Re: [PyMOL] distance atom-protein surface

[Andreas H. <ah...@bi...>]

Hi Giacomo,

you can either create an atom at that position
(see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than 
use the distance command (or wizard).

Or you can get the position of your first atom and simply calculate the 
distance of the two positions,
sth. like:

class MyAtom:
    def __init__(self, selection = "/1lov//A/1/CA"):  
        model = cmd.get_model(selection)
        self.coordinates = self.model.atom[0].coord ## requires at least 
one atom in the model
      
    def distance(self, coords): ## given some coordinates (list of three),
        from numarray import *
        distanceVector=array(self.coordinates)-array(coords)
        return sqrt(dot(distanceVector, distanceVector))

Hope, that's what you wanted!

Cheers,
Andreas

Giacomo Bastianelli wrote:

>Dear Pymol users,
>
>I would like to measure the distance between an atom and
>a specific point (not another atom) in the surface of the protein.
>Is it possible with pymol?
>do I need additional scripts?
>
>Thanks in advance,
>
>Giacomo Bastianelli
>
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-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...