[Chimera-users] SURF for large proteins

Tom Goddard goddard at sonic.net
Tue Jan 3 11:32:12 PST 2012

Hi Vijay,

   Chimera molecular surface calculation (using MSMS) fails for most 
molecules larger than 5,000 atoms.  The main trick that can help is to 
split large multi-chain models into a separate model for each chain 
using the split command (e.g. "split #0").  Then use a separate 
molecular surface on each chain.  The attached photo shows the result of 
that for chaperone 1aon with 21 chains with one subunit colored yellow 
so you can see its shape.

   If you use Coulombic Electrostatic Coloring (menu Tools / Surface & 
Binding Analysis) doing it on the split model gives a slightly different 
result than with an unsplit model.  The potential on each surface is 
just the potential for one chain.  Doing the calculation without split 
would use the potential for the entire model.  The split version can be 
more useful if you are interested in complementary charges on interfaces 
between chains.

   Sometimes you can get a molecular surface computation that fails on 
one computer to work on another computer.  Mac Chimera produces surfaces 
for larger models, and Windows Chimera has the most failures, and the 
failure rate for 64-bit Windows Chimera is much higher than 32-bit 
Windows Chimera which is higher than Mac (all versions).  Not sure where 
Linux fits in.

   Another approach is to use a different kind of surface, one generated 
from a density map made by placing Gaussians at each atom.  The molmap 
command creates this surface (e.g. "molmap #0 5" for a 5 Angstrom 
resolution surface).  You'll probably want to use a high resolution (< 
5A) since the electrostatics can vary on short distances.  You might 
want to use the molmap "gridSpacing" option to get a finer mesh for the 
(e.g. "molmap #0 5 gridSpacing 1" for a 1 Angstrom grid).  Currently 
only molecular surfaces can be colored by Chimera's Coulomb potential 
coloring code, so that won't work on these molmap surfaces.  You would 
need an externally computed potential (e.g. from APBS or DelPhi) and 
then use the Chimera Electrostatic Surface Coloring tool (menu Tools / 
Surface & Binding Analysis) which uses those externally computed 
potential grids.  Those external potential calculations can take a long 
time and a huge amount of memory for large models.  I submitted a 
Chimera enhancement request to allow the Chimera built-in Coulomb 
coloring to work on any surface, but Eric who wrote that code has many 
other things to work on, so it probably won't happen soon.


-------- Original Message --------
Subject: SURF for large proteins
From: Vijay Reddy
To: Tom Goddard
Date: 1/3/12 7:32 AM
> Hi Tom,
> Happy New Year! Wish you the best for you and yours in the New Year!
> I was wondering if are there tricks to calculate and display MSMS 
> surface for large proteins, even with the coarse representations. I am 
> trying to display electrostatic potential.
> Many thanks,
> Vijay

-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1aon-esp.jpg
Type: image/jpeg
Size: 73927 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120103/a48e0e6e/attachment.jpg>

More information about the Chimera-users mailing list