From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Fri Feb 22 2008 - 11:40:52 CST

Hi Axel,

Thanks for letting me know that animate is obsolescent and providing
me the script. It works nicely when I remove the "set" in line
"molinfo top set frame $i".

Thanks again,
Jufang

On Thu, Feb 21, 2008 at 11:40 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Thu, Feb 21, 2008 at 8:06 PM, Jufang Shan <jufang.shan_at_gmail.com> wrote:
> > Hi,
> >
> > I wanted to monitor the helicity change of a protein during
> > simulations and write a script as the following:
> >
> > mol new pro.psf
> > animate read dcd pro.dcd beg 0 end -1 skip 10 waitfor -1
>
> animate read is obsolescent. please use mol addfile and waitfor all
>
>
>
> > set outfile [open helicity.dat w]
> >
> > set sel [atomselect top "protein and name CA"]
> >
> > animate goto start
>
> here you should use molinfo top set frame 0
>
>
> > set nf [molinfo top get numframes]
> > for {set i 0 } {$i < $nf } { incr i } {
> > animate goto $i
>
> molinfo top set frame $i
> $sel set frame $i
>
>
> > mol ssrecalc top
> > set helicity [$sel get structure]
> > puts $outfile "$helicity"
> > }
> >
> > close $outfile
> >
> > But in the output file, the secondary structures for all the frames
> > are the same although they are different when I checked them in tcl
> > console.
>
> you have to step molinfo and the selection frame.
> if that does not work, you may need an display update.
> check the docs for details.
>
> cheers,
> axel.
>
>
> >
> > Can anyone tell me why $helicity does not get updated in the loop?
> >
> > Many thanks,
> > Jufang
> >
> > ------------------------------
> > Jufang Shan
> > Postdoctoral Associate
> > Department of Physiology & Biophysics
> > Weill Medical College of Cornell University
> > New York, NY 10065
> >
> >
>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>