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:[log in to unmask]] On Behalf Of
> rohit kumar
> Sent: Friday, September 15, 2017 13:33
> To: [log in to unmask]
> 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" <[log in to unmask]>
> 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 <[log in to unmask]>
> 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
>
>
>
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