VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 22 2002 - 10:39:38 CST

Hi Margaret, (and VMD-L)
  It sounds like the new version of NetPBM was the solution to the
original problem. Now you'll need to make sure that you are generating
movies of a resolution and size that are playable by PowerPoint, we
usually use resolutions around 320x240 for the movies we make for
PowerPoint. You can go a bit larger, but the movie file size will
increase dramatically, and PowerPoint's ability to play it back
smoothly will also suffer as you approach the limits of the machine
you're playing back on.

I haven't used ffmpeg to display or decode animations, so I don't have
any specific comment there. In general I found ffmpeg to be pretty buggy,
which is actually why I switched to generating the animations using ppmtompeg.
 (ffmpeg crashes or malfunctions when displaying images that aren't
  coincidentally divisble by a block or macroblock size, as I recall.
  This is something that's a bit tricky to get right in an MPEG encoder,
  and I think they have to fix their code to deal with that still..)

Let us know as you make progress with your animations..

I got one really nice bit of information from one of your other
notes with the warning about ppmtompeg not encoding the last B frame,
this explains a tiny glitch I had seen with looping animations in
PowerPoint, so I'm going to see if I can fix that by forcing ppmtompeg
to encode the last B frame whether it wants to or not. :)
I'll announce when a new version of the code is available that fixes
that missing B frame.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 22, 2002 at 12:32:22AM -0800, Margaret Cheung wrote:
> Dear John,
>
> Thank you for your prompt reply.
> I installed netpbm 9.23 as suggested. Compile the source code
> and copied several executables (as suggested) to /usr/bin/. Reload vmd and
> vmdmovie. Now the compiled .mpg file is not null. Somehow I can't view it
> with ffmpeg (I did "ffmpeg -i *.mpg" to view it). So I have to use quick
> time to view it and it looks ok ( I've only tested for two frames.
> Don't know how it goes with large files yet.).
>
>
> Sincerely,
> Margaret S. Cheung
> Biophysics Program
> Physics Department 0319
> University of California, San Diego
> 9500 Gilman Drive,
> La Jolla, CA 92093-0319
> http://www-physics.ucsd.edu/~cheung
>
> On Fri, 22 Mar 2002, John Stone wrote:
>
> >
> > Margaret,
> > We're using NetPBM version 9.23, your version may be too old.
> > I compiled the version we're using from the source rather than
> > using an RPM, but we can determine if this is going to matter for
> > you or not by having you test a few things.
> > Can you do a quick test for me?
> >
> > Try this:
> > Edit the vmdmovie.tcl script, commenting out, or deleting the
> > this line of the code:
> > cleanframes ;# delete temporary files and single frames
> >
> > Once you've done that, restart VMD (if you still had it running)
> > and then run the movie maker as usual. Everything will be the same,
> > except that none of the files will be delete when it finishes.
> >
> > When its done, look at see what files it left in the directory,
> > and mail me the list.
> >
> > Then, try running ppmtompeg manually by changing to the working
> > directory where the animation files were stored, then run ppmtompeg
> > with this command:
> > ppmtompeg foo.par (where "foo" is the name you chose in the movie gui)
> >
> > Send me any errors or interesting looking output from ppmtompeg.
> >
> > In the case that it looks like NetPBM is bombing on you, I have
> > copied the Linux binaries that I built, which work fine for us,
> > into a directory on our FTP server where you (and others) can
> > download them if you like:
> > ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/netpbm-linux
> >
> > You'll need ppmtompeg, sgitopnm, tgatoppm, and probably a
> > couple others that might be called by ppmtompeg.
> >
> > Let me know how it goes and if you still need help getting it running.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Mar 21, 2002 at 10:17:58PM -0800, Margaret Cheung wrote:
> > > Dear John,
> > >
> > > Thank you for your prompt reply. I'm installing
> > > netpbm-progs-9.14-2.i386.rpm for ppmtompeg. I didn't get any error
> > > messages. Instead, "complete" was shown in the window. I'll appreciate it
> > > because I'm preparing my movie for a talk next Monday..... please help.
> > >
> > > Sincerely,
> > > Margaret S. Cheung
> > > Biophysics Program
> > > Physics Department 0319
> > > University of California, San Diego
> > > 9500 Gilman Drive,
> > > La Jolla, CA 92093-0319
> > > http://www-physics.ucsd.edu/~cheung
> > >
> > > On Thu, 21 Mar 2002, John Stone wrote:
> > >
> > > >
> > > > Hi Margaret,
> > > > Can you tell me which version of the netpbm software you have
> > > > installed? I found that some of the older versions are buggy,
> > > > so you may have to have a newer version if the old one fails to
> > > > work for you. I'm not sure that's your problem, but its a
> > > > possibility if everything except for the last phase of the
> > > > movie compression is working correctly. Do you get any errors
> > > > in your VMD console window, or in any Tk dialog boxes? Let me know
> > > > if you see any other indications of the source of the problem.
> > > >
> > > > Thanks,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Thu, Mar 21, 2002 at 08:34:58PM -0800, Margaret Cheung wrote:
> > > > > Dear VMD users and developers,
> > > > >
> > > > > I installed the vmdmovie plugin. However, I can not make movies.
> > > > > I use linux redhet 7.2. vmd is 1.7.1. I installed ppmtompeg package
> > > > > (netpbm-progs*.rpm). I can see the script is making rgb and ppm files.
> > > > > However the final test.mpg is size 0! I got a null output. Please help
> > > > > me. Thank you very much.
> > > > >
> > > > >
> > > > > 1640 -rw------- 1 cheung user 1673853 Mar 21 20:40 test.0000.ppm
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0000.rgb
> > > > > 1640 -rw------- 1 cheung user 1673853 Mar 21 20:40 test.0001.ppm
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0001.rgb
> > > > > 1640 -rw------- 1 cheung user 1673853 Mar 21 20:40 test.0002.ppm
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0002.rgb
> > > > > 1640 -rw------- 1 cheung user 1673853 Mar 21 20:40 test.0003.ppm
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0003.rgb
> > > > > 416 -rw------- 1 cheung user 405504 Mar 21 20:40 test.0004.ppm
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0004.rgb
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0005.rgb
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0006.rgb
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0007.rgb
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0008.rgb
> > > > > 1640 -rw------- 1 cheung user 1674350 Mar 21 20:40 test.0009.rgb
> > > > >
> > > > >
> > > > > Sincerely,
> > > > > Margaret S. Cheung
> > > > > Biophysics Program
> > > > > Physics Department 0319
> > > > > University of California, San Diego
> > > > > 9500 Gilman Drive,
> > > > > La Jolla, CA 92093-0319
> > > > > http://www-physics.ucsd.edu/~cheung
> > > > >
> > > > > On Wed, 16 Jan 2002, John Stone wrote:
> > > > >
> > > > > >
> > > > > > Dear VMD-L,
> > > > > > I have been developing a movie making script for VMD that
> > > > > > is a complete solution for creating Animated GIF, AVI, Quicktime,
> > > > > > and MPEG movies with VMD. The movie script uses several helper
> > > > > > programs to do its work, but provides a completely automatic way
> > > > > > to generate movies without having to do a lot of manual script
> > > > > > processing and running of batch jobs etc. The script is available
> > > > > > as part of the VMD script library here:
> > > > > > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmdmovie/
> > > > > >
> > > > > > Since the script is a test release, I am still in the process of
> > > > > > adding new movie encoder support, improving the GUI, and finding/fixing
> > > > > > bugs. If you would like to try it out, please go ahead and give us
> > > > > > feedback if you have questions or run into problems. In order to
> > > > > > use the script you'll need these programs installed
> > > > > > (and in your path, on Unix systems):
> > > > > > Windows:
> > > > > > The "VideoMach" package, see the movie script page for links and
> > > > > > information.
> > > > > >
> > > > > > Unix:
> > > > > > NetPBM (frame conversion)
> > > > > > ImageMagick (animated GIF format, frame conversion)
> > > > > > SGI dmconvert (AVI, MPEG, Quicktime)
> > > > > > 'ffmpeg' (MPEG-1 generator, works on Linux)
> > > > > >
> > > > > > The script now runs on Windows and Unix systems, with the two
> > > > > > best-supported platforms being Windows and SGI IRIX at the
> > > > > > present time using "VideoMach" (Windows) and "dmconvert" (SGI).
> > > > > > These platforms provide AVI and MPEG encoding presently, and are
> > > > > > pretty reliable.
> > > > > >
> > > > > > For other Unix platforms, the "animated GIF" option is currently the
> > > > > > most reliable output medium. I'm working on getting several MPEG encoders
> > > > > > working on Linux and Solaris, but at the present moment only the
> > > > > > 'ffmpeg' option is ready, and even so the 'ffmpeg' utility is somewhat
> > > > > > buggy.
> > > > > >
> > > > > > If you have questions, pleast let me know. I have several more updates
> > > > > > to complete on this script today and tomorrow, adding support for more
> > > > > > MPEG encoders, after that I'll be working on improving the user interface
> > > > > > again.
> > > > > >
> > > > > > I'll be updating the movie script page over the next few days as
> > > > > > improvements are made to the script, etc.
> > > > > >
> > > > > > Thanks, and enjoy!
> > > > > >
> > > > > > John Stone
> > > > > > vmd_at_ks.uiuc.edu
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > ----- End forwarded message -----
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > >
> > > > --
> > > > 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
> > > >
> >
> > --
> > 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
> > 

-- 
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