What happens if you do a round of refinement in phenix.refine after you have done the mutations? Note: Phenix Autobuild is a tool to build your model, not refine it (though it does some refinement internally but may not be as fine tuned as your data/model may require).
Pavel On Wed, Jul 18, 2012 at 9:50 AM, Deepthi <deept...@gmail.com> wrote: > I tried opening the model with other spacegroups MTZ file. The map doesn't > fit well for other spacegroups. The initial model was refined using Phenix > Autobuild software. I tried MR with every spacegroup possible in primitive > hexagonal. Only p3221 worked. There is no twinning in the crystal. I will > try using other softwares for refinement but this is annoying. I also tried > mutating the model to poly alanines and refine but this made it worse. The > R-free went up to 0.546. > I initially thought it might be a space group problem but trying other > space groups doesn't work either. > > Thank youvery much for the help > Deepthi > > > On Wed, Jul 18, 2012 at 9:36 AM, Vellieux Frederic < > frederic.velli...@ibs.fr> wrote: > >> Hi there, >> >> Not much information provided. How was the initial model refined ? Phenix >> ? It could be a problem with the Refmac refinement protocol (difficult to >> say with so little information) if you switched from Phenix to Refmac. >> >> How certain are you 1 - of the space group; 2 - that the crystal wasn't >> twinned ? You can have both and it can be "annoying". >> >> Further, at this resolution I think you could use one of the SHELXes >> (forgot the terminology) for refinement, that could be more appropriate. >> >> F.V. >> >> >> Deepthi wrote: >> >>> Hi all >>> >>> I am working with a small mutant protein which is 56 amino acids long. >>> The crystal diffracted at 1.4A0 and the space group is p3221. I did >>> molecular replacement using Phenix software with all the data (1.4A0) and >>> got a solution. Phenix did auto building with waters and R-free was 0.3123. >>> >>> I mutated some residues which don't align with the model protein to >>> Alanines. When i change the residues back to their respective side chains >>> Refmac5 won't refine it well. The maps looks clear( you can guess its >>> 1.4A0 data) but R-free is shooting up to 0.41. It is not accepting any >>> changes to the Phenix generated model. I have no idea what is going on. Can >>> anyone help me? >>> >>> Thank You in advance >>> Deepthi >>> >>> >>> > > > -- > Deepthi >
