[phenixbb] Problem with AutoBuild and Alternative Conformations

Dale Tronrud dale at uoxray.uoregon.edu
Sun Dec 16 22:43:04 PST 2007

    Thanks for the quick response.  I have been using the GUI so I'll
see if I can figure out what box to put this file in.

    AutoBuild did do an outstanding job, despite the problem with the
Bchl-a's and I'm looking forward to digging into the map, when I
get this stuff straightened out.


Thomas C. Terwilliger wrote:
> 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:
> input_lig_file_list=lig.pdb
> 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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