[phenixbb] Problem with AutoBuild and Alternative Conformations

Thomas C. Terwilliger terwilliger at lanl.gov
Sun Dec 16 20:46:54 PST 2007

Hi again Dale,

I spoke too quickly...it is not so easy to change the code as I hoped.

However here is a work-around that may be preferable anyhow:

1. Remove your ligand from the PDB file to be rebuilt and put it in "lig.pdb"

2. add to your commands for autobuild:


This will put all the contents of lig.pdb at the end of all PDB files just
before refinement.

All the best,
Tom T

Hi Dale,

Your hypothesis:  "I suspect that the coder assumed that all alternative
conformations mutually exclusive and involve the same subset of the
residue."  is quite correct. (I am the coder in question).

I think that I may be able to fix this particular problem and take care of
the cases you have in this structure by simply allowing all conformations
of ligands in the input file to be kept during rebuilding.  With luck,
this will work and will be in the final 1.3b version due out very shortly.

The autobuild wizard still will not know how to build multiple
conformations into a structure. For the time being it will have to stick
with building one conformation.

Thanks very much for the suggestion!
-Tom T

> Hi,
>     I desire to resolve a crystal, who's structure factors I've downloaded
> from the PDB, using my new high resolution model of this protein from a
different species.  I have decided to use the AutoMR wizard from Phenix
for the chore.  The MR seems to work just find, but I've run into a
problem with the follow-up AutoBuild.
>     This protein has a peptide chain that I would like rebuilt with the
> proper amino acid sequence and seven Bchl-a molecules that I would like
to be carried through to the end.  Since the probe is from a high res
refinement it contains quite a few groups with alternative
conformations. This is not a problem in the protein part as it is being
rebuilt and comes back with a single conformation for each residue.  The
Bchl-a molecules, however, are being horribly mutilated.
>     In the Bchl-a groups, the "A" conformation is being promoted to
> be the "main" (and only) conformation and the "B", "C", "D", "E", and,
yes, the "F" conformations are lost.  A Bchl-a molecule is much larger
than an amino acid so it is quite possible, and reasonable, for one part
to have a "A" and "B" pair of conformations, another part to have a "C"
and "D" pair, and somewhere else for there to be a "E" and "F" pair. 
When conformation "C", "D", "E", and "F" are discarded whole sections of
the Bchl-a molecule disappear
> completely.  This is bad.
>     I suspect that the coder assumed that all alternative conformations
> mutually exclusive and involve the same subset of the residue.  I would
prefer a more careful analysis to uncover the fact that "A" and "B" go
together, and "C" and "D" go together.  If there is a need to reduce the
complexity of the model, (and I would prefer that all the alternatives
make it through to the end) could the program keep "A", "C", and "E", or
whatever makes sense for any particular residue? Better yet, instead of
always keeping the first alternative of a set, could it keep the one
with the highest occupancy?
>     I'm using phenix-1.3b-rc6 on a Fedora 6 PC.
> Thanks,
> Dale Tronrud

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