[phenixbb] phenix.superpose_pdbs_1.4

[David Garboczi]

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 
need?

thanks,
Dave



>  > 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.
>
>Ralf
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://www.phenix-online.org/mailman/listinfo/phenixbb


-- 
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


The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient.  If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices.  The National Institute
of Allergy and Infectious Diseases (NIAID) shall not accept liability
for any statement made that are the sender's own and not expressly made
on behalf of the NIAID by one of its representatives.