Hi Donghyuk, I feel you went ahead with right strategy. For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong indicator, i believe. If you have already build all possible model, using tls can be of further help.
Cheers, Vipul On Thu 10 Jan, 2019, 3:52 PM Donghyuk Shin <sdh...@gmail.com wrote: > Dear all, > > I am having tough time with my Xtal data sets those seem to be twinned or > have translational NCS, and it will be greatly appreciated if you can give > me some advices or comments! > > Data was initially processed with XDS and scaled with aimless without > specifying certain space group (SG). > Aimless picked the P 63 2 2 for the best SG, but the xtriage indicates > there is non-origin peak after patterson analysis. (attached log) > And, I could not get the proper MR-solution from this data sets. > > Because I read that twinning and tNCS cannot be properly distinguished at > high SG, I went down to subgroup either P32 or P6 assuming that there is > twinning which make data set seems to have apparently high SG. (procedure > was same XDS->aimless but I specified the SG to keep them) > Then, xtriage still indicates there is non-origin peak as before, but > found twin laws for the data sets (attached log). > However, I still could not get the right MR-solution. > Then, I went even further down to P3 or C2, and xtriage found more twin > laws which is make sense because of the lower SG. (attached log) > Again, I could not get the MR-solution. > For all the MR running above, I assumed that phaser(ccp4 module) > automatically applied tNCS if they present. or should I have to tick on > button in the expert parameters? > > Then, I went back to the image and processed the datasets with mosflm by > checking the indexed spots. > During this step, I played with the threshold for indexing to follow the > strong spot for get correct SG. > I am not sure whether this is correct or not, but by putting high > threshold for indexing (e.g. ~15) I could index the data with C2 which has > half dimension for a,b axes (116.348, 67.218, 182.861, 90, 90, 90) to the > original unit cell (232.533, 134.202, 182.67, 90, 90, 90). > With this, I could put 3 molecules in ASU by MR. During refinement, I felt > that the R values were not dropping, and I applied twin refinement. > without twin refinement the R values were (0.39/0.44, work/free), and > applying twin refinement gave me significantly better values (0.23/0.26). > Because there were 6 twin operators which may cause this huge R value > drop, I speculate whether this is true or not. > > Your comments will be greatly helpful! > > With you all the best, > Donghyuk > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
