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 );
>
>
>
>
>
>
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