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
> >> PyMOL-users@lists.sourceforge.net
> >> 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!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
