[Chimera-users] APBS maps

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Apr 12 07:49:25 PDT 2012

Hi Rebecca,

You might also want to try showing the actual isosurfaces side-by-side. If
the differences are dramatic, that might make a more impressive visual.

Open your ".dx" files from APBS in Chimera and then use "Tools > Volume
Data > Volume Viewer".

Click on the histogram or change the "step" to display the isosurfaces.
Adjust one threshold to have a "Level" of "-1"  or maybe "-2" and color it
blue. Then adjust the other threshold to have a "Level of "1" or maybe "2"
and color it red.

See attached for an example.

My $0.02,

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office  301-402-0095
Mobile 301-758-3559
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On 4/11/12 1:54 PM, "Rebecca Swett" <rswett at chem.wayne.edu> 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.
>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).
>> 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,
>> ...and sum over atom values to get the residue values with Attribute
>> ...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
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu

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