[phenixbb] SA-omit map

Thomas C. Terwilliger terwilliger at lanl.gov
Tue May 5 13:47:05 PDT 2009

Hi James,

As you found, if you put you multiple conformations in for the protein
autobuild will take only conformation 1 and it will ignore the others. In
the longer term, we plan to have autobuild deal properly with multiple
conformations, but that will take some time...

As a work-around, you could try this:  call all  the protein a "ligand"
and put it in this way (you need to give it one complete residue in the
model as "one_residue.pdb" (or any part of the model that has just one

phenix.autobuild data=data.mtz \
 model=one_residue.pdb \
 input_lig_file_list=model.pdb \

Autobuild treats ligands as a fixed structure during model building and in
omit maps, only adjusted during refinement, which is what you want in this

Let me know if that doesn't do it!

All the best,
Tom T

>> Is there anyway to get phenix.autobuild to NOT delete multiple
>> conformers when doing a SA-omit map?
>> Thanks,
>> jf
>> --
>> James Fraser
>> jamesfraser at berkeley.edu
>> Alber Lab
>> 356 Stanley Hall, QB3
>> UC Berkeley
>> Berkeley, CA 94720
>> http://ucxray.berkeley.edu/~jfraser/
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

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