[phenixbb] ramachanran plot refinement or restraint?

Pavel Afonine pafonine at lbl.gov
Wed Jul 25 20:33:02 PDT 2007


I'm absolutely agree with you.

Jianghai Zhu wrote:
> 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
> +++++++++++++++++++++++++++++++
> 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
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