[phenixbb] Remove distant restraint between two atoms
pafonine at lbl.gov
Thu Mar 3 08:16:01 PST 2016
> I would like to unrestrain the distance between two atoms in a ligand
> – how can I do this? I found instructions for writing a
> remove_restraints_selections.params file in the phenix.refine manual,
> but it does not seem to address bond distances.
bonds are not there indeed. Currently you can do it as following
(admittedly rather ugly!)...
Edit ligand CIF file to remove the definition of bond in question, then
run refinement providing this CIF file. If CIF file is part of Phenix
a) Find its location:
you will see something like this
b) Copy it to your place
Then edit ATP_edited.cif to remove the bond in question (I guess you
would want to remove angle too) and give it to phenix.refine along with
all other inputs.
Let me know how this worked (or didn't) for you!
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