[Chimera-users] electrostatic surface coloring

James Starlight jmsstarlight at gmail.com
Fri May 20 00:35:14 PDT 2016


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 at 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 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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>



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