[phenixbb] geometry in phenix.refine

[Jianghai Zhu]

OK, there is more.  Apparently the huge difference between the rmsd  
bond came from phenix.reduce.  After adding the riding hydrogens by  
phenix.reduce, the rmsd bond jumped a lot.  Shouldn't the hydrogen  
atoms be added with perfect geometry?

Jianghai


On Feb 21, 2008, at 11:24 AM, Jianghai Zhu wrote:

> 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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>
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