REFMAC (CCP4: Supported Program)

User's manual for the program refmac version 5.0.36

DICTIONARY

Links to non-commercial editors to derive coordinates from chemical description

CORINA

This site gives very good coordinates if you supply SMILES strings. It can recognise simple or stereo SMILES strings. The best way of accessing this site is to draw a molecule using CACTVS and using SMILES derived from CACTVS to send to CORINA to derive coordinates.

Monosaccharide Database

It contains various monosaccharides. They could be taken in a PDB format and used as a building block for ligands containing sugars. PDB file may have to be edited to replace charges with B-values.

Disaccharide Database

It contains various disaccharides. Various conformations can be chosen using pictures provided. Output will be PDB file. This PDB file can be used to create a ligand description or as building blocks for the ligand under investigation

Enhanced NCI Database Browser

Using this site one can search for structure with a given substructure.

Sweet2 - Sweet II

This site can give you polysaccharides.

NOTE: In some cases atom names may not be as you wish them to be. Before running REFMAC or LIBCHECK to create a dictionary, it is better to rename atoms to your or IUPAC or somebody's satisfaction.