[phenixbb] geometry in phenix.refine
Jianghai Zhu
jzhu at cbr.med.harvard.edu
Thu Feb 21 17:19:40 PST 2008
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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> phenixbb at phenix-online.org
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