[phenixbb] geometry in phenix.refine

Jianghai Zhu jzhu at cbr.med.harvard.edu
Thu Feb 21 07:47:52 PST 2008


I recently noticed that the geometry in my structure is much worse  
than my previous model.  Here are some examples.

The RMSD results after a refinement by phenix 1.3b.

stage       angl   bond   chir   dihe   plan   repu
3_bss:   0.711  0.009  0.059 18.282  0.002  3.917

after switching to cci version 2008_02_08_1610, I tried to do a  
geometry minimization by setting wxc_scale = 0. The RMSD I got from  
the previous model is as following.

stage       angl   bond   chir   dihe   plan   repu
0    :   1.394  0.124  0.147 20.782  0.004  3.925

and after 6 macro cycles of geometry minimization,

stage       angl   bond   chir   dihe   plan   repu
6_bss:   0.622  0.011  0.120 13.143  0.003  3.822

It funny that the RMSD are so different for the same model.  What  


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

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