Dear Sir,
> 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. I check it, the unit cell dimensions are identical as I did not reprocess the data. I used the same processed data for both with change only during scaling by adding the native Rfree set. > 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. Ok. > 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. ;-) That would probably be the ultimate aim of CCP4!! Thank you Regards Kavya > > -----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. > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
