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 <r...@post.queensu.ca>:
Hi,
* Joel Tyndall <joel.tynd...@otago.ac.nz> [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
<r...@post.queensu.ca> 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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