[phenixbb] Elbow problem
Nigel Moriarty
nwmoriarty at lbl.gov
Fri Mar 11 11:27:19 PST 2011
Jerome
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.
Nigel
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
>
> _______________________________________________
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> 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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