VMD-L Mailing List

From: Saumik Sen (smksenn_at_gmail.com)
Date: Mon Dec 02 2019 - 07:42:15 CST

Dear John,

Just a gentle reminder that I am awaiting your reply to my earlier email.

Thank you,

Best Regards,
Saumik

On Wed, Nov 27, 2019 at 10:45 PM Saumik Sen <smksenn_at_gmail.com> 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?
>
>
>> 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
>
> 

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