Re: [PyMOL] How to get the coordinates of the center of a group of atoms?

[Jason V. <jas...@sc...>]

Hi Cun,

That's a good start.  Just a couple things needs to be changed.
First, frames don't track coordinates, states do.  Frames are for
movies; states are for coordinates.  Next, instead of using center,
use the origin command with the state parameter specified.  Here's
example code for 1NMR a multi-state protein, adjust his for your
application:

python
cmd.fetch("1nmr", async=0)
coord=[]
for i in range(1,cmd.count_states()+1):
 cmd.origin("i. 1-24", state=i)
 coord.append(cmd.get_position())
print coord
python end

Cheers,

-- Jason

On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang <apz...@gm...> wrote:
> hi,
> I have a pdb file with serveral frames, I hope to get the trajectory
> of the center of a selected group of atoms.
> I use the following commands, but return the same coord.
>
> cmd.load("a.pdb")
> coord=[]
> for i in range(cmd.count_frames()):
>   cmd.frame(i+1)
>   cmd.center('id 1-24')
>   coord.append(cmd.get_position())
>
>
> What should I do?
>
> Thank you!
>
> Zhang Cun
>
> --
> Blog: http://www.edwardpku.com/cun
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
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