[phenixbb] modify_start_model.adp.set_b_iso doesn't seem to work on PDB files with ANISOU cards

Stephen Graham stepheng at strubi.ox.ac.uk
Mon Jan 21 10:11:53 PST 2008

Hi all,

I just tried to reset my B values to the wilson B before TLS
refinement (in an attampt to shake some model bias that I am sure is
hiding somewhere in my temperature factors...).  My start model was a
TLS-refined PDB file from phenix.refine (hence with ANISOU cards).  I
issued the following command:

> phenix.refine my_model.pdb my_data.mtz modify_start_model.adp.set_b_iso=60 output.prefix=my_model_resetB main.number_of_macro_cycles=0

As far as I can tell, this should reset my B values to 60 and then
exit.  However, when I look at the resultant PDB file the Bs for all
the solvent molecules 60 but for the protein they are not; rather the
protein Bs are almost identical to the starting PDB file.

If I try to remove the TLS-derived ANISOU cards by adding the command
line option "adp.convert_to_isotropic=true" the result is the same
(except the output PDB file no longer has ANISOU cards).

However, if I strip out the ANISOU cards from my starting pdb file and
_then_ run the above command the resultant PDB file _does_ have the
correct values for both protein and solvent.

It seems like modify_start_model.adp.set_b_iso=60 does not work when
atom has an ANISOU card.  The behaviour I would *expect* would be for
the adp be reset to an 'isotropic' 60 (i.e. set the diagonal elements
to 1 and the off-diagonals to 0).  Is this a bug, or am I doing
something silly?



Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

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