[Chimera-users] Solvent Occupancy Calculation

Elaine Meng meng at cgl.ucsf.edu
Mon May 18 10:28:10 PDT 2009

Hi Sai,
It is only a simple count in each grid cell, no special algorithm.  So  
if the contour level is 80 and you input 100 frames, the contour  
surface in Volume Viewer will enclose the tiny cubes in the grid that  
contained an atom (out of whatever set you specified) 80% of the time,  
i.e. in 80 of your 100 frames.  Actually if the grid spacing is large,  
it might be possible for there to be >1 count per frame, but with the  
recommended spacing of 1.0 Angstrom this should not occur.

Thus, the meaning of the contour level depends on (a) the total number  
of frames input to the occupancy calculation and (b) the grid  
spacing.  If those are the same, then a higher count means higher  
occupancy.  If you are leaving the spacing the same but calculating  
over different numbers of frames, then dividing as you suggested would  
allow comparison.  I would not use "density" interchangeably with  
"occupancy" because they can mean different things; density can be  
evaluated at a moment in time, whereas the occupancy depends on  
multiple measurements through time.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 18, 2009, at 8:25 AM, Saikumar Ramadagu wrote:

> 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 occupancy?
> Thanks very  much for your time
> Sai

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