VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 30 2004 - 14:05:36 CDT

Axel,
  Even better, as it turns out, there's already a Tcl command
to delay for a specified number of milliseconds.

Compare this:
  foreach {i} [info functions] {
    puts $i;
  }

To this:
  foreach {i} [info functions] {
    # sleep for 250 milliseconds
    after 250
    puts $i;
  }

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 30, 2004 at 01:32:28PM -0500, John Stone wrote:
>
> Axel,
> We've already got a portable millisecond delay routine in VMD itself,
> so if you think it would be useful to have that accessible via scripting
> I could probably add a Tcl binding for it.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 30, 2004 at 09:25:26AM +0200, Axel Kohlmeyer wrote:
> >
> > On Tue, 29 Jun 2004, Heshe Peshkin wrote:
> >
> > heshe,
> >
> > perhaps you can live with just loading all your
> > configurations as separate molecules and then
> > use a small tcl script to loop over the molecule
> > indices and toggle the displayed status for the
> > molecules.
> >
> > please see the attached vmd script.
> >
> > this will load 5 frames as molecules and then define a procedure
> > molmovie that takes two (optional) arguments, the
> > number of loops (default 10) and the delay between
> > two frames (default 1 second).
> >
> > please modify it appropriately and then type
> >
> > molmovie 1 0
> >
> > at the vmd prompt. you should then see vmd display
> > all loaded molecules, one after the other, as fast
> > as possible.
> >
> > please let me know, if this works for you.
> >
> > regards,
> > axel kohlmeyer.
> >
> > p.s.: for this kind of setup it would be nice, if VMD
> > would allow sub-second precision delays with the sleep
> > command.
> >
> > on a wide variety of unix platforms the following code
> > has worked very well for me. i don't know how well this
> > translates to windows, though.
> >
> >
> >
> > /*! sleep for some milliseconds */
> > void ms_sleep(const int ms) {
> > struct timeval tv;
> >
> > // convert milliseconds into seconds and microseconds
> > tv.tv_sec = ms / 1000; tv.tv_usec = 1000 * (ms % 1000);
> >
> > if (select(0, NULL, NULL, NULL, &tv) < 0) {
> > cerr << "ms_sleep: select error: "
> > << strerror(errno) << endl;
> > }
> > }
> >
> >
> >
> > HP> Hello.
> > HP>
> > HP> I have the following problem: I am trying to make an "inbox" (wrapped)
> > HP> movie of a polymer system with periodic boundaries. Contrary to the
> > HP> unwrapped version, where I only have one PSF file for all the steps and
> > HP> all the frames can be incorporated into one unit, here each step has its
> > HP> own PSF (connectivity) and PDB (coordinates) file and each frame behaves
> > HP> as separate. It is important that I make the movie exactly in the wrapped
> > HP> version because there are some association going on in the system and I
> > HP> might not capture all of it if I am looking at the unwrapped version (for
> > HP> example if two elements are exactly one box away i will see them as
> > HP> separate but in fact they will be associated).
> > HP> Working with dynamic bonds doesn't help because it creates artificial
> > HP> bonds between neighboring but not connected atoms, and between the
> > HP> associating elements as well (or if the cutoff distance is too big then a
> > HP> part of the existing bonds disappears). And last but not least, loading
> > HP> all the frames, opening them one by one and rendering snapshots will take
> > HP> forever.
> > HP> So - how can I make my movie?
> > HP>
> > HP> Thanks in advance for any ideas.
> > HP>
> > HP> __________________________________________________
> > HP> Do You Yahoo!?
> > HP> Tired of spam? Yahoo! Mail has the best spam protection around
> > HP> http://mail.yahoo.com
> > HP>
> > HP>
> >
> > --
> >
> >
> > =======================================================================
> > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_rub.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > =======================================================================
> >
>
> >
> > # create a movie from separate molecules.
> >
> >
> > # load frames as separate molecules. of course in case of psf+pdb files,
> > # this has to be 'mol new step-1.psf ; mol addfile step-1.pdb'
> > mol new step-1.pdb
> > mol new step-2.pdb
> > mol new step-3.pdb
> > mol new step-4.pdb
> > mol new step-5.pdb
> >
> > # now disable all molecules
> > for {set i 0} {$i < [molinfo num]} {incr i} {
> > mol off $i
> > }
> >
> >
> > # now create an animation by sequentially
> > # turning the molecules on and off
> > # default is to wait a second between frames
> > proc molmovie {{loops 10} {delay 1}} {
> > global molmovie_last
> >
> > set nmols [molinfo num]
> > display update on
> > if {![info exists molmovie_last]} {
> > set molmovie_last [expr $nmols - 1]
> > }
> >
> > for {set i 0} {$i < $loops} {incr i} {
> > for {set n 0} {$n < $nmols} {incr n} {
> > display update
> > display update ui
> > mol on $n
> > mol off $molmovie_last
> > set molmovie_last $n
> > sleep $delay
> > }
> > }
> > }
>
>
> --
> 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 

-- 
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