Re: [PyMOL] Movie to export
What codec do I need to install?? MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team Option x264encopts: Unknown suboption nodct_decimat success: format: 16 data: 0x0 - 0x0 MF file format detected. [mf] search expr: *.png [mf] number of files: 537 (4296) [demux_mf] file type was not set! trying 'type=png'... VIDEO: [MPNG] 0x0 24bpp 25.000 fps0.0 kbps ( 0.0 kbyte/s) [V] filefmt:16 fourcc:0x474E504D size:0x0 fps:25.000 ftime:=0.0400 Opening video filter: [expand osd=1] Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.00, round: 1 == Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG) == Could not find matching colorspace - retrying with -vf scale... Opening video filter: [scale] Movie-Aspect is undefined - no prescaling applied. [swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2 FATAL: Cannot initialize video driver. Movie-Aspect is undefined - no prescaling applied. FATAL: Cannot initialize video driver. Exiting... 2011/11/9 Marius Retegan marius.s.rete...@gmail.com On a Linux system you can use the following commands to stick them all together mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25 -ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264 This will create a x264 compressed file which you will have to put in a mp4 container using the following command. You can modify the bitrate which is now set to 3000 and the framerate 25 fps. MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4 Best regards, Marius -- Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y 2011/11/8 Jason Vertrees jason.vertr...@schrodinger.com: Hi Troels, One benefit of the Incentive version of PyMOL is the Files Save Movie as ... MPEG feature. If you don't have that or you want to use a different compressor that's cool. In the past I had great luck with mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I think everyone's using VLC (http://www.videolan.org/) or ffmpeg (http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel free to update it. Cheers, -- Jason 2011/11/8 Troels Emtekær Linnet tlin...@gmail.com: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] Movie to export
I used this a long time ago, but after googling for the error from bgra to yuv420p I guess that is a problem with the color space conversion that memcoder tries to enforce by default. Maybe you could try imposing the color space by adding -vf format=bgra, but I think that the video codec is not going to be happy about that. Try looking around for other options... Marius 2011/11/9 Troels Emtekær Linnet tlin...@gmail.com: What codec do I need to install?? MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team Option x264encopts: Unknown suboption nodct_decimat success: format: 16 data: 0x0 - 0x0 MF file format detected. [mf] search expr: *.png [mf] number of files: 537 (4296) [demux_mf] file type was not set! trying 'type=png'... VIDEO: [MPNG] 0x0 24bpp 25.000 fps 0.0 kbps ( 0.0 kbyte/s) [V] filefmt:16 fourcc:0x474E504D size:0x0 fps:25.000 ftime:=0.0400 Opening video filter: [expand osd=1] Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.00, round: 1 == Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG) == Could not find matching colorspace - retrying with -vf scale... Opening video filter: [scale] Movie-Aspect is undefined - no prescaling applied. [swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2 FATAL: Cannot initialize video driver. Movie-Aspect is undefined - no prescaling applied. FATAL: Cannot initialize video driver. Exiting... 2011/11/9 Marius Retegan marius.s.rete...@gmail.com On a Linux system you can use the following commands to stick them all together mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25 -ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264 This will create a x264 compressed file which you will have to put in a mp4 container using the following command. You can modify the bitrate which is now set to 3000 and the framerate 25 fps. MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4 Best regards, Marius -- Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y 2011/11/8 Jason Vertrees jason.vertr...@schrodinger.com: Hi Troels, One benefit of the Incentive version of PyMOL is the Files Save Movie as ... MPEG feature. If you don't have that or you want to use a different compressor that's cool. In the past I had great luck with mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I think everyone's using VLC (http://www.videolan.org/) or ffmpeg (http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel free to update it. Cheers, -- Jason 2011/11/8 Troels Emtekær Linnet tlin...@gmail.com: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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] Movie to export
Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] CIF support?
Hi all I'm trying to visualize a small molecule . The format is CIF (from SHELX small molecule refinement). Is there support for this file format? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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] Put scripts in a svn folder
Hi Pymolers. I sometimes find small errors in my scripts, which I then correct. But then I get a little sad, that now my unfinished script still lives out there. So I think, why is the pymolwiki scripts not under subversion control? Then authors could push corrections to their scripts to the subversion directory, and users would get these corrections. I dont know if the pymol wiki could fetch and display the scripts from the subversion folder. How does this idea sounds? Bes Troels -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] Movie to export
have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte tim.schu...@ki.se wrote: ** Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] Movie to export
one more thing: ffmpeg script at that link didn't work for me so i had to modify it like that ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg On Wed, Nov 9, 2011 at 11:22 PM, Vitali Stanevich stanev...@wisc.eduwrote: have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte tim.schu...@ki.se wrote: ** Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] PyMOL-users Digest, Vol 66, Issue 4
-原始邮件- 发件人: pymol-users-requ...@lists.sourceforge.net 发送时间: 2011年11月10日 星期四 收件人: pymol-users@lists.sourceforge.net 抄送: 主题: PyMOL-users Digest, Vol 66, Issue 4 Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Re: Movie to export (Tim Schulte) 2. CIF support? (Francis E Reyes) 3. Put scripts in a svn folder (Troels Emtek?r Linnet) 4. Re: Movie to export (Vitali Stanevich) 5. Re: Movie to export (Vitali Stanevich) -- Message: 1 Date: Wed, 9 Nov 2011 15:14:34 +0100 From: Tim Schulte tim.schu...@ki.se Subject: Re: [PyMOL] Movie to export To: pymol-users@lists.sourceforge.net Message-ID: 4eba8aca.6030...@ki.se Content-Type: text/plain; charset=iso-8859-1 Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtek?r Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtek?r Linnet Slotsvej 2 4300 Holb?k Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- next part -- An HTML attachment was scrubbed... -- Message: 2 Date: Wed, 9 Nov 2011 11:45:44 -0700 From: Francis E Reyes francis.re...@colorado.edu Subject: [PyMOL] CIF support? To: Pymol List pymol-users@lists.sourceforge.net Message-ID: 73c296ba-cee6-4053-a54f-420e72064...@colorado.edu Content-Type: text/plain; charset=us-ascii Hi all I'm trying to visualize a small molecule . The format is CIF (from SHELX small molecule refinement). Is there support for this file format? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- Message: 3 Date: Wed, 9 Nov 2011 23:57:11 +0100 From: Troels Emtek?r Linnet tlin...@gmail.com Subject: [PyMOL] Put scripts in a svn folder To: pymol-users@lists.sourceforge.net PyMOL-users@lists.sourceforge.net Message-ID: ca+cbx2oznwc1cg2nv0h2yv4xjke285jnkvpmyho-o8pbolh...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Pymolers. I sometimes find small errors in my scripts, which I then correct. But then I get a little sad, that now my unfinished script still lives out there. So I think, why is the pymolwiki scripts not under subversion control? Then authors could push corrections to their scripts to the subversion directory, and users would get these corrections. I dont know if the pymol wiki could fetch and display the scripts from the subversion folder. How does this idea sounds? Bes Troels -- next part -- An HTML attachment was scrubbed... -- Message: 4 Date: Wed, 9 Nov 2011 23:22:09 -0600 From: Vitali Stanevich stanev...@wisc.edu Subject: Re: [PyMOL] Movie to export To: pymol-users@lists.sourceforge.net Message-ID: caenuloojshg7ngz_rweb2eb9azcp8micogm+yi0r4y535vc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 have a look at this link: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera disregard morph part. you can modify script to contain frames instead of states. i installed ffmpeg from repositories on ubuntu and don't remember any issues with kodecs. vitali On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte tim.schu...@ki.se wrote: ** Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtek?r Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the
