grade tutorial: different ways to use grade to produce cif dictionaries

1 starting from SMILES

grade -resname LIG 'c1cc(c(cc1CCN)O)O'
grade-LIG.cif  grade-LIG.pdb
coot --dict grade-LIG.cif
EditREFMAC grade-LIG.cif grade-LIG.pdb LIG

2. starting from a picture

3. Starting from ideal coordinates (with hydrogen atoms)

grade -in L37831.sdf -ocif L37831.cif -opdb  L37831.pdb

4. Producing cif dictionary for an existing PDB ligand

grade_PDB_ligand LDP
coot -p  2ar3_dopamine201.pdb --auto LDP.grade_PDB_ligand.cif

Page by Oliver Smart 08 Feb 2011, updated for for Grade Web Server 09 March 2012. Any questions regarding our software or this wiki should be directed to