I am having issues using the 'stepped refine' (Extensions > All Molecule > Stepped Refine) feature in coot (0.7 rev 4459) for windows. It appears to ignore residues with multiple conformations as expected, but only when they are 'alone'. If a structure contains more than one residue with an alternate conformation in a row, the refinement moves one or both of the residues completely out of the density.
Is this a known issue, or is there a fix? Temporarily, I have been breaking up the alternate conformers in a series and rebuilding them after the refinement is complete. Thanks. Neil
