VMD-L Mailing List

From: Samir Unni (srunni_at_gmail.com)
Date: Mon Jul 21 2008 - 12:16:53 CDT

Hi,

That could prove problematic. Using the 'snapshot' renderer requires only
about 10 seconds on this machine (octo-core 2.8 GHz Intel Xeon Mac Pro) with
the command I mentioned earlier (using the modified vmdmovie.tcl). But the
the 'tachyon' renderer requires upwards of 7 minutes. Is there no other
renderer option that could be used without X/OpenGL?

Thanks,

Samir

On Mon, Jul 21, 2008 at 11:44 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/><
> > > > >> 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/><
> > > 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
>