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Peter,<br>
<br>
adptbx.u_as_b(-1) = -78.96.<br>
<br>
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.<br>
<br>
Pavel.<br>
<br>
<br>
Peter Zwart wrote:
<blockquote
cite="midbbd5677f0706130840l7406a6b5jb14f185452fcb7dc@mail.gmail.com"
type="cite">
<pre wrap="">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 <a class="moz-txt-link-rfc2396E" href="mailto:Kate.Kavanagh@sgc.ox.ac.uk"><Kate.Kavanagh@sgc.ox.ac.uk></a>:
</pre>
<blockquote type="cite">
<pre wrap="">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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