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

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Jan 21 14:34:26 PST 2008

    There is another task which should be considered when designing
this interface.  I can imagine situations where I would like to
change the isotropic component of some atoms while preserving
the anisotropic axial ratios.  If I wanted to slide up or down
the overall motion/disorder of a molecule but believed it reasonable
to assume the internal motions are the same I would like such a

Dale Tronrud

Pavel Afonine wrote:
> Hi Stephen,
> what you are seeing is actually a feature. If you have a PDB file with a 
> mixture of isotropic and anisotropic B-factors and you use a command 
> "modify_start_model.adp.set_b_iso=60" the program sets all isotropic 
> B-factors to 60 and leaves anisotropic ones unchanged (this is what the 
> command name suggest: set_b_iso).
> The easiest way to do what you want is to use phenix.pdbtools -- it is 
> very powerful tool for PDB file manipulations:
> 1) First, convert all atoms to isotropic:
> phenix.pdbtools model.pdb convert_to_isotropic=True 
> output.pdb.file_name=model_iso.pdb
> 2) Then set all isotropic b to a desired value:
> phenix.pdbtools model.pdb adp.set_b_iso=60 
> output.pdb.file_name=model_iso_60.pdb
> You can do these manipulations with the whole PDB file content or its 
> any selected part.
> I think in future we can change the behaviour of "convert_to_isotropic" 
> so if you say "convert_to_isotropic=True", then it just converts all 
> anisotropic B-factors to isotropic and if you say 
> "convert_to_isotropic=60", then it set all b to 60 regardless anything. 
> Something like this. Please let me know if you have a better idea.
> For more information on phenix.pdbtools:
> http://www.phenix-online.org/documentation/pdbtools.htm
> Cheers,
> Pavel.
> Stephen Graham wrote:
>> 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?
>> Cheers,
>> Stephen
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