Dear Shiva, Refining against weak and strong reflections separately only works if your intensity distribution is bimodal, because the problem arises from the assumptions of the scaling protocol (that typically assumes a unimodal distribution) that leads to underestimating the sigmas of the strong reflections and overestimating those of the weak reflections. So the first thing to look at is the cumulative intensity distribution (e.g. from Truncate) and if it looks normal, this trick won't help you. If you do see a cumulative intensity distribution biased towards weak reflections, then you could try scaling the pseudo-absent reflections separately, as explained in (doi:10.1107/S0907444906031519). I would expect that in this case the R-values will remain high, since the data are correlated and the normal assumptions for the expected values of R don't really hold any more.
HTH, Esko _____________________ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ESS AB P.O Box 176, SE-221 00 Lund, Sweden Visiting address: Tunavägen 24, Lund Switchboard: +46 46 888 00 00 Phone: +46 46 888 30 36 Mobile: +46 721 79 20 36 E-mail: [email protected] www.esss.se The European Spallation Source is a Partnership of 17 European Nations committed to the goal of Collectively building and operating the world's leading facility for research using neutrons by the second quarter of the 21st Century On Mar 22, 2012, at 11:28 PM, Shiva Kumar wrote: > Dear CCP4bb members > > I have a 3.0 Å dataset which has an off-origin peak of height 36% in > patterson map. The peak is at fractional co-ordinates 0, 0.5, 0.5. Data has > been indexed in P2(1)22(1) SG using HKL2000. I have located all the > molecules in asu (as far as I know) using Molrep with the 'locked rotation' > and 'Use' PST feature. After 1 round (20 cycles) of rigid body and 1 round > (10 cycles) of restrained refinement (Refmac), the R and Rfree are 49 and 53 > %. Although the R factors are very high, I feel the solution might be correct > because the electron density follows c-alpha trace in almost all places. To > be sure, I deleted a beta strand from the structure's core and repeated the > refinement and found that the electron density for the strand was still > present (I have no experimental phases). I have the following questions: > > 1) Are the final R factors never expected to reduce to acceptable values > given the 36% off-origin peak? > > 2) What is the best way to settle the SG? I was considering P2(1)2(1)2(1), > P2(1)22, P2(1)2(1)2 and P2(1)22(1), considering the off-origin peak is at > 0,0.5,0.5. I found all the molecules in asu only using the P2(1)22(1) data in > Molrep. Is this the best way to settle my SG? > > 3) Some CCP4bb archives advise either refining against weak and strong > reflections alternatively > (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=ccp4bb&D=0&1=ccp4bb&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=204490) > or refining against medium intensity reflections. Should I also be doing > these things? If yes, then what is the best way of doing it? > > Your suggestions and corrections to my interpretation of our data would be > appreciated. > > Regards > Shiva
