1) Check free R flag. It may be related with free flag being 1 instead of 0. If it is the case then you can use newer version of refmac: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
or from ccp4 v 6.3 2) Try arp/warp Garib On 19 Jul 2012, at 18:29, Deepthi wrote: > Hi > > Yes i did check my MTZ file header. It shows p3221. For the same reason i > reprocessed the data again in both p3221, p3121 and p321. Except for p3221 > none of the other space groups fit the model. The packing looks good and the > map shows side chains very clearly. When i add the respective side chain its > just not accepting. May be it is not the correct solution? Is it possible? > > Thank You > Deepthi > > On Thu, Jul 19, 2012 at 7:04 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > It isn't that your space group is wrong, but are you sure that your mtz file > has that space group in its header? > MR will test all possible alternatives - in this case P3121 or P3221 - but > won't change the symmetry information in the input mtz. > You need to do that with a utility like > mtzutils hklin1 p3121.mtz hklout p3221.mtz > SYMM P3221 > end > > And there are various options in the REFLECTION UTILITIES. > > The integration and data processing are exactly the same for either space > group, but REFMAC does not check that your mtz and pdb have the SAME symmetry > information, and by default uses that in the mtz file. So you could have a > perfectly good solution in P3221 but be running refinement in P3121, which is > NOT GOOD! > Eleanor. > > > 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 > > > > > -- > 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
