id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3502 """realistic"" lipid bilayer depiction" Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Just a thought that came to mind while looking at this behemoth (new mitochondrial complex I structure - paper hopefully going in this week)... a potentially really nice feature for people working with membrane proteins would be the ability to add a ""fake"" membrane for visualisation without the need to actually explicitly model and equilibrate one. The idea I'm thinking is that you'd ask them to specify sufficient atoms representing the positions of the phosphate head groups to fit planes through top and bottom, then add some realistic random bumpiness and remove the portions intersecting the protein itself. Could make it much easier to turn structures like this into cover-worthy illustrations. 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 working.cif Summary of feedback from opening working.cif --- warnings | Unknown polymer entity '1' near line 380 Unknown polymer entity '2' near line 2758 Unknown polymer entity '3' near line 5436 Unknown polymer entity '4' near line 8587 Unknown polymer entity '5' near line 15226 25 messages similar to the above omitted Atom H1 is not in the residue template for MET /A:1 Atom H1 is not in the residue template for LEU /B:14 Atom H3 is not in the residue template for ALA /C:4 Atom H3 is not in the residue template for ASP /D:2 Atom HH11 is not in the residue template for 2MR /D:65 Atom H1 is not in the residue template for MET /E:1 Atom H3 is not in the residue template for GLN /E:9 Atom H3 is not in the residue template for ALA /G:2 Atom H1 is not in the residue template for ALA /H:2 Atom H4 is not in the residue template for P5S /H:1003 Atom H1 is not in the residue template for ALA /I:2 Atom H1 is not in the residue template for MET /J:1 Atom H1 is not in the residue template for MET /K:1 Atom H4 is not in the residue template for P5S /L:2003 Atom H1 is not in the residue template for MET /M:1 Atom H3 is not in the residue template for ALA /P:3 Atom H1 is not in the residue template for MET /Q:1 Atom H1 is not in the residue template for THR /Z:2 Atom H4 is not in the residue template for P5S /a:1017 Atom H1 is not in the residue template for ALA /b:212 Atom H1 is not in the residue template for ALA /e:212 Atom H1 is not in the residue template for GLN /h:30 Atom H1 is not in the residue template for ALA /i:2 Atom H3 is not in the residue template for THR /j:8 Atom H1 is not in the residue template for GLN /l:30 Atom H1 is not in the residue template for ALA /m:2 Atom H1 is not in the residue template for THR /n:8 Atom H3 is not in the residue template for PHE /o:2 Atom H1 is not in the residue template for PHE /p:2 Atom H1 is not in the residue template for MET /q:1 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for working.cif #1 --- Chain | Description A | ? B | ? C | ? D | ? E | ? F | ? G | ? H | ? I | ? J | ? K | ? L | ? M | ? N | ? P | ? Q | ? R | ? Z | ? a | ? b e | ? c | ? d | ? f | ? g k | ? h l | ? i m | ? j n | ? o | ? p | ? q | ? > set bgColor white > lighting soft > hide H > show ~protein&H > select clear > surface protein > ~surface > cartoon > hide protein > surface protein > select clear > cofr centerOfView showPivot true > save /home/tic20/Desktop/complex_i.jpg > save /home/tic20/Desktop/complex_i_top_view.jpg OpenGL version: 3.3.0 NVIDIA 450.51.05 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 7.3G 47G 213M 8.0G 54G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: complex_i_images.tar.gz }}} [attachment:""complex_i_images.tar.gz""] " enhancement accepted minor Depiction Elaine Meng all ChimeraX