Hi,

you may want to read this before (yes, I remember, you deal with low resolution structure and the information from this link may not be 100% relevant to your case, but it is good to have a look anyway):

http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html

Cheers,
Pavel.



Ralf W. Grosse-Kunstleve wrote: 
Hi Jianghai,

  
I am refining a low resolution huge protein structure.  There are  
about 20% residues in the disallowed region of ramachandran plot.  Is  
there a way in phenix.refine to refine the phi, psi angles to get a  
better ramachandran plot?  or a phi, psi restraints in refinement?
    

If you add

  discard_psi_phi=False

to the phenix.refine command line the psi and phi dihedral angles
are restraint according to the CCP4 monomer library definitions
in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get
the full path name). Look for data_link_TRANS and data_link_CIS,
scroll down to _chem_link_tor.value_angle, to see the restraint
definitions.

We don't have much experience using the phi, psi restraints.
If you don't mind, please let us know how it goes!

Ralf
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