[phenixbb] How to keep a custom bond planar ?

[Ralf W. Grosse-Kunstleve]

Hi Mathieu,

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

  phenix.where_mon_lib_list_cif
  
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
(http://www.phenix-online.org/download/cci_apps/).

Let me know if you need more specific help.

Ralf