[Chimera-users] electrostatic surface coloring

Elaine Meng meng at cgl.ucsf.edu
Thu May 19 14:15:22 PDT 2016


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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