VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 21 2019 - 09:27:22 CST

If what you want only needs to be accurate to the nearest voxel, you could
use one map to mask another. You would have to choose a density threshold
that you consider to be "occupied" and then any voxels above that value
would contribute to the volume. Essentially you'd be multiplying to
binary maps together, and then counting the up the resulting "1s".
If you want to do something more sophisticated with partial occupency
of voxels then you could probably do something similar, but there
would undoubtably be some density renormalization required.

Best,
  John Stone

On Thu, Nov 21, 2019 at 01:39:16PM +0200, Saumik Sen wrote:
> Dear VMD community,Â
> Is it possible to calculate the overlap of two volume maps?
> I have generated the volume maps for each points (geometries) along a
> molecular dynamics trajectory. I want to calculate how much the volumes of
> two geometries overlap with each other. Is it possible to do?Â
> Thanks in advance,
> Best Regards,
> Saumik
> Â --
> Saumik Sen
> Ph. D., Chemistry
> [1]Email-smksenn_at_gmail.com
> Â Â Â Â Â [2]saumik.sen_at_mail.huji.ac.ilÂ
>
> References
>
> Visible links
> 1. mailto:Email-smksenn_at_gmail.com
> 2. mailto:saumik.sen_at_mail.huji.ac.il 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/