2009/8/24 Warren DeLano <war...@delsci.com>
> Carlos,
>
> The complication is that align outputs RMS values for only those atomic
> pairs remaining following sequence matching following by a refined structure
> alignment (which omits atoms above a cutoff), whereas rms outputs the value
> for all atoms matched by identifier (without any optimization).
>
> To run align without optimization, issue:
>
> align selection1, selection2, cycles=0
>
> where selection1 and selection2 are replaced with your atom selections, but
> remember that unmatched residues will not be included in the output RMS
> value.
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: Carlos Ríos Vera [mailto:crosv...@gmail.com]
> > Sent: Monday, August 24, 2009 1:44 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] RMS
> >
> > Hello people,
> >
> > I'm trying to use pymol from a custom python scrypt. What I have done
> > is to align two structures, but I need get the RMS value from that
> > align but I have no idea how to do it.
> >
> > I tried to use the RMS command but the value differs from the value
> > that I get from the align.
> >
> > Any Idea how to get that value?
> >
> > cheers
> >
> > ps: Sorry if my English is not so good
> >
> > --
> > http://crosvera.blogspot.com
> >
> > Carlos Ríos V.
> > Estudiante de Ing. (E) en Computación e Informática.
> > Universidad del Bío-Bío
> > VIII Región, Chile
> >
> > Linux user number 425502
> >
> >
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> >
> >
Thank you very much Warren,
Now I have a question about PyMOL api, because when I align two structures,
the outpur (rms value) is printed in te screen, but I need to store that
value into a variable, is that possible?
I mean, when I do this:
pymol.cmd.do("align %s, %s" %(name_struct1, name_struct2) )
How can I get the rms value into a variable?
cheers, and Thanks
--
http://crosvera.blogspot.com
Carlos Ríos V.
Estudiante de Ing. (E) en Computación e Informática.
Universidad del Bío-Bío
VIII Región, Chile
Linux user number 425502
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