pymol-users

[PyMOL] distance atom-protein surface

[Giacomo B. <gba...@pa...>]

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

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
>
>-------------------------------------------------------------------------
>Take Surveys. Earn Cash. Influence the Future of IT
>Join SourceForge.net's Techsay panel and you'll get the chance to share your
>opinions on IT & business topics through brief surveys - and earn cash
>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>  
>

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

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

Re: [PyMOL] distance atom-protein surface

[Praedor A. <pr...@ya...>]

I needed to have a measurement of the "actual" physical long dimension of a 
protein model to compare with x-ray scattering data.  I activated the surface 
mesh feature and at the extreme ends of the longest axis, right at the 
surface boundary, created a carbon atom at each position, then simply used 
the distance measurement wizard to measure the distance between the too 
points.  

praedor

On Wednesday 10 January 2007 11:29, Andreas Henschel wrote:
> 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).
[...]
> 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,

-- 
Reichstag fire is to Hitler as 9/11 is to Bush