VMD-L Mailing List

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Mon Nov 19 2012 - 09:04:07 CST

What about Timeline plugin?

http://www.ks.uiuc.edu/Research/vmd/plugins/timeline/

read section 15.

On 19 November 2012 15:05, Bjørnar Jensen <bje076_at_ift.uib.no> wrote:

> Hello,
>
> a quick untested script:
> ---------------------------------------------------------------------------
> //Selection for the two atoms of choice
> set A [atomselect top "index xxx"]
> set B [atomselect top "index yyy"]
>
> //Get number of frames loaded into top molecule
> set numframes [molinfo top get numframes]
>
> //Open file for writing output
> set output [open "Distance.dat" w]
> //Write a short header to the file
> puts $output "Frame\tDistance"
>
> //Loop over all frames
> for {set i 0} {$i < $numframes} {incr i} {
> //Advance to frame $i
> animate goto $i
> //Get the positions, find the vector from B to A, calculate the length
> of vector
> set distance [veclength [vecsub [lindex [$A get {x y z}] 0] [lindex
> [$B get {x y z}] 0] ]
> //Write the frame number and distance to file. Separated by a
> 'tabulator'
> puts $output "$i\t$distance"
> }
> //Close and clean up everything
> $output close
> $A delete
> $B delete
> unset numframes
> unset output
> --------------------------------------------------------------------------
>
> This is likely to contain a bug or two and may be inefficient.
> It should, at least, get you started.
>
> The whole "how do I write a script" is found in the user guide and in
> several tutorials. If you are using VMD on a day to day basis learning
> to write scripts for VMD should be mandatory.
>
>
> Best regards,
> Bjørnar Jensen
>
> On 2012-11-17 14:33, 肖富贵 wrote:
>
> Hi guys,
> I have 1000 conformations of a protein, and i want to measure the distance
> between two atoms in this protein.
> I know the "measure bond" command can measure the disance of two atoms.
> However, i have 1000 conformations, and i cannot measure each one by one,
> so can anyone tell me how to write a script?
> Best wishes
> Xiao Fugui
>
>
>
> 

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/