Hi Alicia,
the DistancesRH script seems to do a lot of specific stuff beyond simple
distance matrix calculation. If you have scipy installed, this will give
you a distance matrix:
from pymol import cmd
from scipy.spatial.distance import cdist
coords = cmd.get_model('guide').get_coord_list()
distances = cdist(coords, coords)
Note the "guide" selection, which are all the polymer CAs.
See also:
http://pymolwiki.org/index.php/Get_Coordinates_I
http://pymolwiki.org/index.php/Single-word_Selectors
http://docs.scipy.org/doc/scipy/reference/spatial.distance.html
Cheers,
Thomas
Hersey, Alicia wrote, On 08/21/13 00:59:
> Hi all,
>
> I am trying to make a data matrix of pairwise distances between all
> alpha carbons of a protein. Currently I am using the script DistancesRH
> but this spits back the distances from one alpha carbon to all other
> atoms. Any way to only do CA to CA or is there another script to use? Thanks
>
> - Alicia
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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