[Chimera-users] APBS maps

Rebecca Swett rswett at chem.wayne.edu
Wed Apr 11 10:18:33 PDT 2012

Thanks for the quick reply. I have the side by sides. I'll see if I get 
anything particularly wonky if I try the subtract. Alternatively, can 
you think of a way I could output per-residue charge from an APBS map? I 
might be able to do a simple subtract and render by attribute to get a 
rough approximation.

On 4/11/2012 1:03 PM, Elaine Meng wrote:
> 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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