[Chimera-users] APBS maps
Hurt, Darrell (NIH/NIAID) [E]
darrellh at niaid.nih.gov
Thu Apr 12 07:49:25 PDT 2012
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.
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
http://bioinformatics.niaid.nih.gov (Within NIH)
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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
>> 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
>> Maybe I misunderstood the question, though. Best,
>> 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.
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>Chimera-users at cgl.ucsf.edu
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