VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 13 2019 - 13:15:20 CST

Hi,
  I have written answers to your questions below:

On Wed, Nov 27, 2019 at 10:45:34PM +0200, Saumik Sen wrote:
> 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?

If you're computing the maps entirely using volmap, you shouldn't need to
use any mask maps since you can simply select appropriate parameters when
you compute the maps in the first place.

> > 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?

That's not the right approach, you've confused "occupancy" being used as
a per-atom "weight" vs. an "occupancy map". You don't want to use the
occupancy field as a weight, rather, you might want to compute an
occupancy map...

Rather than using "volmap density", you could use "volmap occupancy", that
creates a different kind of map altogether.

> 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?

You could do that, or you could just multiply the maps together and sum the
resulting voxel values, normalize and/or threshold them. Do you understand
these concepts? If not, you may want to use a different approach that is
more familiar to you. You'll have to work out the details for yourself,
the concepts are simple, there's no ready-made tool for this in VMD, so
you are essentially having to write the tool you want/need using what VMD
can compute for you already. If this isn't something you're comfortable
with, then you might want to look harder to find an already-developed tool
for this sort of calculation. One may exist if you look long/hard enough...

> > 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.

Well, I think you can get various metrics of value this way, but you'll
have to decide exactly what you want and you'll have to get deep enough
into scripting/programming to write the analysis code needed to get it.

Best regards,
  John Stone

>
>
> 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 

-- 
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/