[phenixbb] Defining planarity for Phenix.refine

[Alan Cheung]

Hi Peter - i've managed to do this for some nucleic acids by using a 
custom cif file that contained planar restraint links for each type of 
base pair, and then specifying a phenix .params file that applies these 
cif links to specific base pairs in my model.

e.g. for a G-C base pair (DNA-RNA hybrid), the cif file would have...

data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
GdCr  Gd . . Cr . . GdCr

data_link_GdCr

loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
GdCr   p  1 N1  0.02
GdCr   p  1 C2  0.02
GdCr   p  1 N2  0.02
GdCr   p  2 O2  0.02
GdCr   p  2 C2  0.02
GdCr   p  2 N3  0.02
GdCr   p  1 N1  0.02
GdCr   p  1 C6  0.02
GdCr   p  1 O6  0.02
GdCr   p  2 N4  0.02
GdCr   p  2 C4  0.02
GdCr   p  2 N3  0.02


...and in the .params file...


refinement.pdb_interpretation.apply_cif_link {
   data_link =  GdCr
   residue_selection_1 = chain T and resname Gd and resid 23
   residue_selection_2 = chain P and resname Cr and resid 7
}



I also had to combine it with h-bond base pair restraints with the usual 
refinement.geometry.restraints.edits settings.

Alan






On 19/04/2010 12:23, Peter Grey wrote:
> Dear all,
>
> I have an RNA/Protein big complex at low resolution (roughly 4A). I
> would like to have the base pairs in the RNA as close as possible to
> ideal base pairs.
> I added restraints for distances between base pair hydrogen-bonding
> atoms but this is not enough to ensure that the bases will be  in the
> same plane.
> Could you suggest how to define for  Phenix.refine this planarity ?
>
>
> I am grateful for your advice,
>
>
> Peter
>
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
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-- 
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: cheung at lmb.uni-muenchen.de