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

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 3 08:32:49 PDT 2010

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.

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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