[Chimera-users] query regarding volume viewer

[Nidhi Batra]

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
> >
> > 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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