Wei

I ran your SMILES string in the latest version of eLBOW and generated the attached file which has a more reasonable bond length for C9-C10. I notice you are using version 1.8.2 which is from Feb 2013. I suggest you upgrade your Phenix installation to 1.9 (or a nightly build) to obtain all the great new features.

http://www.phenix-online.org/download/nightly_builds.cgi

Cheers

Nigel

On Wed, Aug 20, 2014 at 1:27 PM, Wei Shi <[log in to unmask]> wrote:

Thank you guys so much!
Hi Matthias, yes, the bond length in the ligand in my structure is much longer than expected... I got the cif file from Phenix. eLBOW. I am wondering how I can check whether there is cif file already exiting for my ligand. Thank you so much!

Best,
Wei

On Wed, Aug 20, 2014 at 11:57 AM, Matthias Zebisch <[log in to unmask]> wrote:

Hi Wei,

your double bond is clearly not correctly defined in your cif file.
It should be significantly shorter - 1.3A instead of 1.5A.
However, it is easy to edit the expected values manually into your cif file.

Try to find PAM.cif in your coot directory (palmitoleate) to find the correct value.
Be careful that you edit the correct bond. Your numbering might be different.

Are you sure that there is no cif file for your ligand already existing?

Best, Matthias

-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK

Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email [log in to unmask]
Website http://www.strubi.ox.ac.uk
-----------------------------------------

On 8/20/2014 3:45 PM, Wei Shi wrote:

Hi all,
I am working on solving a X-ray crystallographic protein-ligand structures.
Attached please find initial oleoyl-CoA structure (elbow.001.pdb) and the ligand structure in the final model (ligand in structure.pdb). When open these in pymol and use "show as lines and set valence, 0.1" to show double bond, the double bond between C9 and C10 in oleoyl-CoA fatty acid part is only visible in the initial ligand structure (elbow.001.pdb) but not in the ligand in the final model (ligand in structure.pdb). I got the initial ligand using smile string by Phenix. eLBOW and fit the initial ligand to the electron density, and then refine the structure in the presence of cif file.
I am wondering whether any of you happen to know why in the final model (ligand in structure.pdb), double bond (C9) is not visible. Is it because the double bond is missing or is it because I didn't display it correctly? Thank you so much!

Best,
Wei

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Nigel W. Moriarty
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Lawrence Berkeley National Laboratory
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