VMD-L Mailing List

From: qwang_at_mail.uh.edu
Date: Mon Sep 29 2008 - 11:44:35 CDT

Hi,

Thank you very much for the tip. Now it works after your suggestion.

Sincerely yours,
Wang Qian

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Monday, September 29, 2008 11:24 am
Subject: Re: vmd-l: question about sscache
To: "Margaret S. Cheung" <mscheung_at_uh.edu>
Cc: "Alexander A. Vakhrushev" <makaveli.lcf_at_gmail.com>, "qwang_at_mail.uh.edu" <qwang_at_mail.uh.edu>, vmd-l_at_ks.uiuc.edu

>
> 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
> variabletracing 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
>