[phenixbb] geometry in phenix.refine
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 21 17:35:19 PST 2008
Hi Jianghai,
I'm confused about what you're comparing with what. Could you please try
this:
1) Take a model;
2) Run phenix.refine with it:
% phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0
strategy=none
3) Run phenix.pdbtools with it:
% phenix.pdbtools model.pdb --show-geometry-statistics
Is the geometry statistics reported by phenix.refine and phenix.pdbtools
different? If it is different then there is a problem and to fix it I
will need to look at that PDB file.
Pavel.
On 2/21/2008 5:19 PM, Jianghai Zhu wrote:
> Here are the results.
>
> phenix.pdbtools, riding H in the model.
>
> |-Geometry
> statistics---------------------------------------------------------|
> | Type | Count | Deviation from ideal | Targets |
> Target (sum) |
> | | | rmsd max min | |
> |
> | bond | 99522 | 0.004 0.085 0.000 | 0.028 |
> |
> | angle | 179035 | 0.793 21.106 0.000 | 0.099 |
> |
> | chirality | 7686 | 0.126 4.889 0.000 | 0.396 |
> 0.060 |
> | planarity | 15814 | 0.004 0.089 0.000 | 0.060 |
> |
> | dihedral | 24985 | 15.478 87.363 0.000 | 1.129 |
> |
> | nonbonded | 99522 | 3.939 4.900 1.125 | 0.725 |
> |
> |-----------------------------------------------------------------------------|
>
> phenix.pdbtools, without H in the model.
>
> |-Geometry
> statistics---------------------------------------------------------|
> | Type | Count | Deviation from ideal | Targets |
> Target (sum) |
> | | | rmsd max min | |
> |
> | bond | 51167 | 0.005 0.085 0.000 | 0.054 |
> |
> | angle | 69163 | 1.030 21.106 0.000 | 0.194 |
> |
> | chirality | 7686 | 0.126 4.889 0.000 | 0.396 |
> 0.142 |
> | planarity | 9110 | 0.005 0.089 0.000 | 0.104 |
> |
> | dihedral | 18756 | 17.864 87.363 0.000 | 1.504 |
> |
> | nonbonded | 51167 | 4.092 4.900 1.434 | 0.639 |
> |
> |-----------------------------------------------------------------------------|
>
> phenix.refine reports at the end of the refinement with riding H.
>
> stage angl bond chir dihe plan repu geom_target
> 0 : 1.394 0.124 0.147 20.782 0.004 3.925 1.1922e+00
> ...
> 6_bss: 0.622 0.011 0.120 13.143 0.003 3.822 2.6112e-02
>
>
> They are all different.
>
> Jianghai
>
> On Feb 21, 2008, at 6:01 PM, Pavel Afonine wrote:
>
>>
>>> Is it possible that phenix.pdbtools ignored the H atoms when
>>> calculating the geometry statistics?
>>>
>>
>> Currently no. But you can easily do it in two steps:
>>
>> 1) phenix.pdbtools model.pdb remove="element H"
>> output.file_name=model_noH.pdb
>>
>> 2) phenix.pdbtools model_noH.pdb --show-geometry-statistics
>>
>> Pavel.
>>
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>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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>
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