On Thu, Apr 15, 2010 at 5:46 AM, Claudia Scotti
I'm trying to rebuild a model with Autobuild. The protein has a ligand, whose density is already well defined, thus that the input for the new autobuild run includes its coordinates as well.
When I start the autobuild run, however, I see that the ligand is removed before rebuilding, which leads the program to use the ligand density to try to rebuild loops, thus introducing errors.
How can I keep the ligand in place, please? Or is there any alternative solutions?
I believe the answer is to move the ligand to a separate PDB file, and add these parameters: input_files.input_lig_file_list=ligand.pdb input_files.keep_pdb_atoms=False (Or if you're using the GUI, add the ligand PDB file and change the type to "Ligands", and uncheck Settings->Input files->Keep pdb atoms. -Nat