[Chimera-users] query regarding volume viewer

Nidhi Batra nidhi.batra at igib.in
Wed Jun 8 05:35:31 PDT 2016

Dear Sir/Madam
I have carried out MD simulations on a set of proteins belonging to a
protein family. Further, I computed the water density around the protein
and have the output in .dx format. I want to use Chimera to visualize the
water density around the protein within 4  A.

For this, I loaded the protein and the .dx file in volume viewer, selecting
the protein and changing the zone to 4 and generating results.  I want to
have a comparison of water density across all proteins. I am unable to
understand how to normalise the settings so that the results are
comparable.  What I understand is to keep the step same. Additionally,  all
the .dx files have different ranges which is obvious, what should be the
value of level so that I can compare the water density across  different
proteins? Should it be kept at a median value of the range or something
else? Please help. If I keep everything default, the results are

Thanking you

Yours sincerely
Nidhi Batra
DBT-Research Associate
Institute of Genomics and Integrative Biology (IGIB),
Mathura Road, Sukhdev Vihar
New Delhi, INDIA 110020
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