Also check if you have correctly estimated no. of molecules in asymmetric unit.
On Fri, May 21, 2010 at 4:58 PM, Tim Gruene <[email protected]> wrote: > Dear intekhab, > > a few suggestions: > - are you sure of the space group or might there be alternatives? > - is you protein globular or modular, i.e., is it worth running MR with > stable > subdomains one after the other? > - try a poly-alanine model (e.g. chainsaw can do this for you, pdbset > probably, > too) > - did you get overloads? If so, collect a low resolution pass to get > correct > intensities even at the poor resolution end. > - what is your low resolution limit? Did you use the default or could you > extend > it? > - did your crystal(s) suffer from radiation damage? It might be worth > collection > only a complete data set with not too high multiplicity. > > Good luck, Tim > > On Fri, May 21, 2010 at 08:01:10PM +0900, intekhab alam wrote: > > Hi all > > I am trying to do molecular replacement with low resolution (4Å) using > > Molrep and Phaser. > > > > Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95. > > > > Identities between my protein and templates were more than 80%. > > > > I couldn’t get correct solution. > > > > Rotation function, translation score, and contrast were low, and they had > no > > significance, though I changed the range of resolution. > > > > Molrep suggested solution coordinates clashed with symmetry molecules. > > > > I tried MR after remove clashed regions, but another clashes happened. > > > > In the case of phaser, there were many clashes, too. > > > > Please, give me any suggestion. > > Should I concern about any options when I run MR programs? > > > > Hope you guys will be interested to answer!!!!!! > > Thanks in advance > > > > > > -- > > INTEKHAB ALAM > > LABORATORY OF STRUCTURAL BIOINFORMATICS > > KOREA UNIVERSITY, SEOUL > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > > iD8DBQFL9m5wUxlJ7aRr7hoRAnJRAJkBglzDPgqcJ07lOf8wLpGTornFyACeMxwB > XCPdN9n9Km6Gdn2SK+jv8WY= > =ncth > -----END PGP SIGNATURE----- > >
