[Chimera-users] APBS maps

Tom Goddard goddard at sonic.net
Wed Apr 11 10:53:14 PDT 2012

Hi Rebecca,

   I think the variation in electrostatic potential is not too rapid 
across the surface and a difference map could be useful and reasonably 
smooth if the surfaces of the two conformations are nearly the same.  
Chimera colors the solvent excluded surface according to the potential 
1.4 Angstroms away from the surface (that is about how close a ligand 
atom could get).  At that distance from the charges the potential will 
not vary too rapidly.  It varies rapidly near the charges (e.g. within 1 
Angstrom of a charged atom).  As long as the conformations are nearly 
the same so the surface you use for display is not too close to the 
atoms of either conformation then I think that difference map will be 
smooth enough.


> Hi Rebecca,
> Chimera has a command for calculating difference maps: vop subtract
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
> *However, this is intended mainly for electron density maps.  I suspect the result for ESP maps would be too noisy to be very useful, since the ESP varies rapidly with small changes in atom positions and from positive to negative and vice versa.  That is, even a difference ESP map for slightly different conformations of the same protein might have a lot of potentially (pun partially intended) misleading features.
> What I usually see for published ESP comparisons is side-by-side images of either molecular surfaces colored by potential value or isopotential contour surfaces (at the same levels for the two molecules).  In that case you would superimpose the proteins to get the corresponding orientation and then translate one of them along the X-axis (left or right) without changing its orientation.  You'd translate the corresponding map along with the protein, of course, and then create the ESP displays for both proteins.  Or equivalently you could create the displays while they are superimposed, then move them apart.
> 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 Apr 11, 2012, at 9:50 AM, Rebecca Swett wrote:
>> Hey guys, i'm working with some electrostatic potential maps and am interested in doing a difference map. Two nearly homologous proteins with nearly identical surface shapes, and radically different electrostatics. I"m thinking a difference map would illustrate the differences well, but in looking at the APBS output I have no idea how to do that manually. Does anyone here have an idea about how to do that in chimera?
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