From: Yunfeng Hu <yu...@sc...> - 2004-10-11 18:32:50
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Hi, I wonder if people can give a summary of how pymol makes movies out of gromacs trr (or xtc) files without having to use all the individual frame pdb files. Thanks! Eric |
From: Tsjerk W. <t.a...@ch...> - 2004-10-12 08:08:44
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Hi Yunfeng Hu, Frankly, with Pymol, people don't as far as I know. What I usually do is determine for the first frame of the individual pdb files (obtained with trjconv -sep) the orientation, viewing point and appearance. This I save in a .pml script. Then with a bit of python code, looping over the frames, calling them, processing the script, raytrace, write the image and delete the object again. It's at present the best I can think of. It appears that Dino is capable of processing a gromacs trajectory and outputting raytraced frames, but I haven't felt like starting at the bottom of that learning curve... To help out a bit, the loop code could look like this: for i in range(nr_of_frames): cmd.load('frame_' + repr(i) '.pdb', 'prot') cmd.do('@script.pml') cmd.delete('prot') Everything to go in script.pml could ofcourse also be explicitly given in the loop... Hope it helps, Tsjerk Yunfeng Hu wrote: > Hi, I wonder if people can give a summary of how pymol makes movies > out of gromacs trr (or xtc) files without having to use all the > individual frame pdb files. Thanks! > > Eric > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > Use IT products in your business? Tell us what you think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out > more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
From: Bruno A. <bru...@de...> - 2004-10-14 16:19:49
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Hello, It's possible to convert to a single pdb file containing all the frames using: trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr You can then load it into pymol using: pymol trajout.pdb And it will load all the frames. If you render a movie into png you will have lots of *.png files, which you can convert into a movie using the following command: convert *.png ppm:- | ppmtoy4m | yuvscaler -O SVCD | mpeg2enc -f 3 -b 4500 -q7 -o mpegfile.m2v For this you need imagemagick (convert) and mjpeg-tools (rest) I've just started out doing some MD simulations and I was trying to use pymol to see the simulations (vmd is more widely used for this) and this is what I've came up so far. Next I will need to make a pymol script to automatically render the png files, preferably without running X as my number crunching box isn't even connected to a monitor. Best, BA Tsjerk Wassenaar wrote: > > Hi Yunfeng Hu, > > Frankly, with Pymol, people don't as far as I know. What I usually do is > determine for the first frame of the individual pdb files (obtained with > trjconv -sep) the orientation, viewing point and appearance. This I save > in a .pml script. Then with a bit of python code, looping over the > frames, calling them, processing the script, raytrace, write the image > and delete the object again. It's at present the best I can think of. It > appears that Dino is capable of processing a gromacs trajectory and > outputting raytraced frames, but I haven't felt like starting at the > bottom of that learning curve... > > To help out a bit, the loop code could look like this: > > for i in range(nr_of_frames): > cmd.load('frame_' + repr(i) '.pdb', 'prot') > cmd.do('@script.pml') > cmd.delete('prot') > > Everything to go in script.pml could ofcourse also be explicitly given > in the loop... > > Hope it helps, > > Tsjerk > > Yunfeng Hu wrote: > >> Hi, I wonder if people can give a summary of how pymol makes movies >> out of gromacs trr (or xtc) files without having to use all the >> individual frame pdb files. Thanks! >> >> Eric >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal >> Use IT products in your business? Tell us what you think of them. Give us >> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out >> more >> http://productguide.itmanagersjournal.com/guidepromo.tmpl >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > -- Bruno Afonso http://brunoafonso.net http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs! http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum |
From: <T.A...@ch...> - 2004-10-14 18:07:44
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Hi Bruno, Sure I'm aware of that, but for a bit of a system (as I usually have) and a good bit of trajectory (as I usually have), that will ask for quite some memory. Did it a few times, but prefer to use separate pdb's instead. Though admitted that for small systems, a multistate pdb works great. Cheers, Tsjerk On Thu, 14 Oct 2004, Bruno Afonso wrote: > Hello, > > It's possible to convert to a single pdb file containing all the frames > using: > > trjconv -f cpeptide_md.trr -o trajout.pdb -s cpeptide_md.tpr > > You can then load it into pymol using: > > pymol trajout.pdb > > And it will load all the frames. > > If you render a movie into png you will have lots of *.png files, which > you can convert into a movie using the following command: > > convert *.png ppm:- | ppmtoy4m | yuvscaler -O SVCD | mpeg2enc -f 3 -b > 4500 -q7 -o mpegfile.m2v > > For this you need imagemagick (convert) and mjpeg-tools (rest) > > I've just started out doing some MD simulations and I was trying to use > pymol to see the simulations (vmd is more widely used for this) and this > is what I've came up so far. Next I will need to make a pymol script to > automatically render the png files, preferably without running X as my > number crunching box isn't even connected to a monitor. > > Best, > BA > > > Tsjerk Wassenaar wrote: > > > > Hi Yunfeng Hu, > > > > Frankly, with Pymol, people don't as far as I know. What I usually do is > > determine for the first frame of the individual pdb files (obtained with > > trjconv -sep) the orientation, viewing point and appearance. This I save > > in a .pml script. Then with a bit of python code, looping over the > > frames, calling them, processing the script, raytrace, write the image > > and delete the object again. It's at present the best I can think of. It > > appears that Dino is capable of processing a gromacs trajectory and > > outputting raytraced frames, but I haven't felt like starting at the > > bottom of that learning curve... > > > > To help out a bit, the loop code could look like this: > > > > for i in range(nr_of_frames): > > cmd.load('frame_' + repr(i) '.pdb', 'prot') > > cmd.do('@script.pml') > > cmd.delete('prot') > > > > Everything to go in script.pml could ofcourse also be explicitly given > > in the loop... > > > > Hope it helps, > > > > Tsjerk > > > > Yunfeng Hu wrote: > > > >> Hi, I wonder if people can give a summary of how pymol makes movies > >> out of gromacs trr (or xtc) files without having to use all the > >> individual frame pdb files. Thanks! > >> > >> Eric > >> > >> > >> > >> ------------------------------------------------------- > >> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > >> Use IT products in your business? Tell us what you think of them. Give us > >> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out > >> more > >> http://productguide.itmanagersjournal.com/guidepromo.tmpl > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyM...@li... > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |