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()
# f
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 transiti
