"realistic" lipid bilayer depiction

[Tristan Croll]

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

complex_i_images.tar.gz​

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

Hi Tristan

Some fraction of this is already available as the "define plane" command, which given a set of atoms will draw a plane that best fits them. It doesn't have artificial bumpiness nor does it make a hole for the protein, but it can be reasonably effective as per: ​http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopamineReceptor.html

--Eric

[Tristan Croll]

That's rather nice!

On 2020-07-13 17:12, ChimeraX wrote:

[Tristan Croll]

There are multiple maps arising from this particular experiment... the 
largest is a supercomplex of 4(!) of these (each of which is made up of 
9700 residues). I think the only workable approach with regard to an 
overview depiction will be to go for "realism". I can probably hack 
together something for immediate use starting from the plane definition 
code you pointed out, but I do think it would be something with wider 
applicability.

On 2020-07-13 17:32, ChimeraX wrote:

[Elaine Meng]

As an aside, those planes were calculated from entries in OPM which put a bunch of fake atoms in the plane:
<https://opm.phar.umich.edu/>

The images for membrane proteins in the RCSB PDB also use this database.
<https://www.rcsb.org/news?year=2016&article=57e55ccd90f5613003407f0c&feature=true>

For a full atomic model see the MemBuilder web service:
<http://bioinf.modares.ac.ir/software/mb/>