Dear Kavya, There used to be a chaos with H3 and R3 settings so you first thing you might want to check that the same setting is used in both cases. Easiest would be to check the CRYST1 record in your pdb files to make sure that the same cell is used.
If you did not start for the second data set from the refined coordinates from the first one but reran molrep instead, your molecule might have landed in a different asymmetric unit/unit cell/origin. In that case I would superimpose the coordinates from the second refinement on those of the first refinement and maybe run one more cycle of refinement to get rid of rounding errors. The should solve your problem. Herman PS: I like the Effortless program, especially if they would add an option to write the paper as well with some buttons to select the desired journal e.g. Nature, Science, Cell etc. The cheat button should only be available for experienced users though. ;-) -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree Manjunath Sent: Friday, May 03, 2013 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] A small clarification Dear users, I wanted a small clarification, I was solving a ligand data in H3 space group with a dimer as the asymmetric unit. Initially, I had solved and refined this without using the same Rfree reflections as that of native data. So I resolved and refined the same data by considering the native Rfree reflections. In both the cases after the final refinement, the R and Rfree had reasonably good values. The problem arose when I compared the maps of data - (1) solved without same Rfree as that of native and (2) solved with same Rfree as that of the native They did not superpose at all. How is this possible? Although it is originally the same data and in each case the map traced the molecule very well, but when both maps are opened in coot they do not superpose at all. I would like to mention that the data has a pseudo translation symmetry with 17% peak. Is this responsible for the results I am getting? I hope one day there will be a program in CCP4 called "EFFORTLESS" which gives a structure from a given sequence!! :) Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
