VMD-L Mailing List

From: h9826299_at_hkusua.hku.hk
Date: Wed Jan 18 2006 - 16:19:52 CST

Dear John,

  Thank you very much for the quick reply and it really works!

  Thanks a lot.

cheers,
Chung

Department of Zoology,
The University of Hong Kong

>
> 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
>