Subject: CCL: SUMMARY of MPEG and molecular animation tools

From: Rick Venable <rvenable.-at-.pollux.cber.nih.gov>
Date: Thu, 22 May 2003 17:43:17 -0400

I recently asked about animation formats in the context of making movies
> from simulation trajectories (from CHARMM in my case), and a slightly
edited summary of responses follows, along with my original question.
Some general comments to the responses:

[1] A few suggested GIF animations, but I worry about color information
loss in going from TrueColor to a PseudoColor format like GIF; I'll
probably try it anyway.

[2] I also thought MPEG1 was a standard format, but nonetheless I've had
a great deal of trouble trying to use Windows Media Player to play
animations created with the venerable mpeg_encode program.

[3] I plan to try a couple of the alternate encoders, which allow
setting the frame rate (mpeg_encode does not); I've found 10 fps works
well for the MD simulation animations I've made.

Thanks to everyone for their replies.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable.-at-.nih.gov
ALT email:  rvenable.-at-.speakeasy.org
-------------------------------------
"Don't blame me, I voted for Kang."
                         Homer
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=

	=============== original question =========================

I've been making molecular animations from CHARMM trajectories in MPEG1
format using mpeg_encode* for a while, but I'm having trouble finding
good MPEG1 players for M$ Windows and MacOS these days.  The only 2 that
were decent were VMPEG for M$, and Sparkle on the Mac; in particular,
they allow the user to set the frame rate for playback.  However, these
haven't been updated in some time; I don't think there's a native OSX
version of Sparkle, for instance.

    * from a series of still frames rendered via POV-Ray

In contrast, newer apps either don't play MPEG1 at all (M$ Media Player,
for instance) and others will play the MPEG1 files, but offer no means
of controlling the frame rate (QuickTime, RealPlayer).  My questions
are:

Are there other inexpensive or free media players for M$ and Mac that
can handle MPEG1 and can provide a way to set the playback speed?

Can anyone recommend other inexpensive animation software for making
"movies" in a common format from a series of still frames?

Is anyone aware of conversion tools, that might convert MPEG1 to
QuickTime or other common format?

I prefer Linux tools, but I'll use whatever works.  Thanks.

	================ summary of responses ====================

From: Jason D. Gans <jgans.-at-.lanl.gov>

While not the exact solution you were looking for, Qmol (windows only)
can directly render DCD files and multi-model pdb files as AVI movies.
Both frame rate and compression level can be specified, as well as a
host of different graphics and display styles (ribbons, surfaces,
clipping plane, etc).  The source code and executable can be found at:

http://lancelot.bio.cornell.edu/jason/qmol.html

	==========================================================

From: Bill Ross <ross.-at-.cgl.ucsf.edu>

ImageMagick will make animated GIFs from a series of stills,
and I think it allows frame rate control.

	==========================================================

From: Lee Woodcock <hlwoodc.-at-.helix.nih.gov>

I have used Gimp in the past to do animations. It can do animated gifs
well. However, I also have used the animation tool in paint shop pro, it
works pretty well. Also, ffmepg in linux can convert from mpeg to avi
and there should be plenty of avi players for winblows and macOS. The
last thing that may help is imagemagick in linux, it can make some nice
animations. I am not sure if you have tried all that I have mentioned
above but I have used them to make some animations recently.

	==========================================================

From: Etienne Derat <etienne.derat.-at-.univ-reims.fr>

Currently, I use mencoder from the package MPlayer

http://www.mplayerhq.hu

There is a lot of options and exportation's types.
With PNG or JPEG from Povray you can make movie with command's line like
this:

mencoder -mf on:w=800:h=600:fps=25 -ovc divx4 -o output.avi \*.jpg

It's a little bit complicated at the beginning but very powerful after.
Ask me if you have some problems

	==========================================================

From: Fabian Boes <fabian.boes.-at-.po.uni-stuttgart.de>

i am using the following windows based software for doing my animations:

"Pymol" -> for creating the animation and saving single .png files for
each frame
"IrfanView" -> for converting the .png into .bmp files
"pjBmp2Avi" -> for creating an uncompressed .avi file out of the bitmap
(or .tga ) files. frame rate can be specified as well as the keyframes.

the resulting animation in uncompressed .avi format is very large
(approx. 900 MB for 40 sec. with 640x480 resolution, 25fps). thus i
compress it using the programm "Virtualdub" with the open-source video
codec "Xvid", which is similar to the popular "DivX" codec.

"Virtualdub" is not able to save .mpeg files, but you can use "TMPGEnc"
to create .mpeg files out of your uncompressed .avi file.

all of the programs i mentioned are - as far as i now - open-source,
freeware or shareware, excluding "TMPGEnc" which is free only for
personal use (see their website for more details).

here are the links:

"Pymol" -> http://www.pymol.org
"IrfanView" -> http://www.irfanview.com
"pjBmp2Avi" -> http://www.cspltd.ndirect.co.uk/graphics/anim.htm
"Virtualdub" -> http://www.virtualdub.org/
"XVid" -> http://www.xvid.org (just the source-code, a comiled version
can be
found here: http://www.roeder.goe.net/%7Ekoepi/xvid.shtml)
"TMPGEnc" -> http://www.tmpgenc.net/

	==========================================================

From: David F. Green <dfgreen.-at-.ai.mit.edu>

I believe that mencode (the encoder associated with mplayer, one the
most functional movie players for linux available) will convert to and
> from a number of formats, including MPEG-1, AVI, and Quicktime.  I don't
have a lot of experience with the encoding side of this software, but
> from my experience with the mplayer, it is very good software.  Plus,
it's open source, and RPMs are available if you're running RedHat.

> From the playback under M$/Mac side of things, you also might want to
check out some of the DVD players, since they should all read MPEG just
fine.  I'm not sure if these have adjustable playback speed, but they
may.

	==========================================================

From: Surjit Dixit <sdixit.-at-.wesleyan.edu>

you could try using "VideoMach" with VMD (VMD has scripts to to use this
program). the user can also adjust the frame rate while generating the
mpeg file using VideoMach. You can employ videomach with images
generated from other sources too. check:
http://www.gromada.com/products.html They seem to have other media
players that i have not used. it might have the option you are looking
for.

	==========================================================

From: Tru Huynh <tru.-at-.pasteur.fr>

you might want to check vlc from:
http://www.videolan.org/vlc/features.html
Although, I don't know if you can set the frame rate.

You can also use the MPlayer encoder/player from:
http://www.mplayerhq.hu/homepage

	==========================================================

From: Bogdan Costescu <bogdan.costescu.-at-.iwr.uni-heidelberg.de>

Windows can play MPEG1 files with Media Player with some filter that
comes with the OS by default, however there are some limitations that
show up especially when embeeding MPEG1 files into PowerPoint
presentations for example. The MPEG1 file has to be constrained to some
"standard"  settings:  720x576 pixels in size (352x288 and 320x240 seem
to also work), only in 25 or 30 (possibly 24 and 29.8) frames/second,
encoded using constant bit rate, all coming from the television
standards. I have had no problems playing such files with Media Player
in Windows98SE, Windows2000 (Pro and Server) and WinXP, without
installing any extra players/filters.

MEncoder for Linux (http://www.mplayerhq.hu) can import still frames and
output AVI and (experimental) MPEG; the content of AVI can be compressed
with a variety of codecs. The drawback of this method is that the
respective codec has to be installed on the Windows/MacOS/whatever
machine in order to play back the movie, which is sometimes impossible
(administrative reasons, inexistance of the codec for a particular
platform, etc.).

What do you call a "common format" ? I'd call MPEG1 a common format
because it's an industry (video) standard. TMPGEnc has profiles for
generating movies in VCD format (MPEG1-based) that can be played by the
majority of standalone DVD players ! MEncoder can import MPEG1 (and
MPEG2) files and convert them to AVI. There are lots of Windows tools
for importing MPEG1/2 files and exporting AVI (and some of them offer
much more functionality, like video editting in VirtualDub
(http://www.virtualdub.org)) mainly used for DVD backup, one starting
point is http://www.doom9.org.

	================ end of summary ======================