How do I use DNA as search model? Can I use it in molrep or phaser?
On Thursday, July 24, 2014, FOOS Nicolas <[email protected]> wrote: > Dear Yang, > > you should try different search model, for example : > 1) DNA only, > > 1) DNA > 2) protein > > 1)DNA+Prot > > etc... You can also try to find a partial solution and keep this solution to place the other molecules with another round of MR. > > Be careful if you use only DNA, if the density doesn't show clear proteic shape, you could have a false positive (a bit like with alpha helix for coil structure) > > One tips, sometimes the DNA could be organised in "infinite Helix" in the crystal, you can try to use DNA 2 times longer than you expect especially if your DNA molecules has over-hang. > > Nicolas > ________________________________________ > De : CCP4 bulletin board [[email protected]] de la part de dusky dew [ [email protected]] > Envoyé : jeudi 24 juillet 2014 13:50 > À : [email protected] > Objet : [ccp4bb] Problem in molecular replacement > > DEAR ALL > I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. > Please suggest. > Thanks > Yang zhang
