[phenixbb] geometry in phenix.refine
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 21 20:11:35 PST 2008
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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