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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