[phenixbb] Death by Big-ass structure&In-Reply-To=62619305-F45C-4B18-BF55-6AC08CA855D8 at lbl.gov

Pavel Afonine PAfonine at lbl.gov
Wed Jun 13 10:24:16 PDT 2007


Peter,

adptbx.u_as_b(-1) = -78.96.

When you read in a model with ANISOU records the equivalent isotropic B 
is ignored but instead the anisotropic one is read in. After you did 
your manipulations you write out a PDB file with isotropic ADP which 
results in -78.96. I quickly looked at your code and it seems to me  
that you don't take this into account. Please use or look for an example 
in  model.py facility to write out a PDB file: this is the common place 
we use to write PDB file after phenix.refine. Please let me know if it 
needs to be adjusted for your particular task or feel free to do it 
yourself.

Pavel.


Peter Zwart wrote:
> NOt sure what happens.
>
> I have to investigate.
> Could you send me example data and model? I'll have a look and see
> where the problem lies.
>
> Thanks
>
> Peter
>
> 2007/6/13, Kate Kavanagh <Kate.Kavanagh at sgc.ox.ac.uk>:
>   
>> Hi Peter,
>>
>> The reindexing works fine but when I try to convert back to R3:H all atoms with ANISOU records are given B-factors of -79.86:
>>
>> ATOM      1  N   MET A   1      16.402  60.069  44.768  1.00-78.96           N
>> ATOM      2  CA  MET A   1      16.316  58.621  44.978  1.00-78.96           C
>> ATOM      3  CB  MET A   1      17.622  57.922  44.573  1.00-78.96           C
>> ATOM      4  C   MET A   1      15.966  58.300  46.432  1.00-78.96           C
>> ATOM      5  O   MET A   1      16.196  59.115  47.326  1.00-78.96           O
>> ATOM      6  N   PHE A   2      15.408  57.114  46.661  1.00-78.96           N
>> ATOM      7  CA  PHE A   2      15.047  56.686  48.013  1.00-78.96           C
>> ATOM      8  CB  PHE A   2      13.750  55.866  48.016  1.00-78.96           C
>> ATOM      9  CG  PHE A   2      13.323  55.436  49.391  1.00-78.96           C
>> .....
>>
>> And since TLS refinement has been used, all protein atoms have ANISOU records.
>>
>> Any suggestions?
>>
>> Kate
>>
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>>     
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