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 <[email protected]> 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 < > [email protected]> 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 [email protected] >> 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 >>> >> >> > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
test.cif
Description: Binary data
test.pdb
Description: Protein Databank data
