VMD-L Mailing List

From: Samir Unni (srunni_at_gmail.com)
Date: Mon Jul 21 2008 - 12:22:20 CDT

Hi,

Does that mean there is a command that I can use in the state file to
manually require the vmdmovie package so it can be used without X, at least
until the support for rendering without a GUI is improved? Do you know the
syntax for including such a command in the state file?

Thanks,

Samir

On Mon, Jul 21, 2008 at 12:01 PM, Axel Kohlmeyer <
akohlmey_at_cmm.chem.upenn.edu> wrote:

> On Mon, 21 Jul 2008, Samir Unni wrote:
>
> SU> Hi,
> SU>
> SU> Yes, that fixed the problem! Is the state variable that's missing one
> of the
> SU> two (or both) that I initialized in my modified version of
> vmdmovie.tcl?
> SU>
> SU> Also, even if this problem is fixed, it seems that the 'makemovie'
> method
> SU> cannot be used unless a GUI is running (i.e. starting vmd with
> '-dispdev
> SU> none' or '-dispdev text' won't work). That isn't an option in my case,
> since
> SU> I will be using the state files I'm creating with instances of VMD that
> are
> SU> on servers where X is not present. Is there a scriptable workaround for
> this
> SU> issue as well?
>
> if you are running without a display you have to
> "require" all packages you want to use.
> all packages with a GUI (and the ones those depends on)
> have to be "required" by VMD during startup to be able
> to register their GUI. if john finds a way to set up the
> initialization properly, then it should work as well
> on machines without display, provided you use a renderer
> different from "snapshot", that is.
>
> cheers,
> axel.
>
>
> SU>
> SU> Thanks,
> SU>
> SU> Samir
> SU>
> SU>
> SU> On Mon, Jul 21, 2008 at 10:31 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> SU>
> SU> > I think I've reproduced the problem you encountered, try doing this
> SU> > and see if you get different behavior:
> SU> >
> SU> > Run the command line script as before, and verify that you get
> SU> > the 1 frame movie, as before.
> SU> >
> SU> > Then, after having done this, try opening the GUI for the movie
> SU> > maker, through the Extensions->Visualization->Movie Maker menu.
> SU> > Once the window is opened, try running the script at the command
> SU> > line again. Let me know if it works correctly for you the second
> SU> > time. I believe that the issue here is an internal state variable
> SU> > that's only being properly initialized when the GUI has been opened.
> SU> > It will be easy to workaround/fix with one or two extra lines of
> SU> > scripting if that's all that's causing your problem.
> SU> >
> SU> > Cheers,
> SU> > John Stone
> SU> > vmd_at_ks.uiuc.edu
> SU> >
> SU> >
> SU> > On Mon, Jul 21, 2008 at 07:57:59AM -0500, Samir Unni wrote:
> SU> > > Hi,
> SU> > >
> SU> > > Sorry I'm so late in getting back to you. Anyway, that code doesn't
> work
> SU> > on
> SU> > > the Mac either. It just briefly opens the video (for one frame, I
> think)
> SU> > and
> SU> > > then closes. I'm using the 1.8.6 version of VMD?is that the one
> you're
> SU> > > using?
> SU> > >
> SU> > > Thanks,
> SU> > >
> SU> > > Samir
> SU> > >
> SU> > >
> SU> > > On Thu, Jul 17, 2008 at 10:19 PM, Samir Unni <srunni_at_gmail.com>
> wrote:
> SU> > >
> SU> > > > Hi,
> SU> > > >
> SU> > > > I tried that, but it didn't work for me. When I attempted to play
> the
> SU> > video
> SU> > > > file with MPlayer, the window appeared for a second and then
> SU> > disappeared,
> SU> > > > just like before. I think only one frame is being recorded.
> SU> > > >
> SU> > > > Right now I'm trying this on my Linux machine at home, but I'll
> try it
> SU> > > > again on the Mac at work tomorrow morning and see if it works
> there.
> SU> > > > However, this was the exact same problem I was previously having
> on the
> SU> > Mac,
> SU> > > > so I don't think it will. If it's working for you, it might have
> SU> > something
> SU> > > > to do with the state file I'm using, which I created by importing
> the
> SU> > DX
> SU> > > > output file from APBS into VMD.
> SU> > > >
> SU> > > > I had meant to attached the modified version of vmdmovie.tcl to
> the
> SU> > last
> SU> > > > email; it's attached now, if you want to take a look.
> SU> > > >
> SU> > > > Thanks,
> SU> > > >
> SU> > > > Samir
> SU> > > >
> SU> > > >
> SU> > > >
> SU> > > > On Thu, Jul 17, 2008 at 9:56 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> SU> > > >
> SU> > > >>
> SU> > > >> Hi,
> SU> > > >> I'm not sure how you changed your copy of the vmdmovie.tcl
> file,
> SU> > > >> but I'd ask that before we delve any further, that you first try
> the
> SU> > > >> original vmdmovie plugin and the command I emailed earlier. If
> that
> SU> > > >> works for you, then we can proceed with debugging whatever has
> been
> SU> > > >> changed in your modified version. Starting with your modified
> version
> SU> > > >> is likely to add more confusion so I'd rather leave that for a
> second
> SU> > > >> step. Please try the example sequence I sent earlier and let me
> know
> SU> > > >> if that works with the unmodified script on your system, or not.
> SU> > > >>
> SU> > > >> Cheers,
> SU> > > >> John Stone
> SU> > > >> vmd_at_ks.uiuc.edu
> SU> > > >>
> SU> > > >> On Thu, Jul 17, 2008 at 09:18:24PM -0500, Samir Unni wrote:
> SU> > > >> > Hi,
> SU> > > >> >
> SU> > > >> > That character resulted from an issue with the email
> formatting; it
> SU> > was
> SU> > > >> not
> SU> > > >> > actually part of the command that I used. The command I used
> was:
> SU> > > >> >
> SU> > > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas 1fas
> SU> > ppmtompeg
> SU> > > >> > snapshot 10
> SU> > > >> >
> SU> > > >> > Also, I sent an update a few hours after my initial email, but
> it
> SU> > seems
> SU> > > >> not
> SU> > > >> > to have made it onto the mailing list. I will repost it here:
> SU> > > >> >
> SU> > > >> > --------------------
> SU> > > >> > I've got a small update. I slightly changed vmdmovie.tcl, so
> that
> SU> > the
> SU> > > >> > framerate can be passed to the 'makemovie' method. When I did
> this,
> SU> > > >> defined
> SU> > > >> > 'framerate' as the extra variable being passed now, and
> defined
> SU> > > >> 'numframes'
> SU> > > >> > as the product of the framerate and the duration, a working
> movie
> SU> > was
> SU> > > >> > created. Though it would seem that only 2 of these 3 variables
> need
> SU> > to
> SU> > > >> be
> SU> > > >> > defined for the program to be able to determine the 3rd, when
> I
> SU> > > >> eliminated
> SU> > > >> > any one of them, the movie was not generated correctly. I have
> SU> > attached
> SU> > > >> the
> SU> > > >> > working version of vmdmovie.tcl, if anyone wants to look at
> it.
> SU> > > >> >
> SU> > > >> > I would still like to know if there is a way to generate a
> movie
> SU> > from
> SU> > > >> the
> SU> > > >> > command line without modifying any files that are a part of
> VMD, if
> SU> > > >> > possible.
> SU> > > >> > --------------------
> SU> > > >> >
> SU> > > >> > I still have not found a workaround for this issue. The
> command I am
> SU> > > >> using
> SU> > > >> > now is:
> SU> > > >> >
> SU> > > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas 1fas
> SU> > ppmtompeg
> SU> > > >> > tachyon 5 40
> SU> > > >> >
> SU> > > >> > Thanks,
> SU> > > >> >
> SU> > > >> > Samir Unni
> SU> > > >> >
> SU> > > >> >
> SU> > > >> > On Thu, Jul 17, 2008 at 5:02 PM, John Stone <
> johns_at_ks.uiuc.edu>
> SU> > wrote:
> SU> > > >> >
> SU> > > >> > >
> SU> > > >> > > Hi,
> SU> > > >> > > The ">" character you have in your example below shouldn't
> be
> SU> > there,
> SU> > > >> > > that would cause some trouble for sure.
> SU> > > >> > >
> SU> > > >> > > Here's a proper example command sequence to make a movie
> from text
> SU> > > >> mode:
> SU> > > >> > > package require vmdmovie
> SU> > > >> > > mkdir /tmp/mytmpdir
> SU> > > >> > > ::MovieMaker::makemovie /tmp/mytmpdir example ppmtompeg
> snapshot
> SU> > 10
> SU> > > >> > >
> SU> > > >> > > This worked fine for me.
> SU> > > >> > >
> SU> > > >> > > Try that and let me know how it goes.
> SU> > > >> > >
> SU> > > >> > > Cheers,
> SU> > > >> > > John Stone
> SU> > > >> > > vmd_at_ks.uiuc.edu
> SU> > > >> > >
> SU> > > >> > > On Wed, Jul 16, 2008 at 09:32:37AM -0500, Samir Unni wrote:
> SU> > > >> > > > Hi,
> SU> > > >> > > >
> SU> > > >> > > > I'm trying to create a Tcl script that will use output
> from APBS
> SU> > to
> SU> > > >> > > create a
> SU> > > >> > > > video file, with no user interaction. So far, I have
> managed to
> SU> > > >> manually
> SU> > > >> > > > create a state file, to which I can then add a few lines
> of code
> SU> > for
> SU> > > >> the
> SU> > > >> > > > Movie Plugin, to automatically generate the video file and
> then
> SU> > exit
> SU> > > >> VMD.
> SU> > > >> > > > However, I can't seem to get VMD to properly generate the
> video
> SU> > file
> SU> > > >> when
> SU> > > >> > > I
> SU> > > >> > > > use the script. It creates a file, but it doesn't seem to
> SU> > contain
> SU> > > >> any
> SU> > > >> > > actual
> SU> > > >> > > > data (it's only about 20 KB), and doesn't play correctly
> when I
> SU> > open
> SU> > > >> it
> SU> > > >> > > with
> SU> > > >> > > > MPlayer. This is the line of code that seems to be the
> problem:
> SU> > > >> > > >
> SU> > > >> > > > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas
> 1fas
> SU> > > >> ppmtompeg
> SU> > > >> > > > > snapshot 10
> SU> > > >> > > >
> SU> > > >> > > >
> SU> > > >> > > > When I load this exact same state file, but with that line
> SU> > removed,
> SU> > > >> and
> SU> > > >> > > > manually use the Movie Plugin, there are no problems. I
> figured
> SU> > out
> SU> > > >> the
> SU> > > >> > > > syntax for the above code by taking a look at
> vmdmovie.tcl, and
> SU> > > >> imitating
> SU> > > >> > > > the calls made when the Movie Plugin is launched from the
> GUI.
> SU> > As
> SU> > > >> far as
> SU> > > >> > > I
> SU> > > >> > > > can tell, I have made no mistakes in the syntax. Does
> anyone
> SU> > know
> SU> > > >> why
> SU> > > >> > > this
> SU> > > >> > > > isn't working correctly?
> SU> > > >> > > >
> SU> > > >> > > > Thanks,
> SU> > > >> > > >
> SU> > > >> > > > Samir Unni
> SU> > > >> > >
> SU> > > >> > > --
> SU> > > >> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> SU> > > >> > > Beckman Institute for Advanced Science and Technology
> SU> > > >> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> SU> > > >> > > Email: johns_at_ks.uiuc.edu Phone:
> 217-244-3349
> SU> > > >> > > WWW: http://www.ks.uiuc.edu/~johns/>
> <http://www.ks.uiuc.edu/%7Ejohns/>
> SU> > <http://www.ks.uiuc.edu/%7Ejohns/><
> SU> > > >> http://www.ks.uiuc.edu/%7Ejohns/>
> SU> > > >> > > Fax: 217-244-6078
> SU> > > >> > >
> SU> > > >>
> SU> > > >> --
> SU> > > >> NIH Resource for Macromolecular Modeling and Bioinformatics
> SU> > > >> Beckman Institute for Advanced Science and Technology
> SU> > > >> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> SU> > > >> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> SU> > > >> WWW: http://www.ks.uiuc.edu/~johns/>
> <http://www.ks.uiuc.edu/%7Ejohns/><
> SU> > http://www.ks.uiuc.edu/%7Ejohns/>
> SU> > > >> Fax: 217-244-6078
> SU> > > >>
> SU> > > >
> SU> > > >
> SU> >
> SU> > --
> SU> > NIH Resource for Macromolecular Modeling and Bioinformatics
> SU> > Beckman Institute for Advanced Science and Technology
> SU> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> SU> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> SU> > WWW: http://www.ks.uiuc.edu/~johns/><
> http://www.ks.uiuc.edu/%7Ejohns/>
> SU> > Fax: 217-244-6078
> SU> >
> SU>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>