[gmx-users] About g_rms and the XPM file format

[Víctor]

Yes, thanks. My first impulse was to do a python script to do the
conversion, but Tsjerk Wassenaar's script works neat :)

On Mon, Jan 23, 2012 at 5:10 PM, lina <lina.lastname at gmail.com> wrote:

> On Mon, Jan 23, 2012 at 9:56 PM, Víctor <victor.gil.sepulveda at gmail.com>
> wrote:
> > Dear all,
> >
> > I've been trying to do a rmsd matrix of  two different trajectories by
> using
> > g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> > uses does something like this:
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> >     superimpose f1 , f2
> >     calculateRMSD f1, f2
> >
> > Or like this (as I've seen in some other rmsd matrix calculation
> scripts):
> >
> > for each frame f in traj1:
> >   superimpose f with first frame
> >
> > for each frame f1 in traj1:
> >   for each frame f2 in traj2:
> >     calculateRMSD f1, f2
> >
> > I've also been trying to convert the resulting xpm file to a readable
> file
>
> BTW, xpm file is readable.
> try:
> more xpm or other tools your preferred to read.
>
>
> > in order to process it using python. Is there any tool to do this kind of
> > conversion?(Btw I've been trying to find this kind of tool with not much
> > luck). There's enough info on the file to be able to parse it easily, but
> > using a 3rd party tested tool would be more convenient.
> >
> > Thanks!
> >
> > --
> >
> > Víctor Gil Sepúlveda
> > E. Informatica - FIB - UPC
> >
> > --
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-- 

Víctor Gil Sepúlveda
E. Informatica - FIB - UPC
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