[Chimera-users] electrostatic surface coloring

Eric Pettersen pett at cgl.ucsf.edu
Thu May 19 14:22:49 PDT 2016


Since coloring surfaces by electrostatics depends upon assigning partial charges to individual atoms, I believe none of these tools will actually work for you since you have a Martini CG trajectory where each of the “atoms” actually represent several individual atoms.  I have no idea how you would attempt to color a CG-trajectory surface by electrostatics.

—Eric

> On May 19, 2016, at 2:15 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Gleb,
> While not specifically for trajectories (i.e. you would have to choose an individual frame, probably wouldn’t want to try to do it on all frames), see
> 
> Coulombic Structure Coloring
> - and/or -
> PDB2PQR
> APBS
> Electrostatic Surface Coloring
> 
> Those are the names of the graphical-interface tools but they all also have commands, see the manual pages and links therein:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
> 
> They are also all covered in the “Surface Properties” image tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On May 19, 2016, at 3:42 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>> 
>> Update:
>> 
>> Assuming that contact map based approach gave me some basic clues
>> regarding interaction patterns established between 2 proteins - which
>> are mostly based on the short-ranged forces e.g mainly vdw surface
>> between hydrophobic side-chains from both proteins involved in the
>> association. Now I'd like to focus on the long-ranged  interactions -
>> mainly mediated by local and global (assuming that concentrations of
>> ions is very high in my system) electrostatics effect. What Chimera's
>> tools might be useful here e.g computation of the electrostatic
>> surface etc?
>> 
>> Thanks!
>> 
>> Gleb
> 
> 
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