Re: [phenixbb] Death by Big-ass structure&[email protected]

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 :

...

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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