|-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.
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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