[phenixbb] geometry in phenix.refine

Pavel Afonine PAfonine at lbl.gov
Thu Feb 21 17:35:19 PST 2008


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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>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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