DEF martin 0.0.1 coot_script_lines 09:40 23/Dec/12 CList 1 CPdbDataFile True True CList CMapCoeffsDataFile 1 True CList CMapCoeffsDataFile 2 True CDictDataFile application/refmac-dictionary Refmac monomer dictionary CIF library encoding ligand geometry Refmac dictionary cif True True True True CString True FILL_PARTIAL_RESIDUES,FIT_PROTEIN,STEPPED_REFINE_PROTEIN_FOR_RAMA,STEPPED_REFINE_PROTEIN,MORPH_FIT,BLANK Fill partial residues,Fit protein,Perform stepped refinement (apply Ramachandran restraints),Perform stepped refinement (no Ramachandran restraint),Iterative morph fit molecule with decreasing blur,Blank script (copy input coordinates to output) Code snippet to start from BLANK CBoolean CString # Input molecules are given internal identifiers "MolHandle_1" etc" # Input maps are given internal identifiers "MapHandle_1" etc" # Input difference maps are given internal identifiers "DifmapHandle_1" etc" # # The appropriate place to put output pdb files to be picked up by the system # is stored in the variable dropDir (see below for how to use this) # # Beware spaces...this is python after all # # Example commands you may wish to try can be explored by uncommenting the lines below # fill_partial_residues(MolHandle_1) # fit_protein(MolHandle_1) # stepped_refine_protein_for_rama(MolHandle_1) # # Per chain operations might look something like: # chainAMol = new_molecule_by_atom_selection(MolHandle_1,'//A') # otherChains = ['B','C','D','E','F','G','H','I','J','K','L'] # for otherChain in otherChains: # molToMove = new_molecule_by_atom_selection(MolHandle_1,'//A') # newMolHandle = superpose_with_chain_selection(MolHandle_1, molToMove, otherChain, 'A', 1, 1, 1) # merge_molecules(newMolHandle, molToMove) # # The following line ensures the output gets written out: write_pdb_file(MolHandle_1,os.path.join(dropDir,"output.pdb")) CList CPdbDataFile CList CDictDataFile