[Chimera-users] Mapping Change in Surface Exposed Residues on Model

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 12 10:59:46 PST 2013


Hi Josh,
Surface area (both SAS and SES) per atom and per residue is automatically calculated when you display a molecular surface.  For any structure, if you can show the surface, you can see a histogram of the surface area values, color by those values, save them to a file, etc. using "Render by Attribute" (in menu under Tools… Structure Analysis). The potential downside of this approach is that surface calculation more prone to failure if you have a large multimolecular complex.   Another approach that doesn't depend on being able to show the surface is to use "Area/Volume from Web"; it gives per-atom values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html>

Maybe you are more interested in the delta or difference in surface areas between two states.  In a test case, I was able to calculate per-residue change in solvent-accessible surface area between the two endpoint states of a morph.  Like the raw areas, the delta values  can be shown by coloring the structure or written to a file. 

Calculating deltaSAS: 
My test case was a single protein, glucose-binding protein (2gbp closed/bound, 2fw0 open/unbound).   I opened those two structures (#0 and #1), superimposed, and created morph trajectory model #2.  Then:

(1) showed surface for morph trajectory frame 1
(2) opened Attribute Calculator (in menu under Tools… Structure Analysis) and simply used it to save the current residue areaSAS values to another attribute name.  I "calculated" attribute named resArea1 for residue with formula: residue.areaSAS
(3) in MD Movie, skipped to last trajectory frame by entering its frame number (you don't want to play trajectory because that would try to calculate the surface for every frame).  Surface was also shown for that frame.
(4) in Attribute Calculator, saved current residue areaSAS to residue attribute named resArea2 with formula: residue.areaSAS
(5) in Attribute Calculator, created residue attribute deltaSAS with formula: residue.resArea1 - residue.resArea2
(6) in Render by Attribute (in menu under Tools… Structure Analysis), see attributes of "residues" for the morph model.  Residue attribute "deltaSAS" will be listed and can be shown with coloring etc. and/or saved to a file using the File menu of that tool.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

This general procedure could also be used for the attributes returned by Area/Volume from Web instead of those from molecular surface calculation.  You could also sum atomic values to get residue values.

Another related feature is command "measure buriedArea" but it is for specific interfaces, i.e. you have to specify the two sets of atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 11, 2013, at 10:07 AM, Joshua Carter <carter_jjc at hotmail.com> wrote:

> Hello,
> My name is Josh Carter and I am an undergraduate at MSU working on some modeling.  I am working in particular on a ribo-nucleo-protein complex that undergoes a conformational change upon target binding.  I am trying to find a good way to map the change in surface exposed residues after this conformational change occurs.  I have a morph model of the two states and was just wondering if there was a way to map using chimera which models are surface exposed or not?
> Thanks,
> Josh




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