Yes, I'm absolutely agree with you. Pavel. 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Frank von Delft wrote:

Jianghai Zhu wrote:

...

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?

No: they are RIDING hydrogens, they do not influence the refinement (i.e. bumps), only the Rfactors/maps. Which is not the same as you ask for with the phi/psi angles.

Not at all. Adding the hydrogen atoms from high to low resolution can be viewed as adding additional anti-bumping restraints. The improvement in the R/Rfree factors in this case is mostly attributed to overall model geometry improvement and less attributed to adding additional scattering power to the structure (depending on resolution). Saying differently, the X-ray gradients for H atoms are zero, H atoms come to Fcalc and hence to X-ray target. However, the geometry restraints target "sees" hydrogens as good as other atoms. Cheers, Pavel.