Dear Elaine, Dear Eric, thank you so much for the explanation! Indeed I suppose I should to convert my trajectory from CG to FG model firstly using back-mapping approach to proceed it to the APBS analysis. With Best Regards, Gleb 2016-05-19 23:22 GMT+02:00 Eric Pettersen <pett@cgl.ucsf.edu>:
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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users