[phenixbb] ramachanran plot refinement or restraint?

Pavel Afonine pafonine at lbl.gov
Wed Jul 25 19:57:43 PDT 2007


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):



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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