VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 22 2008 - 10:15:00 CDT

David,
  You had an extra "top" in your "mol addfile" line which was
causing the waitfor all to be ignored:
  mol addfile ./XTC/trajectory.xtc top waitfor all

The corrected command is:
  mol addfile ./XTC/trajectory.xtc waitfor all

That works for me.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 22, 2008 at 04:35:29PM +1000, David Poger wrote:
> Hi John
>
> Thanks for your help.
>
> David
>
>
>
> The script is:
>
> #################
> # command: vmd -dispdev text -e myscript.tcl
>
> # Axes off
> axes location off
> display antialias on
> display projection Orthographic
>
> # Load the gro file
> mol new firstframe.gro
> mol delrep 0 top
>
> # water: blue lines
> mol selection water
> mol representation Lines
> mol color ColorID 22
> mol addrep 0
> # other: white licorice
> mol selection {not water}
> # Licorice a n m, a=bond radius, n,m=sphere/bond resolutions
> mol representation Licorice 0.2 50 50
> mol color ColorID 8
> mol addrep 0
> # P: yellow vdw
> mol selection {name P}
> mol representation VDW 1.0 50
> mol color ColorID 4
> mol addrep 0
>
> # Periodic images
> mol showperiodic top 0 xzX
> mol numperiodic top 0 3
> mol showperiodic top 1 xzX
> mol numperiodic top 1 3
> mol showperiodic top 2 xzX
> mol numperiodic top 2 3
>
> # Center
> rotate x by 90
> scale by 1.5
> translate by 1 1.4 0
>
> display resize 834 834
>
> # Load the trajectory
> animate style once
> mol addfile ./XTC/trajectory.xtc top waitfor all
>
> set nframes [molinfo top get numframes]
>
> set frame 0
>
> # Loop over the trajectory
> for {set i 0} {$i < $nframes} {incr i } {
> # go to the given frame
> animate goto $i
> # force display update
> display update
> puts "frame $i of $nframes"
> # filename
> set filename ./MOVIE/anim_[format "%04d" $frame].ppm
> # take the picture
> render snapshot $filename
>
> incr frame
> }
>
> exit
>
>
>
>
> John Stone wrote:
> >Hi,
> > The mol addfile command in your script doesn't have the
> >"waitfor all" option specified, so at least the version of the
> >script you sent will not work the way you expect. Please send me
> >the version of the script you've tried previously that had
> >"waitfor all" added so I can see exactly what you're doing,
> >undoubtably there's a small error lurking, still waiting to be found.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Jul 22, 2008 at 02:58:48PM +1000, David Poger wrote:
> >
> >>Hi
> >>Thanks for the tip but I already tried 'waitfor all' and it doesn't
> >>change anything. While the trajectory is loading, VMD still tries to
> >>render the frames as if 'waitfor all' wasn't there.
> >>
> >>Cheers
> >>David
> >>
> >>John Stone wrote:
> >>
> >>>Hi,
> >>> When you load your trajectory, you should be adding
> >>>the "waitfor all" option to your load commands:
> >>> mol new foo.dcd waitfor all
> >>>
> >>>This will prevent VMD from continuing with your script
> >>>until the entire file has been loaded. The problems you
> >>>describe below are caused by running your script while file
> >>>loading is still in progress.
> >>>
> >>>Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Tue, Jul 22, 2008 at 11:19:01AM +1000, David Poger wrote:
> >>>
> >>>
> >>>>Hello
> >>>>
> >>>>I wrote a Tcl script to do a really basic thing: loading a trajectory
> >>>>and taking a snapshot of each frame. However, it doesn't work. It
> >>>>seems the number of frames isn't correct. There are excatly 740 frames
> >>>>(and my file is not corrupted) and VMD invariably finds 4 frames (but,
> >>>>if after the trajectory is loaded, VMD finds the correct number of
> >>>>frames if I type 'molinfo top get numframes' in the VMD console window).
> >>>>Also, if I run VMD interactively (by typing 'vmd -e myscript.tcl'), the
> >>>>first 4 frames are effectively rendered but if I run VMD in batch ('vmd
> >>>>-dispdev text -e myscript.tcl'), the 4 files corresponding to the
> >>>>rendering are created but they are empty...
> >>>>
> >>>>Could anyone help me, please?
> >>>>
> >>>>Thanks,
> >>>>
> >>>>David
> >>>>
> >>>>
> >>>>
> >>>>Here is the script that I use:
> >>>>
> >>>>#################
> >>>># command: vmd -dispdev text -e myscript.tcl
> >>>>
> >>>># Axes off
> >>>>axes location off
> >>>>display antialias on
> >>>>display projection Orthographic
> >>>>
> >>>># Load the gro file
> >>>>mol new firstframe.gro
> >>>>mol delrep 0 top
> >>>>
> >>>># water: blue lines
> >>>>mol selection water
> >>>>mol representation Lines
> >>>>mol color ColorID 22
> >>>>mol addrep 0
> >>>># other: white licorice
> >>>>mol selection {not water}
> >>>># Licorice a n m, a=bond radius, n,m=sphere/bond resolutions
> >>>>mol representation Licorice 0.2 50 50
> >>>>mol color ColorID 8
> >>>>mol addrep 0
> >>>># P: yellow vdw
> >>>>mol selection {name P}
> >>>>mol representation VDW 1.0 50
> >>>>mol color ColorID 4
> >>>>mol addrep 0
> >>>>
> >>>># Periodic images
> >>>>mol showperiodic top 0 xzX
> >>>>mol numperiodic top 0 3
> >>>>mol showperiodic top 1 xzX
> >>>>mol numperiodic top 1 3
> >>>>mol showperiodic top 2 xzX
> >>>>mol numperiodic top 2 3
> >>>>
> >>>># Center
> >>>>rotate x by 90
> >>>>scale by 1.5
> >>>>translate by 1 1.4 0
> >>>>
> >>>>display resize 834 834
> >>>>
> >>>># Load the trajectory
> >>>>animate style once
> >>>>mol addfile ./XTC/trajectory.xtc top
> >>>>
> >>>>set nframes [molinfo top get numframes]
> >>>>
> >>>>set frame 0
> >>>>
> >>>># Loop over the trajectory
> >>>>for {set i 0} {$i < $nframes} {incr i } {
> >>>> # go to the given frame
> >>>> animate goto $i
> >>>> # force display update
> >>>> display update
> >>>> puts "frame $i of $nframes"
> >>>> # filename
> >>>> set filename ./MOVIE/anim_[format "%04d" $frame].ppm
> >>>> # take the picture
> >>>> render snapshot $filename
> >>>>
> >>>> incr frame
> >>>>}
> >>>>
> >>>>exit
> >>>>
> >>>>
> >>>>--
> >>>>
> >>>>_________________________________________________
> >>>>David POGER, Ph.D.
> >>>>Postdoctoral Research Fellow
> >>>>Molecular Dynamics Group
> >>>>School of Molecular and Microbial Sciences (SMMS)
> >>>>Chemistry Building (#68)
> >>>>The University of Queensland
> >>>>Brisbane, QLD 4067
> >>>>Australia
> >>>>
> >>>>Email: d.poger_at_uq.edu.au
> >>>>Tel: +61 7 3365 7562
> >>>>Fax: +61 7 3365 3872
> >>>>
> >>>>
> >>>>** Notice: Unless stated otherwise, this e-mail represents only the
> >>>>views of the Sender and not the views of The University of Queensland.
> >>>>
> >>>>
> >>>
> >>>
> >>--
> >>
> >>_________________________________________________
> >>David POGER, Ph.D.
> >>Postdoctoral Research Fellow
> >>Molecular Dynamics Group
> >>School of Molecular and Microbial Sciences (SMMS)
> >>Chemistry Building (#68)
> >>The University of Queensland
> >>Brisbane, QLD 4067
> >>Australia
> >>
> >>Email: d.poger_at_uq.edu.au
> >>Tel: +61 7 3365 7562
> >>Fax: +61 7 3365 3872
> >>
> >>
> >>** Notice: Unless stated otherwise, this e-mail represents only the views
> >>of the Sender and not the views of The University of Queensland.
> >>
> >
> >
>
> --
>
> _________________________________________________
> David POGER, Ph.D.
> Postdoctoral Research Fellow
> Molecular Dynamics Group
> School of Molecular and Microbial Sciences (SMMS)
> Chemistry Building (#68)
> The University of Queensland
> Brisbane, QLD 4067
> Australia
>
> Email: d.poger_at_uq.edu.au
> Tel: +61 7 3365 7562
> Fax: +61 7 3365 3872
>
>
> ** Notice: Unless stated otherwise, this e-mail represents only the views
> of the Sender and not the views of The University of Queensland. 

-- 
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