[Chimera-users] Query regarding solvent accessible surface area of protein
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.
> 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"
> 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.
> (2) Sometimes surface calculation has numerical failures, as discussed in
> this previous post and links theirein:
> (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:
> (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 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
School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
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