Hi Dr Emsley, Thank you so much for the reply! Would you please let me know how to use Coot's ligand builder or where I could find more information for Coot's ligand builder?
I don't know which is the best way to build the ligand to fit the density in my case. I got the molecular replacement solution using the apo-protein strucutre, but found out that there might be a conformational change in some part of the protein, so the density for that part is bad and also the density for the ligand is not quite continuous....So, I deleted the part that have bad density and do a refinement and then, place the ligand structural model in pymol. I first got the 3D structure of the ligand from 3DMET, which a database for small molecules, and load that PDB onto PRODRG2 website and get a new PDB as described in more detail below. And when I opened the protein with the ligand built back in, and found out that in some part, the ligand needs to be moved in order to fit the density well, so I was trying to move the ligand in coot to fit the density. It seems that the reason coot is not working is because that I used the PDB which is not compatible with the LIB file? Now when I loaded the PDB file of the ligand which I entered the PRODRG2 website instead of the PDB generated on that site, plus mtz and LIB file onto coot, I could move the ligand. Before I used the pdb file generated in the PRODRG2 website (no H's PDB file, since on the website it says that 'to get the ligands pdb file(to build into your structure using a modelling program such as Coot) use the"pdb no H's). Now, when I was trying to move the ligand, Coot didn't give the previous error message, but it is just very slow and didn't quite work the way I expected, and I will play with it.... And, for the CIF, on the PRODRG2 website, it says CIF topology (general<http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/run.html#DRGMAC.LIB> [D]<http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/run/5252D9EEC5880000191A/DRGMAC.LIB?m=1>or PHENIX<http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/run.html#DRGPHE.LIB> [D]<http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/run/5252D9EEC5880000191A/DRGPHE.LIB?m=1>) and I downloaded the general one to load onto Coot. You mentioned that 'I'd use the CIF dictionary that had hydrogens- the one that is compatible with Refmac'. I am wondering how you usually generate the CIF file? And, I am doing all the things I mentioned above and in the previous email because I read in the following link that "If you have a ligand you will need to read the "Refmac" dictionary for that ligand into coot". http://www.ucl.ac.uk/~rmhasek/coot.html Let me know what you think might a better strategy for me to build back in the ligand to fit the density.... Thank you so much! Best, Wei On Mon, Oct 7, 2013 at 7:42 PM, Wei Shi <[email protected]> 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 >
