[phenixbb] ligand cif file
chentiantian2010 at gmail.com
Tue May 31 18:29:45 PDT 2011
Thank you very much, the problem is already solved.
Next time I will let you know if I meet new problems.
On Wed, Jun 1, 2011 at 2:09 AM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> 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
> > _______________________________________________
> > 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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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