VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 12 2006 - 10:57:11 CST

Hi,
  There's nothing wrong with the par file that I can see,
this is undoubtably some new problem with the latest NetPBM distribution.
In any case, if the par file was bad, it clearly should not crash! :-)
I'd suggest filing a bug on their sourceforge page, or else compile
the latest NetPBM from source and see if the fresh build still
has the problem.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 12, 2006 at 06:42:38PM +0200, Dan White wrote:
> Hi John,
>
> when i run ppmtompeg
> with the .par file as as the command line argument
> I get a segmentation fault
>
> I have netpbm-10.31-1.FC3
> which looks like it is very new, from this month infact.....
> so... i wonder if this new netpbm does not work with the par files that
> VMD 1.8.3 is making,
> here is the par file, so you can see if there is anything weird about
> it.
>
> PATTERN IBBPBBPBBPBBPBB
> FORCE_ENCODE_LAST_FRAME
> OUTPUT /home/dan/Desktop/harrytraj/A060108_110.mpg
> INPUT_DIR /home/dan/Desktop/harrytraj
> INPUT
> A060108_110.*.ppm [0000-0118]
> END_INPUT
> BASE_FILE_FORMAT PPM
> INPUT_CONVERT *
> GOP_SIZE 15
> SLICES_PER_FRAME 1
> PIXEL HALF
> RANGE 32
> PSEARCH_ALG LOGARITHMIC
> BSEARCH_ALG CROSS2
> IQSCALE 8
> PQSCALE 10
> BQSCALE 25
> REFERENCE_FRAME DECODED
>
> do you think it is ppmtompeg that isnt working as it should,
> or VMD that isnt making a par file that ppmtompeg understands these
> days..
> or is it a bad .par file?
>
> should I downgrade netpbm to a working version?
> do you know which one?
>
> by the way, in a normal windows installation,
> will the movie maker be there?
> does it require some windows installation of netpbm?
>
> cheers
>
> Dan
>
>
>
> On Jan 12, 2006, at 5:57 PM, John Stone wrote:
>
> >
> >Dan,
> > The VMD movie plugin usese the 'ppmtompeg' binaries that you have
> >installed on your system, so that's the first place I'd look.
> >I've seen several revs of NetPBM that had partially broken builds
> >of ppmtompeg, so you'll probably be in good shape if you get that
> >fixed.
> >One way you can determine for sure if this is ppmtompeg is to invoke
> >it by hand at the command line, using the parameter file that VMD
> >creates in the movie working directory, named filename.par
> >Give that a shot and see if that's what the problem is.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Jan 12, 2006 at 04:13:42PM +0200, Dan White wrote:
> >>Hi VMD users,
> >>
> >>I am trying to make a movie with VMD using the VMD movie generator
> >>extension that comes with vmd 1.8.3 on 32 bit linux (FC3)
> >>
> >>the ppm files are makde jsut fine, but when it makes the mpeg1 file,
> >>the file is empty, 0kb,
> >>
> >>and there are no error messages anywhere in the VMD console
> >>
> >>anyone got any clues?
> >>
> >>does it use its own ppmtompeg binary, or the one installed on the
> >>system,
> >>where should I start trouble shooting?
> >>
> >>cheers
> >>
> >>Dan
> >>
> >>
> >>
> >>Dr. Daniel James White BSc. (Hons.) PhD
> >>Bioimaging Coordinator
> >>Nanoscience Centre and Department of Biological and Environmental
> >>Sciences
> >>Division of Molecular Recognition
> >>Ambiotica C242
> >>PO Box 35
> >>University of Jyväskylä
> >>Jyväskylä
> >>FIN 40014
> >>Finland
> >>
> >>+358 14 260 4183 (work)
> >>+358 468102840 (mobile)
> >>http://www.bioimagexd.org
> >>http://www.chalkie.org.uk
> >>dan_at_chalkie.org.uk
> >>white_at_cc.jyu.fi
> >>
> >>
> >
> >--
> >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
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and Department of Biological and Environmental
> Sciences
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä
> FIN 40014
> Finland
>
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
> http://www.bioimagexd.org
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi
>
> 

-- 
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