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@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