[Chimera-users] Solvent Occupancy Calculation

Saikumar Ramadagu gourmet.sai at gmail.com
Mon May 18 08:25:36 PDT 2009

Hi Elaine,
   I know people in the past have asked a question about the solvent
Occupancy Calculation, but please help me.
I have an oligosaccharide simulaiton trajectory from AMBER9. I used a 100ps
trajectory for solvent occupancy calculation using Chimera.
Everything looks absolutely fine. The questions I have are as follows:
I have 0-220 in my levels section of volume viewer. If I fix the level of
80, what does that mean?
When I'm sliding the bar of levels from left-right what information about
solvent density am I obtaining?
For example does a value of 80 mean low density when compared with a value
of 70? or is it the other way?
When I have two different oligosaccharide simulations and I want to say that
oligosaccharide 1 has more water density around it, what value of levels
should I choose?
What I mean by this statement is do I select same value of levels? or do I
calculate the percentage i.e., 80/220 for first model gives me 36% and for
second sugar if the levels are 0-300 the i should choose a level of 109
which gives 36%?
Also is there any reference paper by which Chimera calculates the solvent

Thanks very  much for your time
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