[phenixbb] geometry in phenix.refine

[Jianghai Zhu]

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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