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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