[Chimera-users] New user-visualizing coulombic

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 19 11:09:07 PST 2013

An important point for users of PDB2PQR (or any web service, for that matter!) is to check the results and not simply use them blindly.  The different force fields may not all handle certain types of structures, and atoms for which there are no parameters are simply omitted from the results. The default force field in PDB2PQR, PARSE, does not handle DNA, so all you get back for PDB entry 2BNA (for example) are several water molecules.

I tried using the PDB2PQR web service (completely separate from Chimera) on 2BNA
...and got the same result.  The file header had this explanation for missing parameters

REMARK   5 This is usually due to the fact that this residue is not
REMARK   5 an amino acid or nucleic acid; or, there are no parameters
REMARK   5 available for the specific protonation state of this
REMARK   5 residue in the selected forcefield.

...suggesting that it was supposed to recognize nucleic acis, but that might be a generic message always given regardless of the chosen force field.


On Feb 19, 2013, at 9:22 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 gre!
> atly appreciated thank you.
>> Armond Minor
>> Student, Biochemistry, SUNY Oneonta
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