[phenixbb] geometry in phenix.refine

[Jianghai Zhu]

Don't mind my email.  I got the wrong file.

Jianghai


On Feb 21, 2008, at 10:47 AM, Jianghai Zhu wrote:

> 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
>
> +++++++++++++++++++++++++++++++
> 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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