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/pymol-users@lists.sourceforge.net/msg10995.html
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html
Hope that helps.
Cheers,
Thomas
On 15 Dec 2016, at 07:02, chemocev marker 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.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net