[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.
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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