[Chimera-users] New user-visualizing coulombic

Francois Berenger berenger at riken.jp
Tue Feb 19 18:04:02 PST 2013

On 02/20/2013 09:23 AM, Francois Berenger wrote:
> Is it possible to launch APBS from within chimera?

Answer to myself: I just saw in the chimera menus that the APBS 
webserver can be used...

> I know there is a pymol plugin, but as I am moving to chimera these days
> ...
> On 02/20/2013 02:22 AM, Elaine Meng wrote:
>> Hi Armond,
>> There are different methods of calculating electrostatic potential.
>> If you want to use Coulomb's law, just use the Coulombic Surface
>> Coloring tool.  It is not necessary to run any other programs or
>> tools.  The Coulombic method is simple and Chimera does all the
>> calculations, as described here:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
>> Some other programs perform a more complicated "continuum
>> electrostatics" calculation: they solve the Poisson-Boltzmann
>> equation.  These programs include APBS, DelPhi, and UHBD.   You used
>> PDB2PQR to prepare the structure for APBS (PDB2PQR associates atoms
>> with charge and radius values and writes out the format needed by
>> APBS), and then you ran APBS, which produced the *.dx file.  That file
>> is the electrostatic potential map.   When someone uses one of the
>> continuum electrostatics programs to calculate an electrostatic
>> potential map, they can open the map in Chimera and then use the
>> Electrostatic Surface Coloring tool to color the molecular surface by
>> the values.
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>> Several years ago I wrote a short explanation of continuum
>> electrostatics calculations.  This is not part of the Chimera manual,
>> but might be useful if you want to know more about them...
>> <http://www.cgl.ucsf.edu/home/meng/grpmt/escalc.html>
>> However, it sounds like you just want to display the  molecular
>> surface and then use Coulombic Surface Coloring, not those other
>> programs or tools.
>> 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 Feb 15, 2013, at 6:04 PM, Minor, Armond wrote:
>>> Hello,
>>>    I am just starting out using the program for a project with my
>>> Biochemistry professor.  We are trying to develop a simple procedure
>>> to visualize the Coulombic surface of short DNA sequences.  I have
>>> very little experience working with Chimera and do not know if I am
>>> going about it in correct way that will yield meaningful data.  I
>>> have tried following the instruction but must of them seem to be for
>>> people who are more familiar with the programs than I am.  Basically
>>> what I have tried is opening a pdb file, running PDB2PQR, opening the
>>> pqr file then running APBS on that. I am not sure what to do with the
>>> .dx file that comes out and how to use it to color the surface.  If I
>>> use it to color the Electrostatic potential map I get a range of
>>> values that seem to be not what my professor is expecting.  If I
>>> instead use the coulombic surface tool I get values like she expects
>>> but I am not sure if these are connected to the .dx file or just the
>>> pdb2pqr file.  Any help would be gr
> e!
>>   atly appreciated thank you.
>>> Armond Minor
>>> Student, Biochemistry, SUNY Oneonta
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