[Chimera-users] query regarding volume viewer
nidhi.batra at igib.in
Thu Jun 9 02:14:46 PDT 2016
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?
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 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
> > 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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