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On 03/05/11 14:08, Nalam, Madhavi wrote: > Hello all: > I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. > It gives an error message like this.. > ------------------------------------------------------ > Failed to match (to the dictionary) the following model atom names: > XXX > "Cl38" "Cl39" > > That would cause exploding atoms, so the refinement didn't start > ------------------------------------------- > > This problem never occurred to me before whenever I generate new cif files. The ligand has two chlorine atoms. I tried to give different three letter codes for the ligand assuming the three letter code I gave may already be in the dictionary and that is why it is giving me the error message. I get the same message irrespective of changing the three letter code. > > I also tried generating a cif file by running it through Refmac5 (the job fails and gives me a cif file which I used in Coot) and again I ended up with the same message. Check that the dictionary names and the atom elements for the Cl atoms are upper-cased in both the PDB file and the dictionary. Paul.