Re: [phenixbb] Searchable phenixbb

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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- ----------------------------------------------------------------- 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