Re: [PyMOL] measure angles in programming

[Thomas H. <tho...@sc...>]

Hi Lei,

those tunnel atoms all have the same name, thus the selection is not unique (not a *single* atom but multiple). For a script like that, it's best to select by atom index.

cmd.iterate("tunnel", 'stored.centers.append("(%s`%d)" % (model, index))')

Cheers,
  Thomas

On 24 Sep 2014, at 23:27, Lei Chen <rai...@gm...> wrote:

> Hi,
> I still have trouble. I am not sure if it is because the tunnel pdb is
> not standard. (it's an output file from another software called
> CAVER.)
> My tunnel pdb looks like:
> ATOM      1  H   FIL T 537     -44.636 -88.973  27.394        5.02
> ATOM      2  H   FIL T 537     -44.620 -88.474  27.363        4.90
> CONECT    1    2
> ATOM      3  H   FIL T 537     -44.574 -87.982  27.350        4.82
> CONECT    2    3
> ATOM      4  H   FIL T 537     -44.568 -87.484  27.315        4.78
> CONECT    3    4
> ATOM      5  H   FIL T 537     -44.561 -86.985  27.279        4.78
> CONECT    4    5
> ATOM      6  H   FIL T 537     -44.554 -86.486  27.243        4.82
> CONECT    5    6
> My codes：
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> stored.centers = []
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
> (model, segi, chain, resn, resi, name))')
> for s in stored.centers:
> print s
> angle = cmd.get_angle(start_point, end_point, s)
> print "%s: %3.2f" % (s, angle)
> cmd.extend( "vertical_distance", vertical_distance );
> 
> output:
> /tunnel//T/FIL`537/H
> GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
> 
> If I use cmd.angle, I get:
> cmd-Error: The 'pk3' selection is undefined.
> 
> 
> On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
>> 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...> 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 );

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.