Hi Mark,
I have an MR solution from a related MAD structure I solved and Arp/Warp rebuilt 99% of this structure without any account for twinning.
Just a remark... You could also do it in PHENIX using AutoMr, Autobuild wizards.
Upon refinement with twinning I get what I think are overly good (refined) R/Rf values (particularily with waters = refine 3). And refinement without twining gives R/Rf on the bad side for my resolution (2A) but not so terrible. And these improve to "reasonable" R/Rf with the inclusion of TLS and waters (= refine 5). I have looked at the structures and maps for both refine3-twin and refine5-notwin and see little differences but nothing major. So my dilemma is which structure to continue refiniing the twinned or not twinned+TLS, how do I know which is correct?
Looking at the numbers, I see no surprises: the most reasonable strategy produces the most reasonable results: refine5 (+TLS+H2O) with 0.1428 / 0.1770 for R-factors. - Yes, definitely accounting for twining is important since it seems to be present and it is supported by the R-factors. - At 2A resolution we normally see many waters, so you need to ask phenix.refine to keep them updated all the time using "ordered_solvent=true" option. The set of water picking parameters gives you a full control over the process, so you can adjust the amount and quality of picked waters. - The total atomic B-factor in phenix.refine is defined as : Btot = Bcryst + Btls + Blocal, where Bcryst comes from overall anisotropic scaling, Btls models the global motion of the domains or molecule as a whole, and Blocal models local atomic vibrations. If you use TLS you utilize a better model for the atomic ADP (providing a correct choice of TLS groups -- it is very important!), and without using TLS you force Blocal to model it which is not great (especially since the similarity restraints are used for ADP). So I would use TLS, but make sure to selects reasonable TLS groups.
My other questions alternate conformations, is it possible to refine the occupancy?
You can do it with the latest version available from http://www.phenix-online.org/download/cci_apps/ however it has a bug that will be fixed in the next release (in a few weeks). Please let me know if you have any other questions! Pavel.