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
Hi Tarun,
you are right, there was a typo in my previous email. The command should indeed
read "run mpng_3d.py". Just copy the file "mpng_3d.py" to a directory, start
pymol from this directory and enter "run mpng_3d.py" on the pymol command line.
Once you ran this command, you can run "mpng_3d m
some additional question about shell scripting (copied from the amber forum
because I'd like to find as more sollutions of this problem as possible):
I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared :
> Hi James -
>
> On Sep 22, 2014, at 4:30 AM, James Starlight
> wrote:
>
> Hi Jared,
>
>
> many thanks for the suggestion!
> your method works perfect (i only slightly modified dir for input file)
>
> #
