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 <jirivit...@gmail.com> 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