[phenixbb] How do I gather the pieces after AutoBuild?

Dale Tronrud det102 at uoxray.uoregon.edu
Sun Dec 23 01:34:01 PST 2007

Hi all,

    I have finished my Autobuild but the resulting model has some residues
that are scattered in distant asymmetric units.  Coot shows their symmetry
images where they belong, next to the rest of the protein.  I could
rebuild these residues by hand in the right place, or collecte together
all the symmetry operators and write a script to gather them, but being
lazy would like a more automated solution.  Surely this happens to
other people and there is a tool that solves this problem.  I've read
a bunch of the web pages for AutoBuild but didn't find a solution there.

   My AutoBuild command was

phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \
                  map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \
                  seq_file=../fmo-ct.pir \
                  resolution=2.2 dmax=20 refinement_resolution=2.2 \
                  cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \
                  input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \

    Shouldn't AutoBuild build a compact model by default?

Dale Tronrud

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