I opened test.cif and test.pdb suggested by Nigel in Coot. I moved the ligand to fit the electron density and saved the ligand, see attached file. When I opened this file in pymol and set valence, 0.1, I cannot see the double bond between C9 and C10. Does any of you happen to know what might go wrong and what I should check? Why in Coot in the presence of the new cif file which says the C9 C10 is double bond with bond length of 1.348A, the double bond between C9 and C10 is not present after moving the ligand to fit the density? Thank you so much!
Best, Wei On Thu, Aug 21, 2014 at 3:38 PM, Wei Shi <wei.shi...@gmail.com> wrote: > Thank you so much, Nigel! I will try as suggested. > > > > On Wed, Aug 20, 2014 at 5:17 PM, Nigel Moriarty <nwmoria...@lbl.gov> > 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 <wei.shi...@gmail.com> 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 < >>> matthias.zebi...@bbz.uni-leipzig.de> 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 matth...@strubi.ox.ac.uk >>>> 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 : nwmoria...@lbl.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> > >
test-coot-2.pdb
Description: Protein Databank data
