there is something on the menu, file->save->molecule after the alignment, choose the molecule you want to save and just save. pymol saves the pdb with new coordinates.
cheers, Abhi On Jan 25, 2008 10:29 PM, Lu Lin <l...@cs.hku.hk> wrote: > Hi Hally, > Thank you for your reply! Could you tell me how to save the alignment > result to a new .pdb file? > Thanks again! > > Best, > Linda > > Hally Shaffer wrote: > > Linda, > > > > To align two proteins, they have to have the same number of atoms. You > can > > manipulate the pdb files to delete part of one protein or remove a small > > molecule ligand if need be. You will need to save the "corrected" pdb > files to > > load for the alignment. > > > > Attached is a picture of two proteins I aligned (one is in the apo form > and the > > other is the ligand-bound holo form of the protein). The major > difference > > between the two is indicated in red. I had to load my two pdb files and > then the > > ligand (rea) as a separate pdb file. The commands are below. > > > > load 1LBDm.pdb, 1LBD > > load 1FBYm.pdb, 1FBY > > load REA.pdb, rea > > > > align 1LBD, 1FBY > > > > > > Good luck, > > Hally > > -- > > Hally Shaffer > > <>< Graduate Student > > Georgia Institute of Technology > > School of Chemistry and Biochemistry > > gth8...@mail.gatech.edu > > > > > > Quoting Lu Lin <l...@cs.hku.hk>: > > > > > >> Hi all, > >> > >> Anyone know which algorithm PyMOL uses to align or super of two > structures? > >> > >> Thanks a lot! > >> > >> Best, > >> Linda > >> > >> > >> > >> > ------------------------------------------------------------------------- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyMOL-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > ------------------------------------------------------------------------ > >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
