Respected Mam, The molecule is not along the C axis. I opened both these molecules along with the pseudo-translation peak generated by patterson function, it could be observed that the origin of the one of the dimer corresponded to the 2nd peak (pseudo translation) peak.
So I guess this is due to phaser recognising once the actual origin and another time the pseudo-origin during MR. However I am not sure whether it randomly selects one of the origin. Thanking you Respectfully KAvya > 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. >> > > -- > 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.
