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Thank you so much, Nigel! I will try as suggested. On Wed, Aug 20, 2014 at 5:17 PM, Nigel Moriarty <[log in to unmask]> wrote: > 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 >>>> >>> >>> >> > > > -- > Nigel W. Moriarty > Building 64R0246B, Physical Biosciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : [log in to unmask] > Fax : 510-486-5909 Web : CCI.LBL.gov >