VMD-L Mailing List

From: Saumik Sen (smksenn_at_gmail.com)
Date: Wed Nov 27 2019 - 14:45:34 CST

Dear John,

Thank you for your quick reply and sorry for my late response. Meanwhile I
was trying to solve the problem as you have instructed. Please check my
replies/doubts as following,

If what you want only needs to be accurate to the nearest voxel, you could
> use one map to mask another.

In the VMD manual it is written that "The mask map is typically used in
combination with other maps in order to hide/mask data that is far from a
region of interest". Therefore, if I generate density maps for two frames
(geometries) of a trajectory and subsequently generate mask maps (within a
cutoff value), these should correspond to the volume maps for the two
respective geometries inside the specified cutoff region. Is this correct?

I looked into the "mask" option in volmap but I am not sure how to use it
in combination with other maps. Do you have any documentation or some
examples where I can find it?

> 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.

I used the following script to generate volume maps for each geometry along
a trajectory,

mol load pdb input.pdb
set sel [atomselect top "all"]
set nf [ molinfo top get numframes ]
for {set i 0} {$i < $nf} {incr i} {
    puts "frame $i of $nf"
    $sel frame $i
    volmap density $sel -res 1.0 -radscale 1.0 -weight mass -mol top -o
output.$i.dat.dx
}
$sel delete
exit

If I replace the option "mass" with "occupancy" then it doesn't generate
the isosurface. Could you please check whether the above volmap script is
correct or not keeping my problem in mind?

Essentially you'd be multiplying to binary maps together, and then counting
> the up the resulting "1s".

By two binary maps do you mean the two maps that will be generated by using
the "mask" option on two density maps?

> 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.

I want to get some numbers or maps that will clearly demonstrate how much
my molecule is rotating along the trajectory. I have calculated the RMSD
but that seems to be not a good parameter in my case. Therefore, I want to
calculate how much the volume of the molecule is changing along the
trajectory. Currently I am not sure whether I will encounter any partial
occupancy of voxels.

Thank you for your help,

Best Regards,
Saumik

On Thu, Nov 21, 2019 at 5:27 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
Saumik Sen
Ph. D., Chemistry
Phone- +919619589914
Email-smksenn_at_gmail.com
          saumik.sen_at_mail.huji.ac.il