Arp/Warp server? JPK
On Thu, Apr 19, 2012 at 9:00 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk>wrote: > Several possibilities. > > 1) Phaser is very prone to reject solutions because of packing clashes.. > (PS How do you reset the packing limit in the current GUI?) > Running chainsaw before you begin the search can help - it prunes out > patches where the sequences don't match and gives a sensibly truncated > search model. > > 2) There is only one molecule - does it pack reasonably or are there great > holes in the map with suspicious density for a 2nd molecule? > > I would refine the molecule you have and rebuild if possible, then use > that model to search again > Eleanor Dodson > > > > On 19 April 2012 03:24, Ed Pozharski <epozh...@umaryland.edu> wrote: > >> 36% solvent sounds too low. Most protein crystals are at ~50%. On the >> other hand, if you assume one molecule, your solvent content jumps to >> 68% - not unheard of, but somewhat high for 1.7A resolution dataset. >> >> But you have a good MR solution, just try to refine/rebuild and see what >> you have in the density. >> >> Is your protein a dimer by any chance? Then you may have two dimers, >> only one is formed by crystal symmetry. Thus you'd have 1.5 molecules >> in asu, which would result in solvent content of ~52% - just right. If >> that is the case, run MR with the monomer. >> >> Cheers, >> >> Ed. >> >> On Thu, 2012-04-19 at 02:26 +0100, Krithika Sundaram wrote: >> > Hi all, >> > >> > I am working on an oxidoreductase and having some trouble during >> molecular replacement. >> > >> > The resolution of the crystal is 1.7 A and the space group is I4122 (a >> = b = 121.086, c =156.93 and alpha = beta = gamma = 90). >> > >> > The cell content analysis results predicted two molecules in the >> asymmetric unit and the solvent content as 36 %. The Matthew's coefficient >> is 1.94. The Wilson plot also looks fine. >> > >> > However, after molecular replacement (using Phaser) the result just >> gives me just a single molecule. ( RFZ = 8.5 TFZ =13.9 PAK = 0 LLG =189 >> TFZ=18.0 LLG = 642) >> > >> > Any suggestions how to solve this problem? >> > >> > Thanks in advance. >> > >> > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
