You knowe there are alternative indexing for H3 - you couldnt have solved one as h k l and the other as k h -l? And alternate origins - H3 is a polar spacegroup so if you redid the molecular replacement you may finish up anywhere along the c axis.. Easiest is to do a superpose of both sets of coordinates and see what the transformation required is - it will almost certainly be a crystallographically acceptable fit Eleanor
On 3 May 2013 10:02, Kavyashree Manjunath <[email protected]> wrote: > 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:[email protected]] On Behalf Of > > Kavyashree Manjunath > > Sent: Friday, May 03, 2013 10:07 AM > > To: [email protected] > > 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. >
