[gmx-users] Questions about Visualization
mgoette at mpi-bpc.mpg.de
Mon Jun 6 12:32:02 CEST 2005
First: There is a VMD-Mailinglist available. I am sure, you will get
much more help there.
Second: If I am right, its not too hard to make a movie of 10 PDBs in
VMD. But, if I remember correctly, every PDB-File has to have the same
number of atoms and the same atom types...
Then, you should be able to use the Movie-Plugin to make your movie.
Perhaps, you also need to RMSD your files, but I am not sure...
Third: There is a nice "new" visualization tool called YASARA. The
viewer is for free, but I don't know, if you are able to use movie
making functions in it. The "commercial" version is still quite cheap,
and my personal opinion is, that this program is one of the best
free/low-cost tools, I have seen...BTW, the guy who wrote that program
is a really nice fellow ;)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
李 猛 wrote:
> Thanks for your reply!
> I have learned VMD by myself for two weeks, I am the only first one in
> my group who use VMD, so I can not find any other people to help me. I
> just know some basic operations of it, Could you please help me out on
> how to make an animation from the 10 PDB input files?
> Is it right that I load the 10 PDB files together?
> Meng Li
>> From: sabuj pattanayek <sabuj.pattanayek at vanderbilt.edu>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Questions about Visualization
>> Date: Wed, 01 Jun 2005 19:57:01 -0500
>> There are several programs that can do what you need: VMD
>> (http://www.ks.uiuc.edu/Research/vmd/), UCSF Chimera
>> (http://www.cgl.ucsf.edu/chimera/), and Pymol (http://pymol.sf.net). You
>> may need to convert your txt file format into a standard coordinate
>> format such as PDB (which itself is a simple txt file) or some other
>> format that these programs can understand. For example you could do
>> something like this:
>> HETATM 1 MG MG A 1 128.591 82.670 19.892 1.00 1.00
>> This would make a single (Mg) ion at x, y, z locations 128, 82, and 19.
>> Note that the spacing is important in PDB format (see
>> Hope that helps,
>> Sabuj Pattanayek
>> 李 猛 wrote:
>> > Hi:
>> > I am a student in St.Francis Xavier University, Canada. I am sorry that
>> > i am rude interrupting you by writing this email. I am a research
>> > student this summer for Physics department of my university.
>> > I am looking for a visualization tool to simulate the movement of
>> > spheres(actually moleculars), they collide with each other and then
>> > to another location in a certain box. The input data are locations of
>> > spheres that generated by another program.
>> > Suppose there are 100 spheres in a box. The input data are 10 txt files
>> > that include position (X, Y, Z) of each sphere at 10 different time. I
>> > want to make an animation of the molecular according to the input
>> > Could you please give me some suggestion on the visualization tools
>> > that take txt file as a input? I am really appreciate your help!
>> > Meng Li
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