VMD-L Mailing List

From: Samir Unni (srunni_at_gmail.com)
Date: Mon Jul 21 2008 - 11:35:51 CDT

Hi,

Yes, that fixed the problem! Is the state variable that's missing one of the
two (or both) that I initialized in my modified version of vmdmovie.tcl?

Also, even if this problem is fixed, it seems that the 'makemovie' method
cannot be used unless a GUI is running (i.e. starting vmd with '-dispdev
none' or '-dispdev text' won't work). That isn't an option in my case, since
I will be using the state files I'm creating with instances of VMD that are
on servers where X is not present. Is there a scriptable workaround for this
issue as well?

Thanks,

Samir

On Mon, Jul 21, 2008 at 10:31 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> I think I've reproduced the problem you encountered, try doing this
> and see if you get different behavior:
>
> Run the command line script as before, and verify that you get
> the 1 frame movie, as before.
>
> Then, after having done this, try opening the GUI for the movie
> maker, through the Extensions->Visualization->Movie Maker menu.
> Once the window is opened, try running the script at the command
> line again. Let me know if it works correctly for you the second
> time. I believe that the issue here is an internal state variable
> that's only being properly initialized when the GUI has been opened.
> It will be easy to workaround/fix with one or two extra lines of
> scripting if that's all that's causing your problem.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Mon, Jul 21, 2008 at 07:57:59AM -0500, Samir Unni wrote:
> > Hi,
> >
> > Sorry I'm so late in getting back to you. Anyway, that code doesn't work
> on
> > the Mac either. It just briefly opens the video (for one frame, I think)
> and
> > then closes. I'm using the 1.8.6 version of VMD?is that the one you're
> > using?
> >
> > Thanks,
> >
> > Samir
> >
> >
> > On Thu, Jul 17, 2008 at 10:19 PM, Samir Unni <srunni_at_gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I tried that, but it didn't work for me. When I attempted to play the
> video
> > > file with MPlayer, the window appeared for a second and then
> disappeared,
> > > just like before. I think only one frame is being recorded.
> > >
> > > Right now I'm trying this on my Linux machine at home, but I'll try it
> > > again on the Mac at work tomorrow morning and see if it works there.
> > > However, this was the exact same problem I was previously having on the
> Mac,
> > > so I don't think it will. If it's working for you, it might have
> something
> > > to do with the state file I'm using, which I created by importing the
> DX
> > > output file from APBS into VMD.
> > >
> > > I had meant to attached the modified version of vmdmovie.tcl to the
> last
> > > email; it's attached now, if you want to take a look.
> > >
> > > Thanks,
> > >
> > > Samir
> > >
> > >
> > >
> > > On Thu, Jul 17, 2008 at 9:56 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > >>
> > >> Hi,
> > >> I'm not sure how you changed your copy of the vmdmovie.tcl file,
> > >> but I'd ask that before we delve any further, that you first try the
> > >> original vmdmovie plugin and the command I emailed earlier. If that
> > >> works for you, then we can proceed with debugging whatever has been
> > >> changed in your modified version. Starting with your modified version
> > >> is likely to add more confusion so I'd rather leave that for a second
> > >> step. Please try the example sequence I sent earlier and let me know
> > >> if that works with the unmodified script on your system, or not.
> > >>
> > >> Cheers,
> > >> John Stone
> > >> vmd_at_ks.uiuc.edu
> > >>
> > >> On Thu, Jul 17, 2008 at 09:18:24PM -0500, Samir Unni wrote:
> > >> > Hi,
> > >> >
> > >> > That character resulted from an issue with the email formatting; it
> was
> > >> not
> > >> > actually part of the command that I used. The command I used was:
> > >> >
> > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas 1fas
> ppmtompeg
> > >> > snapshot 10
> > >> >
> > >> > Also, I sent an update a few hours after my initial email, but it
> seems
> > >> not
> > >> > to have made it onto the mailing list. I will repost it here:
> > >> >
> > >> > --------------------
> > >> > I've got a small update. I slightly changed vmdmovie.tcl, so that
> the
> > >> > framerate can be passed to the 'makemovie' method. When I did this,
> > >> defined
> > >> > 'framerate' as the extra variable being passed now, and defined
> > >> 'numframes'
> > >> > as the product of the framerate and the duration, a working movie
> was
> > >> > created. Though it would seem that only 2 of these 3 variables need
> to
> > >> be
> > >> > defined for the program to be able to determine the 3rd, when I
> > >> eliminated
> > >> > any one of them, the movie was not generated correctly. I have
> attached
> > >> the
> > >> > working version of vmdmovie.tcl, if anyone wants to look at it.
> > >> >
> > >> > I would still like to know if there is a way to generate a movie
> from
> > >> the
> > >> > command line without modifying any files that are a part of VMD, if
> > >> > possible.
> > >> > --------------------
> > >> >
> > >> > I still have not found a workaround for this issue. The command I am
> > >> using
> > >> > now is:
> > >> >
> > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas 1fas
> ppmtompeg
> > >> > tachyon 5 40
> > >> >
> > >> > Thanks,
> > >> >
> > >> > Samir Unni
> > >> >
> > >> >
> > >> > On Thu, Jul 17, 2008 at 5:02 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > >> >
> > >> > >
> > >> > > Hi,
> > >> > > The ">" character you have in your example below shouldn't be
> there,
> > >> > > that would cause some trouble for sure.
> > >> > >
> > >> > > Here's a proper example command sequence to make a movie from text
> > >> mode:
> > >> > > package require vmdmovie
> > >> > > mkdir /tmp/mytmpdir
> > >> > > ::MovieMaker::makemovie /tmp/mytmpdir example ppmtompeg snapshot
> 10
> > >> > >
> > >> > > This worked fine for me.
> > >> > >
> > >> > > Try that and let me know how it goes.
> > >> > >
> > >> > > Cheers,
> > >> > > John Stone
> > >> > > vmd_at_ks.uiuc.edu
> > >> > >
> > >> > > On Wed, Jul 16, 2008 at 09:32:37AM -0500, Samir Unni wrote:
> > >> > > > Hi,
> > >> > > >
> > >> > > > I'm trying to create a Tcl script that will use output from APBS
> to
> > >> > > create a
> > >> > > > video file, with no user interaction. So far, I have managed to
> > >> manually
> > >> > > > create a state file, to which I can then add a few lines of code
> for
> > >> the
> > >> > > > Movie Plugin, to automatically generate the video file and then
> exit
> > >> VMD.
> > >> > > > However, I can't seem to get VMD to properly generate the video
> file
> > >> when
> > >> > > I
> > >> > > > use the script. It creates a file, but it doesn't seem to
> contain
> > >> any
> > >> > > actual
> > >> > > > data (it's only about 20 KB), and doesn't play correctly when I
> open
> > >> it
> > >> > > with
> > >> > > > MPlayer. This is the line of code that seems to be the problem:
> > >> > > >
> > >> > > > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas 1fas
> > >> ppmtompeg
> > >> > > > > snapshot 10
> > >> > > >
> > >> > > >
> > >> > > > When I load this exact same state file, but with that line
> removed,
> > >> and
> > >> > > > manually use the Movie Plugin, there are no problems. I figured
> out
> > >> the
> > >> > > > syntax for the above code by taking a look at vmdmovie.tcl, and
> > >> imitating
> > >> > > > the calls made when the Movie Plugin is launched from the GUI.
> As
> > >> far as
> > >> > > I
> > >> > > > can tell, I have made no mistakes in the syntax. Does anyone
> know
> > >> why
> > >> > > this
> > >> > > > isn't working correctly?
> > >> > > >
> > >> > > > Thanks,
> > >> > > >
> > >> > > > Samir Unni
> > >> > >
> > >> > > --
> > >> > > 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/>
> <http://www.ks.uiuc.edu/%7Ejohns/><
> > >> http://www.ks.uiuc.edu/%7Ejohns/>
> > >> > > 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/><
> http://www.ks.uiuc.edu/%7Ejohns/>
> > >> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>