[phenixbb] Elbow problem

Nigel Moriarty nwmoriarty at lbl.gov
Fri Mar 11 11:27:19 PST 2011


If you are using a PDB file without hydrogens, there can often be
ambiguous bonding assignments so it can be better to add hydrogens or
use a "better" chemical input like SMILES, Mol2 etc that explicitly
states the bonding. You can also use REEL to define bond orders and
run eLBOW.

Either way, send me the input file (off list) and I'll take a look.


On Fri, Mar 11, 2011 at 11:15 AM, Jerome Nwachukwu <JNwachuk at scripps.edu> wrote:
> Hi all:
> For some reason, phenix.elbow converts a specific double-bond (C=C) in my
> ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is
> there away to avoid or correct this problem?
> Thank you,
> -Jerome
> Jerome C. Nwachukwu, PhD
> Kendall Nettles' Lab
> Dept. of Cancer Biology
> The Scripps Research Institute-Florida
> 130 Scripps Way, 2C1
> Jupiter, FL 33458
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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

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