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

Aditya Padhi adi.uoh at gmail.com
Wed Nov 3 23:36:28 PDT 2010

Hi Elaine,
    Thank you so much for answering all my doubts. I am now able to
calculate SASA for all frames by modifying the code posted on the site.

Thanks alot.


On Wed, Nov 3, 2010 at 9:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Aditya,
> There is no way to get the average without calculating it for each step
> first.  Or, you could calculate average coordinates (with some other
> program, Chimera does not have this function now) and then calculate the
> SASA for those coordinates, but it would be different than the average of
> SASA over all the steps.
> The way to do anything automatically for a whole trajectory is to use the
> "per-frame scripting" in the MD Movie tool, as described in #3 of my earlier
> reply.  That would not make it any faster, however, but it would
> automatically use the python script to save a file with SASA information at
> each step.  See that earlier message for how to get and use the script.
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005693.html
> >
> 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 2, 2010, at 8:43 PM, Aditya Padhi wrote:
> > Hi Elaine,
> >     As per your guidance, I am now able to calculate SASA for the
> trajectories of AMBER MD simulation of my protein. But I have 1200 frames
> and I need to calculate SASA for each and every frame. As u told, I can
> calculate by fixing each frame. But it seems to be very time taking and not
> favorable. Is there any way so that I can calculate SASA as an average among
> all the frames or most favorable would be to get SASA for all 1200 frames
> automatically rather going for individual ones.
> >     If you have any such script/relevant idea , kindly help me in this
> regard.
> >
> > Thanking you.
> > Aditya.
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