Hi all, I was solving a protein-ligand complex structure and got a molecular replacement solution with the protein as the search model and now trying to fit the ligand to the electron density in coot. It seems that the ligand needs to change conformation to fit the density well. So, I created the dictionary using PRODRG2 (the following link), and downloaded CIF topology (general) from the results file page. Is this the CIF library which I should include in order to move the ligand to fit the density in coot?
http://www.ucl.ac.uk/~rmhasek/dictionary.html And in coot, I loaded the pdb file, mtz file and the click 'import CIF dictionary' to load the DRGMAC.LIB file, but when I was trying to move the ligand, coot gave the error message as follows: No restraints found! No existent or minimal description of restrained residues. Are you sure that you read a non-minimal mmCIF dictionary for this monomer. Are you sure the PDB reside name matches the dictionary residue name? If not, try File -> Import CIF Dictionary Alternatively, did you check that the atom names of the PDB file match those of the restraints. I am wondering whether any of you have any suggestions about how to the fix this. Thank you so much! Best, Wei
