Conformer A atoms don’t “see” conformer B atoms so as far as the program is concerned the B conformer only has the last ring. You should set all confA atoms not in the last ring to blank conformers.
So: last ring - A +B conformers rest of ligand - no conformer Thanks, Nick ————————————————— Nick (Nicholas) Pearce Post-doctoral Researcher Lab of Piet Gros Crystal & Structural Chemistry Group Universiteit Utrecht > On 27 Oct 2017, at 13:41, Derek Logan <derek.lo...@biochemistry.lu.se> wrote: > > Hi, > > This is a cross-post to ccp4bb and phenixbb. I'm trying to refine a largish > small molecule ligand. It has two conformations that differ only in the > orientation of a terminal aromatic ring, i.e. variation in the last torsion > angle. I previously refined it as two independent conformations for the whole > molecule, but that showed too much deviation between the conformations in the > region that is "identical", i.e. that can be modelled just as nicely with a > single conformation. With Occam's razor I split the molecule at the last > torsion angle. Conformation A is the whole molecule; conformation B is just > the last ring. Both have the same residue number, just different altloc > labels. However when I refine this using phenix.refine, the B conformation > refines as if it were not attached to the A conformation (see the attached > screen dump). I tried it using Refmac and the two conformations separated > even more. Clearly this didn't work as I was expecting. What am I doing > wrong? Is it even possible to do it this way? > > /Derek > > <PastedGraphic-3.png>
