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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