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 >> > >
