[phenixbb] How to keep a custom bond planar ?
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Tue Jul 24 12:31:49 PDT 2007
Also sorry for the late reply.
> How can I define a plan or some dihedral ??
Sorry, this is not implemented (not hard, but never got to it).
> Or as in the ligand .cif I defined a plan
> LIG plan-2 C1 0.020
> LIG plan-2 C2 0.020
> LIG plan-2 C3 0.020
> I could add the atoms NZ and CE of the lysine to the plan-2.
You can define the bond, angles, dihedrals, chiralities and planarities
with a cif link. Currently we don't generate such links automatically
(it is in the works). To get a start, copy one of the links from the
mon_lib_list.cif file; the command
will give you the absolute path. Give the cif link a unique name and
modify it for your situation. Then use "apply_cif_link" as described
in the phenix.refine documentation, e.g. at the CCI Apps download page
Let me know if you need more specific help.
More information about the phenixbb