I have battled a similar piece of structure in a recent project. There is no software in crystallography that can handle hierarchical alternative conformations w/o tricks. I was refining in Shelxl but the same trick will work elsewhere. I had to define a new residue type, with two heads. The A conformation had atoms for both heads. The B conformation didn't have atoms that couldn't be seen. I was missing the entire side chain in that conformation so the SC had no atoms.
Besides creating the new geometry restraint library, you will have to ensure that no bad contacts are flagged between the two heads. In Shelxl you can tie all the occupancies together properly, with a couple annoyances. In other programs you are on your own. Another possibility is to create four conformations for the entire stretch but then you'll have to have the program keep many pairs of atoms superimposed. I don't know if Refmac has that feature. You will, of course, have difficulties when you deposit this thing with the PDB. There is no way to correctly represent your model in a PDB file, nor I believe in mmCIF. It may be reasonable to switch to the four conformation model for deposition, since you will not have to worry about enforcing the superposition of atoms any longer. That may be clearer to people who use the model at a later date. Dale Tronrud Andy Millston wrote: > I am currently trying to refine a structure where a 5 residue stretch of > a chain is in 2 conformations. Oddly enough, 1 of these 5 residues is in > dual conformations in both the conformations! Is there a conventional > nomenclature for defining such dual-dual conformations? > > Refmac5 does not accept the intuitive way of naming such an atom. > > For example: A normal dual conformer GLY would be named as AGLY and BGLY > in PDB file and this is acceptable to Refmac5 > > When I name a "dual-dual" GLY as AAGLY and BAGLY, Refmac5 fails! Any > idea, WHY?? > > Thank you! > > Here is the error log: > ---------------- > Logical name: ATOMSF, Filename: /programs/ccp4-6.0.2/lib/data/atomsf.lib > > *************************************************************************** > * Information from CCP4Interface script > *************************************************************************** > The program run with command: refmac5 XYZIN "/home/../myfile.pdb" XYZOUT > "...tmp" HKLIN "....mtz" HKLOUT "....tmp" LIBOUT "..._56_lib.cif" > has failed with error message > fmt: read unexpected character > apparent state: internal I/O > last format: (I4) > lately reading sequential formatted internal IO > *************************************************************************** > > > #CCP4I TERMINATION STATUS 0 fmt: read unexpected character apparent > state: internal I/O last format: (I4) lately reading sequential > formatted internal IO > ---------------- >
