Hi Nick, Pavel and Herman, Thanks for the lightning-fast tip about not using an altconf label for the common part of the molecule. That was the solution. So obvious when you think about it... My colleague Esko Oksanen also pointed out offline that I need to include the last atom before the phenyl ring with two conformations, otherwise the torsion angle wouldn't be properly defined. Indeed, without including this atom it blew up when idealising geometry in Coot, but with that minor modification it behaved just fine in both phenix.refine and Refmac.
@Pavel, thanks but it wasn't a visualisation glitch, as the rings were clearly displaced from each other. (BTW my message got bounced from phenixbb because of the screen dump I included). /Derek On 27 Oct 2017, at 13:47, Nick Pearce <n.m.pea...@uu.nl<mailto:n.m.pea...@uu.nl>> wrote: 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<mailto: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>
