How about trying some ARP/WARP? JPK
On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine <pafon...@gmail.com> wrote: > 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 >> > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
