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Of course - none of us has given the best advice of all! Try to find a better ordered crystal! Eleanor On 2 July 2017 at 19:59, Matthias Barone <[log in to unmask]> wrote: > Beside the good propositions of fixing the environment, flip the peptide, > or using PDB_REDO, I would suggest the following additional attempts: > Try > 1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate > directly to Ala. See which ones remain visible in a diff map and bring them > back in during the upcoming ref cycles (refine OCCs in Phenix) > 2) use simulated CART annealing to get the side chains out of your way > 3) use a FEM map against misinterpreted side chains > 4) In very nasty cases, I use MOLOC to do real space refinement and give a > lot of weight to the H-Bond network. This usually helps to keep weakly > defined regions in place. > > good luck, matthias > > > > >>> Vipul Panchal <[log in to unmask]> 02.07.17 19.31 Uhr >>> > I do agree with Eleanor. When I was solving structure at 2.16A resolution, > outlier residues were having stearic clash or required side chain flipping. > > At 2.76A resolution, hydrogen bonds would be difficult to visulize. > > I found phenix.refine more user friendly. You may too find it useful. > > Vipul Panchal, > Ph.D. student > CSIR-IGIB > (M)- 091 7678617949 > > On 02-Jul-2017 9:14 PM, "Eleanor Dodson" <[log in to unmask]> > wrote: > > Just remember - most Ramachandran outliers are due to errors in the > environment - eg: maybe some side chains clash hence refinement tries to > move things to accommodate that bad feature, etc etc etc... > At that resolution it is inevitable you will have some level of > mis-interpretation .. > 4% outliers does not surprise me. > > EDSTATS is a useful tool to find things such as pep flips - you can access > it most simply from CCP4 GUI2 . > > But unless the outliers are in a important part of the structure I would > suggest checking, then living with them. > > Eleanor > > > > > > > On 2 July 2017 at 16:31, Rajesh Kumar <[log in to unmask]> wrote: > >> Dear Meytal, >> >> PHENIX-REFINE has an option for Ramachandran outlier refine. If you check >> this on, it will do the work. But after this refinement, you must check >> every residues to make sure residues are in the density. >> >> Thank you >> Rajesh >> >> >> ---xxxxx---- >> With regards >> Rajesh K. Harijan, Ph.D. >> Schramm Laboratory >> Albert Einstein College of Medicine >> 1300 Morris Park Ave., Bronx, NY 10461 >> Tel: 718.430.2777 | Fax: 718.430.8565 >> >> >> >> On Sun, Jul 2, 2017 at 7:26 AM, Meytal Galilee <[log in to unmask]> >> wrote: >> >>> Dear all, >>> I am refining a 2.76A structure using refmac5. >>> I keep fixing the Ramachandran outliers down to 18 (1.9%), however, upon >>> restrained refinement, the outliers increase back to 35. >>> Do you have any suggestions how can I fix my structure? >>> Thanks, >>> Meytal Galilee >>> >>> >> >> >> > >