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

Dale Tronrud det102 at uoxray.uoregon.edu
Wed Dec 26 23:19:45 PST 2007

Dear Tom,

    I was about to write an answer to my own letter since I have a
solution, but I don't understand it.

    I have a molecular replacement solution in which each molecule
is compact and the two copies are right next to each other.
AutoBuild is tearing pieces out and scattering them about symmetry
space, although most of both molecules stay in the same place.

    My solution that fixes this problem and keeps the molecules
together?  Remove the methinone that the sequence file has as
the first residue.  The first 8 or 9 residues of this molecule
are disordered in both the original crystal and this crystal.
I was using the DNA sequence as the source for the amino acid
sequence but I believe the Met is removed post-translationally.
The first run had the Met and AutoBuild built molecules with
some parts far removed from the majority of the two peptides.
The second run had the Met removed from the sequence file,
and as far as I recall nothing else changed, and this produced
a proper model.

    Could this be a consequence of the sequence renumbering required
by the differing alignments?

    I'm moving on with this model.


Thomas C. Terwilliger wrote:
> 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
> NCS.
> 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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