Christine

The bond lengths (if you didn't use the --opt option) are taken from quantum chemical calculations to generate a simple force field. One of the problems with the PDB format is the ambiguity of bond orders that can arise. You should run eLBOW and look at the result to check that the bond connections and bond orders are correct. You can then use the --opt option to generate a better geometry for your refinement.

Regarding the covalent bonding, you have some options. You can add a CONECT record

CONECT

Overview

The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues. These records are generated by the PDB.

Record Format

COLUMNS       DATA TYPE       FIELD         DEFINITION
-------------------------------------------------------
 1 -  6       Record name     "CONECT"
 7 - 11       Integer         serial        Atom serial number
12 - 16       Integer         serial        Serial number of bonded atom
17 - 21       Integer         serial        Serial number of bonded atom
22 - 26       Integer         serial        Serial number of bonded atom
27 - 31       Integer         serial        Serial number of bonded atom

You can also use the LINK record but lets try this option first.

Nigel

-- 
Nigel W. Moriarty, Ph.D.
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
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Email : [email protected]
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