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.

I used my .sca to create a .mtz with phenix.reflection_file_converter and modifiers twin_law="h,-k,-l" xray_data.r_free_flags.generate=True I used to phenix so the I knew this free set is ok for (at the time possible) twinning. Thanks to you and Pavel for the quick response. Have a good weekend. Mark On Fri, 11 Apr 2008, Peter Zwart wrote:

Hi Mark,

If you have assigned free flags with ccp4, you are in soup. phenix.refine does not enforce a twin consistent free set, which not have unless you made it with cns or within phenix.

you could try autosol / autobuild (which will assign a proper set for you), and use twin info during refinement if you provide it (RTPhM).

hth

P

2008/4/11, Mark Collins :

...

Ok first of all, DOH! I always forget I can do that in google. But as Pavel suggests I put in my questions anyway, here it goes....

...

From the Yeates twinning server and xtriage my data seems to be twinned at approx 22-25%, the log is attached. 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. 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? My other questions alternate conformations, is it possible to refine the occupancy?

Thanks Mark

On Fri, 11 Apr 2008, Francis E Reyes wrote:

...

http://www.google.com/search?hl=en&q=phenixbb+site%3Aphenix-online.org&btnG=Search

Google seems to be indexing it.

On Apr 11, 2008, at 12:33 PM, Mark Collins wrote:

...

Hi phenix community Is there a search function for this bb, as there is for the ccp4bb? I have some questions about twinning, TLS and alternate conformations in phenix.refine. I hate repeating questions that have been answered previously but going thru the Archives month by month is proving to be a little slow. Thanks Mark Collins _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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-- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net ----------------------------------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb