VMD-L Mailing List

From: Dan White (dan_at_chalkie.org.uk)
Date: Thu Jan 12 2006 - 10:42:38 CST

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