Re: [PyMOL] Alpha carbon pairwise distances

[Thomas H. <tho...@sc...>]

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