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

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Dec 26 18:53:29 PST 2007

Hi Dale,

If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the
pieces that you have, try to rebuild them (in nearby locations), and not
reassemble the molecule.  Rebuilding in place is supposed to be a way to
finish off your structure, and that's why it doesn't move it around.

In your case, you are rebuilding in place after Phaser molecular
replacement.  Usually Phaser will make a compact molecule during MR, so
this should not normally be a problem. I gather that in this case it
didn't do so, however.

With rebuild_in_place=No then AutoBuild should try and make a compact
molecule. If you have NCS then it will try to make a compact molecule with

All the best,
Tom T

> 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 \
>                   rebuild_in_place=Yes
>     Shouldn't AutoBuild build a compact model by default?
> Dale Tronrud
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