[Chimera-users] Loading .dx maps to chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 17 10:00:24 PST 2007

Dear Maya,
I don't know much about the display in PMV, but I will assume that in  
both programs you are coloring a surface by electrostatic potential.   
Possible reasons for differences in appearance:

(1) the default display settings may simply be different between the  
two programs, that is, what values are mapped to what colors.  In  
Chimera's Electrostatic Surface Coloring tool, the default is red  
(10% transparent) at -10, white (50% transparent) at 0, blue (10%  
transparent) at +10.


(2) the surfaces may be different.  Chimera shows a solvent-excluded  
surface (probe contact + reentrant), where maybe PMV is showing a  
solvent-accessible surface (where the probe center goes).  Even if  
both programs are showing the solvent-excluded surface, the atomic  
VDW radii used to calculate the surface and the vertex density of the  
surface likely differ.  Another variable is the probe radius,  
although most programs use 1.4 angstroms as the default.

These differences do not mean that either program is wrong.  However,  
in Chimera you can adjust the color/value mapping with Electrostatic  
Surface Coloring (under Tools... Surface/Binding Analysis), and  
surface vertex density and probe radius in the molecular surface  
attributes panel (choose Favorites... Model Panel, and in the Model  
Panel choose the surface model on the left and click "attributes" on  
the right).  You can also change atomic VDW radii, although that is  
more trouble, and we have been careful about using good values.


Currently Chimera does not calculate a solvent-accessible surface.   
If PMV does calculate this type of surface and can write it out in  
GRASP surface format, you could then read it into Chimera.  Finally,  
you could show a "pseudo" solvent-accessible surface in Chimera by  
increasing all radii by 1.4 (one probe radius) and then using a probe  
small as possible, as described in this previous message to chimera- 

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 17, 2007, at 12:34 AM, maya shcushan wrote:

> Dear sir,
> I am trying to load a .dx file (electrostatic potential) onto a  
> molecule in chimera.
> I successfully loaded the map onto a the molecule’s surface.
> The problem is the potentials I get look differently than the  
> original map. That is, the potentials appear different in the  
> visualization tool of PMV, the program which generated the .dx file  
> I tried to e-load on chimera.
> Thanks,
> Maya Schushan,
> Tel-Aviv university, Israel.

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