[Chimera-users] electrostatic surface coloring

[Elaine Meng]

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