Now I see what you did. I tried exact same things myself using an arbitrary structure from PDB. I couldn't reproduce your problem using both: the current development code and the latest CCI Apps: 2008_02_08_1610.

In this case I can only work on this problem if you send us the reproducer so we can reproduce your problem.

Pavel.


On 2/21/2008 6:06 PM, Jianghai Zhu wrote:
Sorry, I should have made it clear.

I started a refinement using phenix.refine with riding H in my model.  After the refinement, I got the following at the end of the log and the header of the pdb file.

 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


Using this refined model, I did phenix.pdbtools model.pdb --show-geometry-statistics.  And I got the following.

 |-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 |              |
|-----------------------------------------------------------------------------|

Using this refined model, I did phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 strategy=none.  And I got the following.

------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   0.608  0.003  0.120 12.395  0.003  3.928   2.9651e-02
------------------------------------------------------------------------

After removing the H from the refined model, I did phenix.pdbtools model_noH.pdb --show-geometry-statistics.  And I got the following.

|-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 |              |
|-----------------------------------------------------------------------------|


Jianghai


On Feb 21, 2008, at 8:35 PM, Pavel Afonine wrote:

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.



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