[Chimera-users] APBS maps

[Rebecca Swett]

That actually might work for me. The odd thing about the structures i'm 
comparing is that while the surface shape is nearly identical, the 
sequence identity is quite disparate. I'll play with it and let you know 
how it turns out. Thanks again for your suggestions.
~Rebecca


On 4/11/2012 1:41 PM, Elaine Meng wrote:
> Hi Rebecca,
> I was also thinking you might try smoothing the difference map to see if that better brings out the major features.  Various kinds of map smoothing (Gaussian filtering, etc.) can be done with "vop" command options or the Volume Filter tool (under Tools...Volume Data).
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html>
>
> Of course, the more processing you do, the more you have to explain to your audience!
>
> I'm not sure what you are getting at with the residue charge issue. The APBS map doesn't have charges, it only has the potential resulting from those charges.  You already know for the most part which residues are charged (Asp/Glu negative, Lys/Arg positive, His being the ambiguous case) and that only involves the structure, not the map.
>
> While you could use the Values at Atom Positions tool to get ESP values mapped to atom positions,
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
>
> ...and sum over atom values to get the residue values with Attribute Calculator,
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>
>
> ...that doesn't seem particularly useful applied to the same atoms that gave rise to the potential.  Typically it would be used to map potential from one molecule (say a receptor) onto other molecules not used to calculate the potential (say different small molecule ligands in the binding site).
>
> Maybe I misunderstood the question, though.  Best,
> Elaine
>
> On Apr 11, 2012, at 10:18 AM, Rebecca Swett wrote:
>
>> 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.
>> ~Rebecca
>