetero
> select ::name="CAH"
28 atoms, 29 bonds, 1 model selected
> color sel magenta
> color sel byhetero
Drag select of 334 atoms, 12 pseudobonds, 509 residues, 302 bonds
> select H
4004 atoms, 1 model selected
> hide sel target a
> select clear
> save /Users/rorygordon/Desktop/image2.png supersample 3
> save /Users/rorygordon/Desktop/image3.png supersample 3
> save /Users/rorygordon/Desktop/image4.png supersample 3
> save /Users/rorygordon/Desktop/P450cam_Putida_Whole.cxs
> open /Users/rorygordon/Desktop/P450cam_putidaredoxin_Poulos.pdb
P450cam_putidaredoxin_Poulos.pdb title:
Crystal structure of cytochrome P450CAM-putidaredoxin complex [more info...]
Chain information for P450cam_putidaredoxin_Poulos.pdb #2
---
Chain | Description
A | camphor 5-monooxygenase
B | camphor 5-monooxygenase
C D | PDX
Non-standard residues in P450cam_putidaredoxin_Poulos.pdb #2
---
1N0 — 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione (bis(maleimido)hexane, bound
form)
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
HEM — protoporphyrin IX containing Fe (HEME)
> open /Users/rorygordon/Desktop/P450cam_putidaredoxin_Poulos.pdb
P450cam_putidaredoxin_Poulos.pdb title:
Crystal structure of cytochrome P450CAM-putidaredoxin complex [more info...]
Chain information for P450cam_putidaredoxin_Poulos.pdb #3
---
Chain | Description
A | camphor 5-monooxygenase
B | camphor 5-monooxygenase
C D | PDX
Non-standard residues in P450cam_putidaredoxin_Poulos.pdb #3
---
1N0 — 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione (bis(maleimido)hexane, bound
form)
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
HEM — protoporphyrin IX containing Fe (HEME)
> hide #!1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1 models
> show #!1 models
> open "/Users/rorygordon/Desktop/MRes Project/Reference Enzymes/P450cam -
> Putidaredoxin Complex/Putidaredoxin-P450cam-Reduced-Cleaned.pdb"
Summary of feedback from opening /Users/rorygordon/Desktop/MRes
Project/Reference Enzymes/P450cam - Putidaredoxin
Complex/Putidaredoxin-P450cam-Reduced-Cleaned.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (344 )
Cannot find LINK/SSBOND residue CYS (19 )
Cannot find LINK/SSBOND residue GLU (198 )
Cannot find LINK/SSBOND residue CYS (39 )
Cannot find LINK/SSBOND residue CYS (39 )
31 messages similar to the above omitted
Putidaredoxin-P450cam-Reduced-Cleaned.pdb title:
Crystal structure of reduced cytochrome P450CAM-putidaredoxin complex bound to
camphor and 5-exo-hydroxycamphor [more info...]
Chain information for Putidaredoxin-P450cam-Reduced-Cleaned.pdb #4
---
Chain | Description
A | camphor 5-monooxygenase
C | PDX
Non-standard residues in Putidaredoxin-P450cam-Reduced-Cleaned.pdb #4
---
CA — calcium ion
CAH — 5-exo-hydroxycamphor
CAM — camphor
FES — FE2/S2 (inorganic) cluster
HEM — protoporphyrin IX containing Fe (HEME)
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1.2 models
> hide #!1 models
> hide #!2 models
Drag select of 326 atoms, 13 pseudobonds, 511 residues, 280 bonds
> select H
7971 atoms, 2 models selected
> hide (#!4 & sel) target a
> select #4/C
1678 atoms, 1578 bonds, 4 pseudobonds, 2 models selected
> color (#!4 & sel) cyan
> hide #!4 models
> select #1
8091 atoms, 8188 bonds, 12 pseudobonds, 3 models selected
> ~select #1.2
1 model selected
> select #2
8154 atoms, 8102 bonds, 32 pseudobonds, 3 models selected
> select #3
8154 atoms, 8102 bonds, 32 pseudobonds, 3 models selected
> select #1.2
8091 atoms, 8188 bonds, 12 pseudobonds, 2 models selected
> select #1
8091 atoms, 8188 bonds, 12 pseudobonds, 3 models selected
No visible models!
> show #!1 models
> show #!1.2 models
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
> show #!2 models
> select #2
8154 atoms, 8102 bonds, 32 pseudobonds, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1
1 model selected
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3
8154 atoms, 8102 bonds, 32 pseudobonds, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!4 models
> select /A
6843 atoms, 6550 bonds, 9 pseudobonds, 2 models selected
> color (#!4 & sel) light gray
> color sel byhetero
Drag select of 303 atoms, 13 pseudobonds, 482 residues, 257 bonds
> color sel byhetero
> select ::name="HEM"
73 atoms, 76 bonds, 4 pseudobonds, 2 models selected
> color (#!4 & sel) byelement
> color (#!4 & sel) #fd988aff
> color (#!4 & sel) #fd9a8cff
> color (#!4 & sel) #fea394ff
> color (#!4 & sel) #fec2aaff
> color (#!4 & sel) #fec5abff
> color (#!4 & sel) #fec6acff
> color (#!4 & sel) #fec7acff
> color (#!4 & sel) #fecaa6ff
> color (#!4 & sel) #feca9fff
> color (#!4 & sel) #fec996ff
> color (#!4 & sel) #fec895ff
> color (#!4 & sel) #fec693ff
> color (#!4 & sel) #fec091ff
> color (#!4 & sel) #feb088ff
> color (#!4 & sel) #fea983ff
> color (#!4 & sel) #fea481ff
> color (#!4 & sel) #fea280ff
> color (#!4 & sel) #fd9a7aff
> color (#!4 & sel) #fd8d71ff
> color (#!4 & sel) #fd836cff
> color (#!4 & sel) #fd816aff
> color (#!4 & sel) #fd846bff
> color (#!4 & sel) #fd866cff
> color (#!4 & sel) #fd8c6eff
> color (#!4 & sel) #fd8a6dff
> color (#!4 & sel) #fd896cff
> color (#!4 & sel) #fd907fff
> color (#!4 & sel) #fd8f7fff
> color (#!4 & sel) #fd8d7fff
> color sel byhetero
Drag select of 303 atoms, 13 pseudobonds, 511 residues, 257 bonds
> show (#!4 & sel) target ab
> select H
3967 atoms, 1 model selected
> hide sel target a
> select ::name="HOH"
487 atoms, 1 model selected
Drag select of 2545 atoms, 13 pseudobonds, 511 residues, 2151 bonds
> hbonds sel
1629 hydrogen bonds found
> select clear
Drag select of 216 atoms, 59 residues, 178 bonds, 30 pseudobonds
> hide (#!4 & sel) target ab
> cartoon hide (#!4 & sel)
Drag select of 278 atoms, 16 residues, 56 bonds, 36 pseudobonds
> hide (#!4 & sel) target ab
> cartoon hide (#!4 & sel)
> select /C:106@CB
1 atom, 1 model selected
> surface style sel mesh
> surface sel
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 4.C
> surface style (#!4 & sel) mesh
> surface hidePatches (#!4 & sel)
> surface style (#!4 & sel) mesh
OpenGL version: 4.1 INTEL-14.6.18
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir6,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 4 GB
Boot ROM Version: 121.0.0.0.0
SMC Version (system): 2.13f15
Software:
System Software Overview:
System Version: macOS 10.15.5 (19F101)
Kernel Version: Darwin 19.5.0
Time since boot: 1 day 4:35
Graphics/Displays:
Intel HD Graphics 5000:
Chipset Model: Intel HD Graphics 5000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0a26
Revision ID: 0x0009
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Rory,
--Eric
Tom, should the command "surface style (#!4 & sel) mesh" actually do nothing (with part of the surface selected)? That seems surprising. Seems like it should change the whole surface into mesh. Is that a bug or am I misunderstanding something?
--Eric