Re: [PyMOL] Video in Ubuntu Linux
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 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
Re: [PyMOL] Video in Ubuntu Linux
Do you have the python code from freemol.org ? -David > On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos > 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 -- 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
Re: [PyMOL] Video in Ubuntu Linux
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
Re: [PyMOL] Video in Ubuntu Linux
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_encode/?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! Folmer > Thank you in advance. > > Best Regards, > > Ioannis -- 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
[PyMOL] Video in Ubuntu Linux
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_encode/?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? 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
