On 01/24/12 11:52, Miguel Ortiz Lombardia wrote: > El 24/01/12 18:56, Greg Costakes escribió: >> Whoops, I misspoke... I meant Rsym and Rmerge increase with higher >> redundancies. >> > > But then suppose that one merges data from a crystal that is degrading > while exposed, sp the data gets degraded. This is not at all unusual. In > the absence of a deep understanding of refinement, intuition suggests > that degraded data should produce degraded models. If Rwork and Rfree > are measuring anything useful they should go up redundancy in those > not-so-unusual cases. Or intuition is misguiding me again. >
Yes, if one has a poorer quality data set one expects the Rw and Rf to be higher, but this is not necessarily a correlation to high redundancy. Surely if you have high redundancy and know the crystal is decaying you have to flexibility to not use the decayed data in the merge. I would expect that decayed data would only be merged with the early data if the redundancy was so low that you had to just to get a full data set. Dale Tronrud > > -- Miguel > >> ------------------------------------------------------------------------------- >> Greg Costakes >> PhD Candidate >> Department of Structural Biology >> Purdue University >> Hockmeyer Hall, Room 320 >> 240 S. Martin Jischke Drive, West Lafayette, IN 47907 >> >> -------------------------------------------------------------------------------- >> ** Hard work often pays of in time, but Procrastination always pays off >> now ** >> >> ------------------------------------------------------------------------ >> *From: *"Dale Tronrud" <det...@uoxray.uoregon.edu> >> *To: *"Greg Costakes" <gcost...@purdue.edu> >> *Cc: *CCP4BB@JISCMAIL.AC.UK >> *Sent: *Tuesday, January 24, 2012 12:43:43 PM >> *Subject: *Re: [ccp4bb] Problem with getting Rfree and Rf down >> >> >> Is this observation about redundancies a general rule that I missed? >> It seems rather surprising to me. What have results have others seen? >> >> Dale Tronrud >> >> On 01/24/12 07:23, Greg Costakes wrote: >>> snip... >> >>> Higher redundancies (>7 or so) do tend to increase overall R/Rfree. >> >>> snip... >>> >> ------------------------------------------------------------------------------- >>> Greg Costakes >>> PhD Candidate >>> Department of Structural Biology >>> Purdue University >>> Hockmeyer Hall, Room 320 >>> 240 S. Martin Jischke Drive, West Lafayette, IN 47907 >>> >>> >> -------------------------------------------------------------------------------- >>> ** Hard work often pays of in time, but Procrastination always pays off >>> now ** >>> >>> ------------------------------------------------------------------------ >>> *From: *"Sam Arnosti" <meisam.nosr...@gmail.com> >>> *To: *CCP4BB@JISCMAIL.AC.UK >>> *Sent: *Monday, January 23, 2012 4:48:50 PM >>> *Subject: *[ccp4bb] Problem with getting Rfree and Rf down >>> >>> Hi every one >>> >>> I have some crystals in the space group P3121. I collect 180 frames of >> data. >>> >>> My crystals do not diffract better than at most 2.0 angstrom, but the Rf >>> barely goes below 23%, >>> >>> and Rfree also remains somewhere between 28-33%. I have tried to refine >>> my data as much as I can. >>> >>> I do not know whether the problem is because of the bad diffraction or >>> collecting extra frames. >>> >>> The structure factors are also high but they get better as the crystals >>> diffract better. >>> >>> Thanks >>> >>> Sam > >
