[Chimera-users] Query regarding solvent accessible surface area of protein

[Elaine Meng]

Hi Aditya,
If you display the molecular surface, the atoms and residues are automatically assigned their surface area values as the attributes named areaSAS (solvent-accessible surface area) and areaSES (solvent-excluded surface area).  You get both values even though the surface displayed in Chimera is the SES.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

You can see histograms of the per-atom or per-residue attribute values and show them with colors using the Render by Attribute tool (under Tools... Structure Analysis).  You can also write out the values into a file using the File menu of that tool.  Another way to do the coloring is with the command "rangecolor"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

It is not necessary to calculate an average.  You can do it by showing a surface at each step, then saving the values or coloring to show them as described above.  However, there are a few issues:

(1) Bubbles inside the structure also have surface area.  If you do not want to include these bubbles in the surface area calculations, use the Preferences (under Favorites menu), New Surface category, turn off "show disjoint surfaces" and click Save.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces>

(2) Sometimes surface calculation has numerical failures, as discussed in this previous post and links theirein:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005689.html>

(3) In MD Movie, you could use a per-model script to show the values with coloring.  There is the rangecolor command as mentioned above, but no Chimera command for saving the attributes to a file.  However, a python script for this purpose has been posted to the mailing list:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003531.html>
(You would need to download "attachment.bin" from that page, which is a misnomer, as it is a python file in plain text.  You could just paste the plain text as a Python script in the MD Movie per-frame script dialog.)

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

On Oct 30, 2010, at 2:54 AM, Aditya Padhi wrote:

> Hi all,
>         I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants?
>         Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)?
> Kindly help me sir. Any other suggestions will be highly grateful.
> Thanks and regards
> Aditya.