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:
It seems due to the fact that youre selection s is not a valid selection.
Try to simplify it by simply giving
(model, chain, resi, name)
It should be enough to define a single atom, as required by get_angle
On 9/25/14 5:27 AM, Lei Chen wrote:
> Hi,
> I still have trouble. I am not sure if it is
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 27.3945.02
ATOM 2 H FIL T 537 -44.620 -88.474 27.363
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
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 al
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
ato
