VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 18 2006 - 16:04:52 CST

Hi,
  It seems that you've encountered a bug of some sort, I'll have to
look into this. For now add this line to the end of the loop over
frames:
  display update ui

That seems to cure the problem for the time being with VMD 1.8.4 test builds.
I'll have to look into why that isn't working when the dislay isn't also
being updated.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 19, 2006 at 05:22:41AM +0800, h9826299_at_hkusua.hku.hk wrote:
> Hi,
>
> I've used John's script (below) to calculate the ss composition of every frame
> of a traj. But it's strange that the results for every frame is the same, which
> is the ss composition of the last frame. Anybody, knows the reason? The the ss
> assignment needed to be updated? I've try the sscache.tcl for updating the ss
> but it don't work, though it works for the animation with changing ss.
> Thanks!!
>
> ### The script I used ###
>
> proc calcsscounts {} {
> set numframes [molinfo top get numframes]
> set sel [atomselect top "name CA"]
> for {set frame 0} {$frame < $numframes} {incr frame} {
> animate goto $frame
> vmd_calculate_structure top
> $sel frame $frame
> $sel update
> set helixlist [$sel get alpha_helix]
> set sheetlist [$sel get sheet]
> set helixcount 0
> foreach i $helixlist { incr helixcount $i }
> set sheetcount 0
> foreach i $sheetlist { incr sheetcount $i }
> puts "Frame: $frame"
> puts " Alpha helix count: $helixcount"
> puts " Beta sheet count: $sheetcount"
> }
> $sel delete
> }
>
> cheers,
> Chung
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078