REFMAC (CCP4: Supported Program)
User's manual for the program refmac version 5.*
Links to non-commercial editors to derive coordinates
from chemical description
- 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
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
- 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.