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

Aditya Padhi adi.uoh at gmail.com
Sun Oct 31 03:31:52 PDT 2010

Thanks alot Elaine. I will try it up. If any problem still resides I will
convey to you.


On Sun, Oct 31, 2010 at 12:00 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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.

Aditya Kumar Padhi
Ph.D Scholar
School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
Contact no:+91-9711539958
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