[phenixbb] ramachanran plot refinement or restraint?
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 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:
>> 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
>>> 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
>>> We don't have much experience using the phi, psi restraints.
>>> If you don't mind, please let us know how it goes!
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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