Hi Lei -
The `get_angle` command needs an atom selection for your “tunnel" atoms, which,
like the B-factor as Matt mentioned, you can also get using `iterate`:
###
# create a list
stored.centers = []
# get the macro selection string for each atom in tunnel
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
segi, chain, resn, resi, name))')
# loop through the list of centers and print each angle
for s in stored.centers:
angle = cmd.get_angle('start_point', 'end_point', s)
print "%s: %3.2f" % (s, angle)
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner
<mp...@pitt.edu<mailto:mp...@pitt.edu>> wrote:
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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