[Chimera-users] electrostatic surface calculation

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 2 15:55:31 PDT 2013


One more idea.  Sometimes the molecular surface calculation chokes up on some singularity and generates a weird shape in a small area.  Even if the coordinates are essentially the same, very small rounding differences might lead to this problem with one set and not the other.  I feel that this is fairly unlikely, but if you think that it is the problem, just use the surface that looks good for both types of coloring.
Elaine

On Oct 2, 2013, at 3:51 PM, Elaine Meng wrote:

> Hi Ursula,
> The molecular surface calculation is the same regardless of what coloring is done.  Thus there must be some difference in the atomic coordinates for which the surface is calculated.  I am guessing one surface is for the coordinates returned by PDB2PQR and another is calculated from the original coordinates.
> 
> You could try looking at those two sets of coordinates (not the surfaces) to see if there are any differences.
> 
> However, I can only imagine that PDB2PQR would ignore/omit coordinates, not acquire additional coordinates as compared to the original coordinates.  It omits residues not handled by the designated force field.  My only other idea is that even if they contain the same number of protein atoms, one set of coordinates has been transformed (rotated and/or translated) differently than the other.
> 
> It is best to figure out what is going on, but I should also note you can re-color the same surface model that was colored by Coulombic ESP with the APBS ESP instead.  Which surface model to color is specified in the Surface Color (Electrostatic Surface Coloring) dialog.
> 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 Oct 2, 2013, at 2:51 PM, Ursula Schulze-Gahmen wrote:
> 
>> I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? 
>> 
>> Thanks
>> 
>> Ursula
>> 
>> -- 
>> Ursula Schulze-Gahmen, Ph.D.
>> Assistant Researcher
>> UC Berkeley, QB3
>> 356 Stanley Hall #3220
>> Berkeley, CA 94720-3220
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> 
> 
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