[Chimera-users] bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein

Anne-Frances Miller afmill3r2 at gmail.com
Thu Oct 1 08:08:05 PDT 2020

Hello Elaine,

This was the the ticket!!

Thank you very much,
and especially for the speed of your answer.


Novel Meritorious Research (and teaching)
A.-F. Miller, Ph. D.
Professor of Chemistry
University of Kentucky

Visiting Fellow, 
        Einstein Foundation of Berlin
Chair, Div. of Biological Chemistry, 
 	American Chemical Society

> On Sep 30, 2020, at 12:50 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Anne-Frances,
> You can use "surfcat" to define which atoms should be enclosed together in a single surface before showing the surface.  These surface categories (groupings) are mutually exclusive.  It's simplest to start afresh by closing everything first and reopening the structure instead of trying to delete the existing surface(s) first.
> Example 3d72 is a dimer with chains A, B each containing FAD and water.  Let's say I want one surface enclosing chain A protein and chain A FAD together.  The trick is that you can't just make the category all of chain A because there might be waters and other stuff you don't want in the surface, so instead of specifying atoms directly in the "surfcat" command, I use one or more "select" commands to get exactly the atoms I want, and then use "sel" in the "surfcat" command.
> open 3d72
> preset apply interactive 2
> select :.a
> ~select solvent
> surfcat blob1 sel
> surface blob1
> ~sel
> repr stick
> color red :fad
> (the other commands use "all atom" preset so you can see all the atoms before selecting, and then afterwards, change representation back to stick, but then change the surface patch for :fad red so that you can see it is combined with the protein)
> This page has more details and examples of using  "surfcat"
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>
> There is also a "measure buriedArea" command that allows specifying any sets of atoms regardless of how they are grouped for the surfaces that are displayed, but that didn't seem to be exactly what you needed in this case.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Sep 30, 2020, at 2:24 AM, Anne-Frances Miller <afmill3r2 at gmail.com> wrote:
>> Dear Chimera,
>> I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein?
>> (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6)
>> Thank you,
>> Anne-Frances

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