CIF files
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CIF files are needed for refinement (e.g. refmac, phenix.refine, buster) and visualization programs (e.g. coot) to describe the topology and parameters of ligands or molecules.
All of these programs are installed with a standard library of CIF files.
There are several options for obtaining a CIF file for a non-standard ligand:
Use the Grade server
- go to en.wikipedia.org and enter your ligand's name, e.g. Dibenzothiophene
- copy the SMILES string provided for many small molecules in Wikipedia (of course there are many other sites where you could find SMILES strings!)
- go to http://grade.globalphasing.org and paste the SMILES string
- download the CIF-file
Use JLigand
JLigand is a graphical CCP4 program. Just start a new ligand, define and link the atoms that make up your ligand, together with the hydrogens. Then regularise and save the restraint file.
Use Phenix tools
See Phenix utilities at e.g. http://phenix-online.org/version_docs/1.9-1688/ .
Use the PRODRG server
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg - see Servers for ligand topologies/parameters