[phenixbb] ligand refinement - elbow

Nigel W. Moriarty nwmoriarty at lbl.gov
Fri Feb 29 16:45:49 PST 2008


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



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*

 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 W. Moriarty, Ph.D.
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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