[Chimera-users] New user-visualizing coulombic

Francois Berenger berenger at riken.jp
Tue Feb 19 16:23:09 PST 2013


Is it possible to launch APBS from within chimera?

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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