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 <rainfiel...@gmail.com> 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 <jared.samp...@nyumc.org>
> 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...@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 );
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
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