Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:
Hi James -
On Sep 22, 2014, at 4:30 AM, James Starlight jmsstarli...@gmail.com
wrote:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly
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
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
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
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,
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
