Dear Wei, I guess it is because your initial model contains protons, which allows pymol to deduce the valence of the carbon atoms, which is missing in the final structure. However, some pymol expert may correct me. Best, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Wei Shi Gesendet: Mittwoch, 20. August 2014 16:45 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] double bonds in oleoyl-CoA 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
