[Chimera-users] density maps

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 24 12:15:10 PST 2017


Of course, the grid spacing that you choose when calculating the occupancy map also matters, i.e., best to use the same spacing for the maps you are planning to compare.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>

Elaine

> On Feb 24, 2017, at 9:09 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Antonio,
> Don’t worry, you aren’t bothering me  :-)
> 
> Yes, in the Volume Viewer dialog, step 1 is recommended for seeing your data in full resolution.  The range is really for your information, you would not change the range itself, but drag the vertical bar lon the histogram left or right to control the isosurface level in the 3D display.  The current position of that vertical bar is reported as the “level” under the histogram. Or, you can just enter a different value as the “level” and it will move the vertical bar to that place on the histogram.
> 
> The only other advice I have for comparing the occupancy in your two simulations is to remember that the map values are just counts, and they are not normalized by the number of observations.  So either you would need to use the same number of frames from the two simulations, or remember to correct for different numbers of frames.  For example, if you used 100 frames from one simulation, a count (map value) of 5 means occupancy near that grid point 5% of the time, but if you used 200 frames from the other simulation, you would need a map value of 10 to mean occupancy 5% of the time.
> 
> 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 Feb 24, 2017, at 1:09 AM, Antonio Coluccia <antonio.coluccia at uniroma1.it> wrote:
>> 
>> Dear Elaine
>> thank you very much for your help.
>> Soory i am boring you
>> I would like to compare the frequency density maps of two different dynamics simulations and to make the comparison easer i thought to set at the volume viewer dialog the step to the higher value (16). If i understood well this sounds to be an error. 
>> I should fix the step at 1 and to use the range field to highlight the most “frequent” surface. This should be more accurate!
>> Do you have any other advise to obtain a meaning comparison of the computed density maps?
> 
> 
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