id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3464 partial surface mesh rory.gordon.19@… Eric Pettersen "{{{ 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 }}} " defect closed normal Surface fixed Tom Goddard Elaine Meng all ChimeraX