RE: [ccp4bb]: planarity restraint in refmac5

[Bart Hazes <bhazes@ualberta.ca>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


If overall geometric distortions are high then it is likely that the X-ray
weight was indeed too high. However, local distortions are more likely due to
errors in the model. If an aromatic ring is distorted there is not much point
in flattening it out again. Same for distorted bond lengths and angles. Fixing
these is well within the radius of convergence of the refinement program. If
you see these localized distortions it normally means that something else in
that area is wrong; e.g. VDW conflict, model error... These may well need
human intervention and should be warning flags to you during the next manual
rebuilding session.

Bart

On Fri, 13 Jul 2001, Huiying Li wrote:

> > My experience in agreement with Garib's advice is that the
> > X-ray weights are probably set high in default. I occasionally
> > run a regularization and refine few cycles with x-ray weights
> > low (Garib suggested 0.1, or lower at low res ( < 3.0)).
> >
>
> Thank you for pointing this out. I re-run the same REFMAC5 refinement with
> a weight at 0.1, the distortion in geometry is negligible. The default
> of X-ray weight in CCP4i (0.5) is apparently way too high for the data
> resolution (2.1 A) I have.

===============================================================================

Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta, T6G 2H7, Canada
phone:	1-780-492-0042
fax:	1-780-492-7521

===============================================================================