[phenixbb] ramachanran plot refinement or restraint?

Jianghai Zhu jzhu at cbr.med.harvard.edu
Wed Jul 25 20:23:36 PDT 2007

Yes, I am aware of the disadvantage that the ramachandran plot is no  
longer a validation tool if the phi-psi angels are restrained.   
However, in the situation of low-resolution structure, the electron  
density is not really good enough to confine the backbones.  Since  
the backbones can move around in the electron density without making  
differences in the refinement, why not restrain the phi-psi angels to  
those we know are correct.  Shouldn't them be better than the  
conformations with phi-psi angles that we know are not correct?  If  
the refinement program can't give me a better ramachandran plot, I  
probably will manually correct them in a modeling program like coot,  
which is tedious.  I heard Paul Emsley has a plan to build  
ramachandran plot target into the real space refinement in Coot.  It  
is not available in Coot last time I checked.

Adding riding hydrogens into the structure was a powerful validation  
tool.  But now we all add riding hydrogens into the refinement since  
it makes the refinement better.  At the same time, we lose some power  
in the validation.  We still think it is worth doing so, don't we?


Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232

On Jul 25, 2007, at 10:57 PM, Pavel Afonine wrote:

> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070725/df81d055/attachment-0003.htm>

More information about the phenixbb mailing list