The self rotation isnt the correct input to the translation function - just run the Auto-Molrep option.. Eleanor
On Thu, 21 Jul 2011 20:57:02 +0800, Hubing Lou <[email protected]> wrote: > I also processed with Imosflm and ran Pointless, it was P21. Also it was > indicated by the "Intensity systematic absences" in HKL2000 scale.log file. > > Best, > Hubing > > On Thu, Jul 21, 2011 at 8:44 PM, > <[email protected]>wrote: > >> ** >> Dear Hubing, >> >> One maybe stupid question: Your are sure the space group is P21 and not >> P2 >> or even something else? Did you test other possible space groups? >> Choosing >> the wrong space group could exactly lead to the results you observe. >> >> Best, >> Herman >> >> >> ------------------------------ >> *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of >> *Hubing >> Lou >> *Sent:* Thursday, July 21, 2011 6:46 AM >> *To:* [email protected] >> *Subject:* [ccp4bb] Phaser and Molrep gave different solutions >> >> Dear all, >> >> I am stuck in a molecular replacement case and looking for advices. >> I have been working on a protein-DNA complex structure. >> Data was processed by HKL2000 to 2.6Ang and some of the data statistics >> are >> shown below: >> >> Space group: P21, >> Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90 >> Redundancy: 2.8 (2.7) >> Completeness: 94.8 (93.1) >> Linear R-fac: 0.051 (0.442) >> >> Data quality was checked by Phenix.xtriage and there's no problem. I then >> prepared a model by Chainsaw. Our protein shares only 30% of sequence >> similarity with the model, but structurally they are in the same group >> and >> almost identical in apo form. Matthrews Coeff indaced two monomers in >> AU. I >> then ran Phaser in "automated search" mode and there's a solution with >> RFZ >> score 4.8, TFZ score 3.8. The electron density map was not bad with DNA >> double helix clearly seen. However Refmac5 couldn't get Rfree lower than >> 50%. >> >> I then changed to MolRep, ran "self rotation function" first then used >> the >> first 10 peaks for translation search. Again there's a solution but it is >> different from that from Phaser. I attached a picture here. Checking in >> coot, the packing is the same. But, the refinement couldn't get Rfree >> lower >> than 50%. >> >> I have tried to include NCS, TLS refinement in Refmac, both not working. >> Hope someone out there can help. >> Thanks very much for your time. >> >> Hubing >> >>
