[Chimera-users] setting solvent density threshold at 2.5 times of the bulk solvent density

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 8 09:14:30 PDT 2015


Dear Mohan,
This sounds like a general issue with EM, independent of Chimera, and may depend on the specific data set, experimental conditions, resolution, etc.

Unfortunately I don’t have an answer… perhaps some users who are expert in EM may be able to respond.
Best,
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 Sep 8, 2015, at 1:52 AM, Mohan Pradhan <mohan.pradhan at ymail.com> wrote:
> 
> Dear Chimera users,
> I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
> 
> My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5
> Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
> 
> Kindly suggest.
> Thanks,
> Mohan




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