[phenixbb] Searchable phenixbb
PAfonine at lbl.gov
Fri Apr 11 14:11:39 PDT 2008
> 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
> 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
however it has a bug that will be fixed in the next release (in a few
Please let me know if you have any other questions!
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