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
<[log in to unmask]> 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