VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 02 2018 - 12:00:45 CDT

Hi,
  I have just removed you from the VMD-L mailing list. You may receive
a couple of pending messages, but today should be the last day you get any.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 01, 2018 at 10:59:12AM +0100, Christine Horejs wrote:
> Thank you
> On 1 August 2018 at 09:39, Ashar Malik <[1]asharjm_at_gmail.com> wrote:
>
> Again the same problem.Â
> You useÂ
> [measure rmsd $sela $selb]
> it should be measure rmsf
> Secondly - this is not how rmsf is calculated.Â
> the simplest way to calculate the RMSF isÂ
> load your trajectory
> make 1 selection (just 1) holding your atoms of interest. (eg.
> roi_atoms)
> now useÂ
> measure rmsf $roi_atomsÂ
> if you use the above command all frames in your trajectory will be used
> to calculate the rmsf.Â
> if you want to limit them as I think you are trying to do (not exactly
> sure) add frame numbersÂ
> soÂ
> measuer rmsf $roi_atoms 50 60Â
> with the above command only frame 50 through 60 will be used.Â
> keep in mind the difference in math between RMSD and RMSF.Â
> RMSD is per frame -- so you get a trend
> RMSF is per set of frames -- so you will get just 1 value (doesn't
> matter if you use 50 frames or 5000).
> check this page for more details:
> [2]https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html
> On Wed, Aug 1, 2018 at 4:17 PM Sasthi Charan Mandal
> <[3]sasthi.phys_at_gmail.com> wrote:
>
> Oh I am sorry. It will be rmsf. So it would be very much helpful for
> me if you would provide me the tcl script. I have one script but using
> this script I could not get the expected result. Could you please
> check my script and let me know what is wrong here?
> The script is:
> set outDataFile [open rmsf.dat w]
> for {set r 491} {$r <= 512} {incr r} {
> set sela [atomselect top "resid $r"]
> set selb [atomselect top "resid $r"]
> $sela frame 0
> for {set f 0} {$f<=9990} {incr f} {
> $selb frame $f
> display update
> set val [measure rmsd $sela $selb]
> set resid $r
> puts $outDataFile "$resid $f $val"
> }
> }
> close $outDataFile
> return
> }
> On Wed, Aug 1, 2018 at 6:10 AM, Ashar Malik <[4]asharjm_at_gmail.com>
> wrote:
>
> The subject of the mail is asking for rmsf where as in the email you
> say rmsd. So which one?Â
> Rmsd and rmsf can both be obtained using the "measure" command.Â
> Remember to remove translational and rotational effects from your
> system prior to their use.Â
> Write back if this doesn't help and an example "script" can be
> provided.
> On Aug 1, 2018 00:06, "Sasthi Charan Mandal"
> <[5]sasthi.phys_at_gmail.com> wrote:
>
> I want to calculate the rmsd of each base pair of dna over a
> specified time.. So if anyone have the script I will be thankful
> to you if you provide me.
> Thanks
>
> --
> Best,
> /A
>
> References
>
> Visible links
> 1. mailto:asharjm_at_gmail.com
> 2. https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html
> 3. mailto:sasthi.phys_at_gmail.com
> 4. mailto:asharjm_at_gmail.com
> 5. mailto:sasthi.phys_at_gmail.com 

-- 
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/