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. Dale 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