Hi Manoj, Following on from Poul's reply, and maybe whilst you are waiting to get derivatives ;) you could try something like the following for getting around the model-bias-after-borderline-MR-issue.
1) generate a prime-&-switch'd map from resolve. 2) use this map to prune your model (be quite brutal here). 3) Re-refine, using refmac and, in parallel, a simulated annealing refinement protocol (CNS/Phenix). 4) Stick your pruned models and all these maps into coot and see what you can build back. I've found that schemes/strategies based around this can break the back of refinement after borderline MR. HTH Dave 2009/8/11 ManojSaxena <mks...@rediffmail.com>: > Hi all, > > I am working with a protein that have 28% similar to my MR template. > I have processed data in HKL2000 for one of my crystal and I got unique sol > in space group > P212121. with LLG 131 and TFZ score 13.5 > I have used buccaneer and coot for model building and my Rfee came to 45%. > I used the PDB file from this crystal ( Rfee of 45%) as my MR model for data > obtained from > another crystal and got sol with TFZ score=40.5 and LLG=2305. > > I used coot and did a round of refmac refinement now my Rfee is 41%. > > My concern is > a) wether my scheme is good or not because I am afraid that this will > increase the model > bias. > b)Now I am stuck at 41% Rfee I have many chain breaks and loop regions have > not good > density. I tried TLS refinement it did not help. what else I shall try?? > > Thanks > > Manoj > PSU > Biochemistry > -- ============================ David C. Briggs PhD Father & Crystallographer http://drdavidcbriggs.googlepages.com/home Skype: DocDCB ============================
