Hi,
you can just use the 'angle' command.
cmd.angle('angle1', 'start_point', 'end_point', a)
To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')
HTH,
Matt Baumgartner
On 09/24/2014 06:35 PM, rainfieldcn wrote:
> Hi all,
> I generate two pseudoatoms "start_point" and "end_point" by
> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
> in one chain.
> I want to measure the angle from each atoms in "tunnel" to "end_point"
> to "start_point". at the same time, I want to print the B-factor of
> atoms in "tunnel".
> To measure the angle, I programmed like this，but it doesn't work.
> I guess it's because get_angle function needs some particular variable
> format.
> By the way, how can I print the b factor of atom?
> Thanks,
> Lei
>
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> centers = cmd.get_model(tunnel,1)
> for a in centers.atom:
> angle= cmd.get_angle(start_point, end_point,a)
> print angle
> return (start_point, end_point, tunnel)
> cmd.extend( "vertical_distance", vertical_distance );
>
>
>
>
>
>
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