[phenixbb] geometry in phenix.refine

[Jianghai Zhu]

Hi,

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  
happened?

Jianghai

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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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