Try this, assuming you have good data. Use one molecule you got to do refinement (rigid body or restraint refinement with tight restraint) and phase the map. Then do a phased map molecular replacement. You might want only use the core of your protein to do the molecular replacement search to avoid the clashing problem. It worked once for me even the map was very bad.
Nian On Tue, Dec 7, 2010 at 3:38 PM, Arnon Lavie <la...@uic.edu> wrote: > Hi there: > > The situation: We are facing difficult molecular replacement: we believe we > have two molecules in the ASU, but phaser/molrep find only one. Using the > electron density calculated using this single molecule, we have manually > placed the 2nd molecule, albeit not good enough for rigid body refinement. > > Our strategy: We are looking for a program to do a 3 dimensional search > around the current position of the 2nd molecule. Maybe one that calculates > R-factor at the different positions, to allow to identify the correct one. > ... > > Does anyone know of such a program, or an alternative approach? > > Thanks. > > Arnon > > -- > *********************************************************** > Arnon Lavie, Professor > Dept. of Biochemistry and Molecular Genetics > University of Illinois at Chicago > 900 S. Ashland Ave. > Molecular Biology Research Building, Room 1108 (M/C 669) > Chicago, IL 60607 > U.S.A. > Tel: (312) 355-5029 > Fax: (312) 355-4535 > E-mail: la...@uic.edu > http://www.uic.edu/labs/lavie/ > *********************************************************** >
