[phenixbb] Searchable phenixbb

[Peter Zwart]

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
>  >
>
> _______________________________________________
>  phenixbb mailing list
>  phenixbb at phenix-online.org
>  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
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