Re: [PyMOL] GROMACS trajectories (Timofey Tyugashev)
Thank you for reply. xtc trajectories do work. Maybe the first time the problem occurred because I was using PyMOL installed from Linux Mint repository. Now I use SVN one. -- ___ 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] GROMACS trajectories
Hi Timofey, This wiki page is obsolete, current PyMOL includes a recent version of the VMD plugins, and it can load xtc files (and probably trr too, but I don't have a test file around). You need to load topology and trajectory in two steps, into the same object. Example: load topology.gro, somename load_traj trajectory.xtc, somename Cheers, Thomas On 06 Oct 2015, at 05:39, Timofey Tyugashev wrote: > Is there any way to load .xtc or .trr files into PyMOL to view trajectories? > This user page on the wiki suggest the way, but it looks like it's > outdated and defunct now. > pymolwiki.org/index.php/User:Speleo3/VMD_plugins -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Full-scale, agent-less Infrastructure Monitoring from a single dashboard Integrate with 40+ ManageEngine ITSM Solutions for complete visibility Physical-Virtual-Cloud Infrastructure monitoring from one console Real user monitoring with APM Insights and performance trend reports Learn More http://pubads.g.doubleclick.net/gampad/clk?id=247754911&iu=/4140 ___ 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] GROMACS trajectories
The safest way to do that would be to convert your trajectory to a format readably by PyMOL, with trajectory manipulation tools such as trjconv (in GROMACS) or catdcd (you can find it in the VMD website). PyMOL recognizes the AMBER .trj format with the "Load_traj" function, so you can use that: http://pymolwiki.org/index.php/Load_Traj Or you can write the frames to a single PDB file, in which case PyMOL will treat it as an NMR ensemble and load all frames (not recommended though, because the file size might be enormous, depending on system size and the number of frames). In both cases, make sure you use the appropriate setting for manipulating long trajectories: http://pymolwiki.org/index.php/Defer_builds_mode 2015-10-06 12:39 GMT+03:00 Timofey Tyugashev : > Is there any way to load .xtc or .trr files into PyMOL to view > trajectories? > This user page on the wiki suggest the way, but it looks like it's > outdated and defunct now. > pymolwiki.org/index.php/User:Speleo3/VMD_plugins > > > > -- > Full-scale, agent-less Infrastructure Monitoring from a single dashboard > Integrate with 40+ ManageEngine ITSM Solutions for complete visibility > Physical-Virtual-Cloud Infrastructure monitoring from one console > Real user monitoring with APM Insights and performance trend reports > Learn More > http://pubads.g.doubleclick.net/gampad/clk?id=247754911&iu=/4140 > ___ > 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 > -- Full-scale, agent-less Infrastructure Monitoring from a single dashboard Integrate with 40+ ManageEngine ITSM Solutions for complete visibility Physical-Virtual-Cloud Infrastructure monitoring from one console Real user monitoring with APM Insights and performance trend reports Learn More http://pubads.g.doubleclick.net/gampad/clk?id=247754911&iu=/4140___ 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] GROMACS trajectories
Is there any way to load .xtc or .trr files into PyMOL to view trajectories? This user page on the wiki suggest the way, but it looks like it's outdated and defunct now. pymolwiki.org/index.php/User:Speleo3/VMD_plugins -- Full-scale, agent-less Infrastructure Monitoring from a single dashboard Integrate with 40+ ManageEngine ITSM Solutions for complete visibility Physical-Virtual-Cloud Infrastructure monitoring from one console Real user monitoring with APM Insights and performance trend reports Learn More http://pubads.g.doubleclick.net/gampad/clk?id=247754911&iu=/4140 ___ 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 + gromacs trajectories
Thank you, Bruno and Tsjerk. I found both approaches work very well.
Eric
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
Re: [PyMOL] pymol + gromacs trajectories
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
> >>
> >>
> >>
> >> ---
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> >
> >
> >
> >
>
>
--
~
-- :)
-- :) 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!
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Re: [PyMOL] pymol + gromacs trajectories
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
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http://brunoafonso.net
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http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum
Re: [PyMOL] pymol + gromacs trajectories
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!
-- :)
~
[PyMOL] pymol + gromacs trajectories
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
