Francis Any formal charge is written in th PDB file in columns 79-80 as per the PDB format. Running elbow.builder --smiles "[OH3+]" results in a PDB file REMARK 99 electronic Ligand Builder and Optimisation Workbench (eLBOW) REMARK 99 - a module of PHENIX version 1.3b (Mon Aug 22 04:38:00 2007) REMARK 99 - file written: Thu Sep 13 09:44:48 2007 REMARK 99 REMARK 99 SMILES string: [OH3+] ATOM 1 O01 LIG A 1 -0.000 0.000 -0.000 1.00 20.00 A O 1 ATOM 2 1H01 LIG A 1 1.080 0.000 -0.000 1.00 20.00 A H 0 ATOM 3 2H01 LIG A 1 -0.540 0.000 0.935 1.00 20.00 A H 0 ATOM 4 3H01 LIG A 1 -0.540 -0.000 -0.935 1.00 20.00 A H 0 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 END Plans are afoot to optionally calculate partial charges and put them in the file. Nigel On 9/12/2007 11:57 AM, Francis E Reyes wrote:

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor))

Thanks

FR

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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