[Chimera-users] query regarding volume viewer

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 9 08:49:49 PDT 2016


Hi Nidhi,
I do not know how VMD calculated the “density” values.  Chimera simply uses the values that are in the dx file, so depending on how you got those values, you may have to do some normalization.  My comments apply only IF the values were simply counts (not densities) of the number of times a water appeared in the grid cell.

I do not know why the numbers are so different.  Some possibilities are that the grid cells were very small, or you didn’t use enough snapshots for a representative sample, or that your simulations were not under constant pressure, or not equilibrated.  Again, you would have to use your detailed knowledge of how you got your data to decide for yourself whether it needs normalization.  It is not really a Chimera question, other than that we can clarify that Chimera does not automatically normalize, it just shows the raw data from the file.
Elaine

> On Jun 9, 2016, at 2:14 AM, Nidhi Batra <nidhi.batra at igib.in> wrote:
> 
> Dear Elaine
> Thanks for the input. You are right, I calculated the water density through VMD. I kept all the parameters same for the calculation as well for the simulation for all the proteins. According to your suggestion, I should keep the contour level same for all the proteins, irrespective of the range? Because the range varies a lot, for some it is 0-2.5, for others it is 0-4.95 and so does the histogram. Is the contour level connected to range in any way?
> 
> Thanking you
> 
> Yours sincerely
> -- 
> Nidhi Batra
> DBT-Research Associate
> Institute of Genomics and Integrative Biology (IGIB),
> Mathura Road, Sukhdev Vihar
> New Delhi 110020
> 
> 
> On Wed, Jun 8, 2016 at 10:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Nidhi,
> It depends on how you calculated the dx files. It sounds like you did it in some other program (not Chimera).
> 
> If you just counted the number of times a water was inside a grid cell, then you would need to normalize for different grid cell sizes (unless they were the same), and the number of samples (frames or snapshots) used for each protein (unless they were also the same).  Also I guess you would probably want to make sure the simulations of the different proteins were under the same conditions.
> 
> After correcting for those differences, if any, you could just use a consistent contour level for all the proteins.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jun 8, 2016, at 5:35 AM, Nidhi Batra <nidhi.batra at igib.in> wrote:
> 
> > 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 misleading.
> >
> > Thanking you




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