RNA, DNA, Prosthetic Groups and Ligands

You may use OS to calculate the occluded surface and raylengths of non-amino acid molecules in a structural model. Simply change the HETATM to ATOM and make sure that the rest of each record corresponds to PDB format.

In addition you should make sure that each element in your PDB file has an entry in the radii file. This file is temporarily deposited in your cwd for the OS run. If you want to make your own, copy it to your directory using the command in os.run. Then edit the file. To prevent it from being overwritten make sure you comment out the command in os.run which calls the $OSDIR/data/radii.

Note: The analysis programs, occsurf and respak recognize only the 20 amino acid names and CYT (for OPLS dissulfide linked residues) and UNK (for all others including ligands). If you want analysis of ligand packing change the PDB file or the "prot.srf" file so that all three-letter residue names are one of the above.