<div dir="ltr"><div dir="ltr"><div dir="ltr">As follow up, the best solution to this problem that I found at the moment is as follows (thanks to Oleg for suggestions/fixes).<div><br></div><div>1. Set occupancy of the first orientation to 0.5.</div><div>2. Set altloc of the first orientation to 1.</div><div>3. Set occupancy of the second orientation to 0.5.</div><div>4. Set altloc of the second orientation to 2.</div><div>5. Rename all the chain IDs of the second orientation (I used lowercase - i.e. A->a, B->b, etc).</div><div>6. If you need to keep two orientations close (I do in this case), define NCS groups as follows</div><div><div>refinement.pdb_interpretation.ncs_group {</div><div> reference = chain A</div><div> selection = chain a</div></div><div>}</div><div>7. Also, define the occupancy groups as</div><div><div>refinement {</div><div> refine {</div><div> occupancies {</div><div> constrained_group {</div><div> selection = chain A</div><div> selection = chain a</div><div> }</div><div> }</div><div> }</div><div>}</div></div><div><br></div><div>This works with phenix.refine. I've seen some adverse effects with coot - basically, LSQ/SSM no longer works. Obviously, splitting the full model into separate orientations helps. And finally, lowercase chains probably need to be renamed back to uppercase for PDB deposition.</div><div><br></div><div>Cheers,</div><div><br></div><div>Ed.</div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Nov 1, 2018 at 2:15 PM Edwin Pozharski <<a href="mailto:pozharskibb@gmail.com">pozharskibb@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Is there some way to make phenix.refine to ignore clashes for specific pair(s) of chains? I am dealing with a rare case of twinning where same protein molecule exists in two orientations in the same unit cell. I tried just to duplicate the molecule and set initial occupancy to 0.5, but refinement fails (as I expected) saying that there are too many close contacts. Ideally, I would like to proceed with ignoring close contacts between, say, chains A/B.<div><br></div><div>I am aware that one can exclude groups of residues from symmetry clashes, but these two copies are in the same cell. I guess I could try shifting one into the next unit cell and then excluding symmetry clashes, but even assuming that will work it is a rather ugly hack.<br><div><br></div><div>The alternative is probably to define the second orientation as an alternative conformation. Aside from aesthetic objections, I don't want to lose the ability to restrain NCS - I need two orientations to be identical structures, and I am not sure yet whether I can use NCS groups defined via alternative conformers.</div><div><br></div><div>Cheers,</div><div><br></div><div>Ed.</div></div></div>
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