[phenixbb] phenix.superpose_pdbs_1.4

David Garboczi dgarboczi at niaid.nih.gov
Sat Feb 7 08:05:03 PST 2009

Yes, I recognize that one cannot arbitrarily move the model.

I have a unit cell and symmetry in which we determined a structure 
and refined a model; call this the reference.  But there are four 
other unit cells and symmetries of datasets that were, for various 
reasons, not sufficient to solve the structure.

After phaser-ing the model into each of the other datasets, I'd like 
to examine the four other packings for common packing interactions 
that may have biological relevance.  I am comparing symmates of the 
reference model with symmates of the superimposed model.

I've found that if I specify on the command line the unit_cell and 
space_group of the moving model, the "fitted" pdb file will have the 
unit_cell and space_group of the moving pdb.  That might be all I 


>  > The default unit cell and symmetry for the "fitted" model (the one
>>  that was moved) is the unit cell and symmetry of the "fixed" pdb.  As
>>  I am superimposing the same model from several space groups to study
>>  the differences in packing, I need the "fitted" pdb to keep its own
>>  unit cell and symmetry.  How might I do this?
>Could you run the superposition "the other way around", i.e. instead
>of fitting A to B fit B to A.
>>  When is the current default of altering the unit cell and symmetry of
>>  the moving model useful?
>In general, you cannot arbitrarily move a model with respect to the
>crystallographic symmetry; you will get clashes due to symmetry.
>If you fit B so that it is in the same place as A, and assuming A
>has no clashes due to symmetry, then B should have no clashes, too.
>phenixbb mailing list
>phenixbb at phenix-online.org

David N. Garboczi, PhD
Phone: 301-496-4773
Head, Structural Biology Section (SBS)
Research Technologies Branch (RTB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742	   
Fax:    301-402-0284
Email: dgarboczi at niaid.nih.gov

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