[phenixbb] Searchable phenixbb

[Mark Collins]

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 <mcollins at convex.hhmi.columbia.edu>:
> >
> >  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
> >  > > phenixbb at phenix-online.org
> >  > > 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
> >  > phenixbb at phenix-online.org
> >  > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >  >
> >
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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
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