VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 21 2008 - 11:44:58 CDT

Hi,
  Ok, that's good to know. Yes, it should be possible to use the makemovie
method in pure text mode, but some state variables will have to be changed
and you won't be able to use the "snapshot" renderer since there's no
OpenGL window to take snapshots from. You'll probably want to try using
tachyon, I'll send you the necessary script tweaks to get it going for you.
I'll also be improving the text mode movie generator routine
for the next release. :)

Cheers,
  John

On Mon, Jul 21, 2008 at 11:35:51AM -0500, Samir Unni wrote:
> 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
> > 

-- 
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