Hi Jianghai,
you need to fix the jumping atoms before doing the refinement. Lets say you
want to fix all chloride ions, it would look like this:
# morph without refinement
rigimol.morph(rin, rout, refinement=0, async=0)
# get rid of the default movie
cmd.mstop()
cmd.frame(1)
cmd.mset()
# fix chlorides and run refinement
cmd.flag(fix, elem CL)
rigimol.refine(5, rout)
Hope that helps.
Cheers,
Thomas
On Mar 7, 2013, at 8:28 AM, Jianghai Zhu j...@idi.harvard.edu wrote:
Hi,
If I turn on the refinement option in morph, the non-covalently bonded atoms
like metals and waters are moving around a lot. However, if I turn off the
refinement, there are some distortions in my protein. Is there a way to make
the non-covalently bonded atoms just move along the transition path?
Thanks.
--Jianghai
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
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