Re: [PyMOL] aligned and cealign command

Hi Jiri,

Try this on the PyMOL command line:

# example structures (use your own here)
fetch 1ake, s1, async=0
fetch 4ake, s2, async=0

# import the "angle_between_domains" command
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py

# align on chain A
align s1 & chain A, s2 & chain A

# measure rotation and displacement of chain B
angle_between_domains s1 & chain B, s2 & chain B, method=cealign

For 1ake and 4ake, this reports:
 Angle: 21.70 deg, Displacement: 56.08 angstrom

See also:
https://www.mail-archive.com/pym...@li.../msg10995.html
https://www.mail-archive.com/pym...@li.../msg13015.html

Hope that helps.

Cheers,
  Thomas

On 15 Dec 2016, at 07:02, chemocev marker <jir...@GM...> wrote:

> Hi Pymol user
> I have a heterodimer protein and I wanted to compare it with homologous structures. The chain B of both the structures can be align with align command and in doing so, the chain A is misaligned and which can be only align by the cealign command. The sequence similarity between chain A is very low but the both chains have similar fold. I am interested to know, how much degree the subunits move or rotate when we aligned the chain A with cealign command.
> best
> Jiri

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.