Hi Elaine,<br>   I know people in the past have asked a question about the solvent Occupancy Calculation, but please help me.<br>I have an oligosaccharide simulaiton trajectory from AMBER9. I used a 100ps trajectory for solvent occupancy calculation using Chimera.<br>
Everything looks absolutely fine. The questions I have are as follows:<br>I have 0-220 in my levels section of volume viewer. If I fix the level of 80, what does that mean?<br>When I&#39;m sliding the bar of levels from left-right what information about solvent density am I obtaining?<br>
For example does a value of 80 mean low density when compared with a value of 70? or is it the other way?<br>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?<br>
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%?<br>
Also is there any reference paper by which Chimera calculates the solvent occupancy?<br><br>Thanks very  much for your time<br>Sai<br clear="all"><br><br>