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Hi all, Thank you guys so much for the useful suggestions. I could fit the ligand to electron density by doing the following: 1. Run Phenix. eLBOW by loading the smile string and generate the pdb file and cif file. 2. Import CIF dictionary and open pdb for the ligand generated in Phenix.eLBOW and pdb for the protein plus the mtz file onto Coot. 3. Now, in coot, I could move the ligand to fit the density by 'real space refine zone'. Thank you so much! Best, Wei On Mon, Oct 7, 2013 at 7:43 PM, Wei Shi <[log in to unmask]> wrote: > 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 >