Hi Rohit, There are many refinement settings you can tweak and some local rebuilding in COOT based on difference density and validation reports can also help. PDB-REDO can help you a bit with this and it should be able to optimize your settings for Refmac. To avoid too much of a black box, while it is running you should probably read some of the Refmac papers to see what these different settings do.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > rohit kumar > Sent: Friday, September 15, 2017 13:33 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PAK=0 problem > > Thanks to all for replying. > > > If my solution is correct, why R/Rfree not going down from 21/25? > I have tried most of the options like Tls, ncs refinement in refmac5 but > these > options are not helping me, might be I am not expert with using these > options. > Could someone guide me how to use these options correctly during > refinement? > > > > > > On 15-Sep-2017 12:36 PM, "Eleanor Dodson" <eleanor.dod...@york.ac.uk> > wrote: > > > PAK=0 is GOOD - i.e. there are no clashes between symmetry > equivalent molecules. > So I think you have solved your structure. > Eleanor > > On 15 September 2017 at 07:20, rohit kumar <rohit...@gmail.com> > wrote: > > > Dear all, > > > During MR using PHASER with a 1.8 A data, I found that the > PAK=0 but all the other values are looking fine. > > When I run REFMAC5 the R/Rfree values are 25/30 (without > water) and 21/26 (after adding water). > > Just want to know whether my solution is correct or not. if > not please let me know what strategies I can use to get correct solution. > As I have tried all the combination in PHASER. > > Here I am attaching the result of PHASER . > > > > Inline image 3 > > > > Thank you in advance > > > -- > > WITH REGARDS > Dr. Rohit Kumar Singh > > >
