You can use molrep or phaser as you prefer with DNA. To do that, you can edit you pdb file by hand with your favorit text editor (vim, emacs...) And you can cure your pdb file with Edit PDB File in ccp4 coordinate Utilities ________________________________________ De : dusky dew [duskyde...@gmail.com] Envoyé : jeudi 24 juillet 2014 14:46 À : FOOS Nicolas Cc : CCP4BB@JISCMAIL.AC.UK Objet : Re: Problem in molecular replacement
How do I use DNA as search model? Can I use it in molrep or phaser? On Thursday, July 24, 2014, FOOS Nicolas <nicolas.f...@synchrotron-soleil.fr<mailto:nicolas.f...@synchrotron-soleil.fr>> 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 > [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] de la part de dusky dew > [duskyde...@gmail.com<mailto:duskyde...@gmail.com>] > Envoyé : jeudi 24 juillet 2014 13:50 > À : CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > 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
