Odd twinning issue (or maybe all twinning issues are odd by default)
All I had a structure that seemed perfectly twinned in P41 21 2, completely built to the observable density (no peaks in 2Fo-Fc map over 2sigma) and refined to 33/35 (R/Rfree). I indexed, scaled, and merged the original unmerged data to P41, molecular replaced using the above model. Three rounds of rigid body refinement of the MR solution with group adp's dropped R/Rfree to 28/30 (while generating new free R flags based on the P41 data). The resolution was to 2.5 so I skipped the NCS. Now I try to do a second round of refinement with this time individual_sites and individual_adps with no change to the input model. The final R/Rfree's are now in the 50's? Am I missing something (fundamental) ? Thanks FR --------------------------------------------- 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
That is not supposed to happen ....
Not sure what the problem is.
Can you send two logfiles?
P
2008/9/11 Francis E Reyes
All
I had a structure that seemed perfectly twinned in P41 21 2, completely built to the observable density (no peaks in 2Fo-Fc map over 2sigma) and refined to 33/35 (R/Rfree). I indexed, scaled, and merged the original unmerged data to P41, molecular replaced using the above model. Three rounds of rigid body refinement of the MR solution with group adp's dropped R/Rfree to 28/30 (while generating new free R flags based on the P41 data). The resolution was to 2.5 so I skipped the NCS. Now I try to do a second round of refinement with this time individual_sites and individual_adps with no change to the input model. The final R/Rfree's are now in the 50's?
Am I missing something (fundamental) ?
Thanks
FR
--------------------------------------------- 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
-- ----------------------------------------------------------------- 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 -----------------------------------------------------------------
I know it's not what you asked, but I can't stop myself:
The resolution was to 2.5 so I skipped the NCS. How on earth does the one justify the other?? In my book, that's still half an Angstrom worse than where one should even start /thinking/ of skipping NCS, no?
(Sorry, it's my hobby-horse /du jour/.) phx.
participants (3)
-
Francis E Reyes -
Frank von Delft -
Peter Zwart