VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 29 2008 - 10:03:46 CDT

Hi,
  You may also need to add "molinfo $index set frame $frame" to your script.
For the purposes you seem to have intended, all of the vmd_frame variable
tracing is just a distraction, and isn't really relevant to what you're doing.
You can also replace the old call to vmd_calculate_structure with the more
current approach of "mol ssrecalc $index". Try cleaning up your code and
eliminating the leftover parts from sscache, and focus on writing a simpler
script that just loops over frames, calls "mol ssrecalc" and does the
secondary structure queries you're interested in.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 28, 2008 at 10:04:56PM -0400, Margaret S. Cheung wrote:
> Hi Alexander and VMD developer and wizards,
> Thank you for the reply. Qian and I took a look at it and it still
> didn't work and this issue was not resolved. Do you have other suggestions?
> Thank you.
> Best,
> Margaret
>
> Alexander A. Vakhrushev wrote:
> >Hi Qian!
> >
> >Try to add after frame selection command
> >
> > # get the protein atoms
> > set sel [atomselect $index "protein"]
> > $sel frame $name
> >
> >following line, updating your selection
> >
> > $sel update
> >
> >2008/9/27, qwang_at_mail.uh.edu <qwang_at_mail.uh.edu>:
> >
> >>Hi,
> >>
> >>I am using the script (sscache.tcl) to compute the secondary structures
> >>of a
> >>protein in a trajectory. I follow the instructions from
> >>http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/sscache.tcl.
> >>
> >>I wrote a tcl script as an attached and tried to execute it on a
> >>trajectory,
> >>but it only showed the results of the last frame. I tried my script using
> >>different modules (functions) but it looped correctly, so I am quite sure
> >>that I have been including the loop correctly.
> >>
> >>Could you please help me take a look at this script and see if there is
> >>something that I could have overlooked?
> >>
> >>Thank you.
> >>Sincerely,
> >>Qian
> >>
> >>
> >>
> >>
> >
> >
> >
>
> --
> Margaret S. Cheung
> Assistant Professor
> Department of Physics
> 629C Science and Research 1
> University of Houston
> Houston, TX 77204-5005
> email: mscheung_at_uh.edu
> (O)713-743-8358 (F)713-743-3589
> http://www.phys.uh.edu/~mscheung/ 

-- 
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