Re: [PyMOL] measure angles in programming

[Sampson, J. <Jar...@ny...>]

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...@pi...<mailto:mp...@pi...>> 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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