Re: [PyMOL] align states

[Andrea S. <and...@gm...>]

Hi,
the command intra_fit was the one! However, if I'd like to visualize
the first, let's say, 20 structures of my bundle?

thanks again

andrea

2006/7/19, Robert Campbell <rl...@po...>:
> Hi,
>
> * Joel Tyndall <joe...@ot...> [2006-07-15 14:29] wrote:
> > Hi andrea,
> >
> > you can easily do this by
> >
> > split_states my_struct
> > dele my_struct
> >
> >
> > for the NMR ensemble, then I would use the action menu, align function
> > and align them  to state_1. This is in effect aligning the separate
> > states as objects, unless I misunderstood you
> >
> > J
> >
> > Andrea Spitaleri wrote:
> > > Hi all,
> > > in pymol is it possible to align states rather than object. I mean, I
> > > have loaded a pdb file with n-structures and I'd like to align each of
> > > them on the first one of the bundle.
>
> If in fact the n-structures contain all the same atoms, then you can use
> the intra_fit command instead:
>
>   PyMOL> help intra_fit
>
>   intra_fit
>
>   DESCRIPTION
>
>      "intra_fit" fits all states of an object to an atom selection
>      in the specified state.  It returns the rms values to python
>      as an array.
>
>   USAGE
>
>      intra_fit (selection),state
>
>   PYMOL API
>
>      cmd.intra_fit( string selection, int state )
>
>   EXAMPLES
>
>      intra_fit ( name ca )
>
>   PYTHON EXAMPLE
>
>      from pymol import cmd
>      rms = cmd.intra_fit("(name ca)",1)
>
>   SEE ALSO
>
>      fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit
>
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Department of Biochemistry, Queen's University
> Kingston, ON K7L 3N6  Canada
>   <rl...@po...>         http://adelie.biochem.queensu.ca/~rlc
>   phone: 613-533-6821            fax: 613-533-2497
>   PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2
>
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