[phenixbb] geometry in phenix.refine

[Pavel Afonine]

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.
>>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20080221/87bf5e1a/attachment-0003.htm>