[phenixbb] ligand cif file

Nigel Moriarty nwmoriarty at lbl.gov
Tue May 31 11:09:04 PDT 2011


You can also improve the results by giving eLBOW all the information
you have in the best possible format. There is a hierarchy of chemical
inputs that provide information about your ligand. One of the best
ways to remove ambiguity about a ligand is to include the hydrogens in
the input. A rough guide to inputs from lowest common denominator to
highest is

1. PDB without hydrogens
2. PDB with hydrogens
3. Mol2D, Mol3D, SDF, SMILES, Tripos, Chemical Components code

I'd be happy to take a long at your input to assist you. Please send
files directly to me.

NB. Any files sent to me will be held in strictest confidence.


On Fri, May 27, 2011 at 6:12 PM, ChenTiantian
<chentiantian2010 at gmail.com> wrote:
> Hi there,
> Now I use phenix.elbow to produce the cif file of the ligand instead of
> using Prodrg.
> but I find a problem with this cif file, the C=N bond is not right, it
> becomes C-N in the
> cif file, so it does not fit the electron density, what should I do to
> modify the cif file to
> chage C-N to C=N ?
> Best Regards,
> Tiantian
> --
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica, Chinese Academy of Sciences
> Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
> Pudong New Area, Shanghai, 201203, P.R. China
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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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