Can you check space group in your mtz and pdb? I have seen this happening when they disagree. It is annoying and I would like it to be sorted out. If you want you can send your data and I can try to sort it out.
Garib On 18 Jul 2012, at 17:50, Deepthi 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 Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
