[Chimera-users] APBS maps

Rebecca Swett rswett at chem.wayne.edu
Wed Apr 11 15:06:16 PDT 2012

Thank you Elaine, your method worked like a charm. And a bit of 
explanation as to why we're doing this. We ran the electrostatics over a 
range of pH's as the two structurally similar but sequentially different 
proteins have quite different behavior in an acidified endosome, We're 
looking for surface hot spots that might be relevant to their different 
behaviors at various pH's. Thanks again for your help.

On 4/11/2012 1:54 PM, Rebecca Swett wrote:
> 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
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