 |
 |
You don't say how many molecules you are looking for? I would try to first work in SG C2 pretending that the pseudo translation is 100% of the origin. Reindex the data as k,l,h, change the SG to C2 and then redo the scaling and merging. You will lose all the reflections k+l =2n+1 in your indexing - h+k = 2n+1 after reindexing, but the MR should be simpler. Once you have a C2 solution you can convert it back to the orthorhombic one with a certain amount of intellectual struggle! The C2 origin along your b axis is free, so you will have to Or you can use ZANUDU from the ysbl software web site which will maybe help. Eleannor On Mar 22 2012, 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 > -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266