Nope! I do not know what I am supposed to do with it (where to find it and how to compile it, if necessary)... Any idea, David?
BTW: The link to the Parallel Berkeley Encoder (mpeg_encode) is not working. Nevertheless, we can still get freemol from bioinformatics.org. I have the feeling that I only need mpeg_encode (and not APBS, PDB2PQR and mengine), right? Ioannis On Friday 08 of July 2016 09:16:40 David Hall wrote: > Do you have the python code from freemol.org ? > > -David > > > On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos <imicha...@bioacademy.gr> wrote: > >> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote: > >> Dear Ioannis, > >> > >>> On 2016-07-08 09:04, Ioannis Michalopoulos wrote: > >>> Dear PyMOL users, > >>> > >>> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on > >>> the > >>> web. This produced the directory: > >>> > >>> /opt/pymol-svn/ > >>> > >>> and a symbolic link to pymol executable: > >>> > >>> /usr/bin/pymol -> /opt/pymol-svn/pymol* > >>> > >>> PyMOL works fine. Nevertheless, when I try: > >>> > >>> File > Save Movie As > MPEG... > >>> > >>> I get the following error message: > >>> > >>> MPEG encoder missing. > >>> The FreeMOL add-ons may not be installed > >>> > >>> I downloaded the source code for mpeg_encode > >>> (freemol-mpeg_encode.tar.gz) > >>> from: > >>> > >>> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_ > >>> en > >>> code/?view=tar > >>> > >>> and I did the following: > >>> > >>> tar zxvf freemol-mpeg_encode.tar.gz > >>> cd mpeg_encode > >>> ./configure > >>> make > >>> sudo make install > >>> > >>> This created the following file: > >>> > >>> /bin/mpeg_encode.exe > >>> > >>> That means that mpeg_encode.exe is in the PATH (it runs from any > >>> directory). mpeg_encode.exe seems to work. Unfortunately, when I try to > >>> produce a movie in pymol, I get the same error message. What have I done > >>> wrong? > >> > >> I hope it is very simple. > >> You need to include an environment variable $FREEEMOL pointing at the > >> directory where > >> freemol is installed > >> > >> If you are using bash that would be > >> export FREEMOL=/your/bath/to/freemol/ > >> where the mpeg_encode.exe file is in > >> /your/bath/to/freemol/bin/mpeg_encode.exe > >> > >> Hope this helps! > > > > I created a directory: > > > > /opt/freemol > > > > with two subdirectories: > > > > /opt/freemol/bin > > /opt/freemol/licenses > > > > which contain the files: > > > > /opt/freemol/bin/mpeg_encode.exe > > /opt/freemol/licenses/mpeg_encode.txt > > > > I created the file: > > > > pymol.sh > > > > with this content: > > > > #!/bin/bash > > FREEMOL=/opt/freemol > > export FREEMOL > > pymol > > > > I ran pymol.sh, but the problem remained the same. Any idea? > > > > Ioannis > > > >> Folmer > >> > >>> Thank you in advance. > >>> > >>> Best Regards, > >>> > >>> Ioannis -- Dr Ioannis Michalopoulos Staff Research Scientist - Associate Professor Level Centre of Systems Biology Tel: +30 210 6597 127 Fax: +30 210 6597 545 Email: imicha...@bioacademy.gr _________________________________________________ Biomedical Research Foundation, Academy of Athens Soranou tou Efessiou 4, 115 27 Athens, Greece ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
