VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 21 2008 - 12:46:17 CDT

I'll send you an email later today with some scripts, I'll cover the
other questions you asked regarding Tachyon speed etc at that time as well.

Cheers,
  John

On Mon, Jul 21, 2008 at 12:22:20PM -0500, Samir Unni wrote:
> 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.
> > 

-- 
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