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From: Troels E. L. <tl...@gm...> - 2011-11-08 20:54:46
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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 |
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From: Jason V. <jas...@sc...> - 2011-11-08 21:15:56
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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 If the PyMOLWiki's out of date, please feel free to update it.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 <tl...@gm...>: > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Marius R. <mar...@gm...> - 2011-11-09 09:03:29
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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 <jas...@sc...>: > 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 <tl...@gm...>: >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Troels E. L. <tl...@gm...> - 2011-11-09 11:00:47
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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: 0.000000, 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 <mar...@gm...> > 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 <jas...@sc...>: > > 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 <tl...@gm...>: > >> 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 (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > >> > > > > > > > > -- > > Jason Vertrees, PhD > > PyMOL Product Manager > > Schrodinger, LLC > > > > (e) Jas...@sc... > > (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 (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > |
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From: Marius R. <mar...@gm...> - 2011-11-09 12:17:35
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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 <tl...@gm...>: > 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: 0.000000, 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 <mar...@gm...> >> >> 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 <jas...@sc...>: >> > 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 <tl...@gm...>: >> >> 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 (PyM...@li...) >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> Archives: http://www.mail-archive.com/pym...@li... >> >> >> > >> > >> > >> > -- >> > Jason Vertrees, PhD >> > PyMOL Product Manager >> > Schrodinger, LLC >> > >> > (e) Jas...@sc... >> > (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 (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pym...@li... >> > > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Tim S. <Tim...@ki...> - 2011-11-09 14:14:44
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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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
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From: Vitali S. <sta...@wi...> - 2011-11-10 05:22:16
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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...@ki...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > |
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From: Vitali S. <sta...@wi...> - 2011-11-10 05:29:42
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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 <sta...@wi...>wrote: > 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...@ki...> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> >> >> >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Save $700 by Nov 18 >> Register now >> http://p.sf.net/sfu/rsa-sfdev2dev1 >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> >> > |
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