Here is one way to do this: change your mouse mode from “viewing” to “editing”. left-click on the atoms at each end of the bond you wish to remove, each atom will highlight with a gray ball around it, In the command line type "unbond pkset” and hit the enter key, your bond will be removed.
> On Jun 3, 2019, at 3:15 PM, Hao Li <hlum...@umich.edu> wrote: > > Dear users, > > I am working on a structure of a protein-ligand complex, and the ligand > contains an azetidine group. Whenever I display this structure in pymol, an > unwanted bond forms between 2 carbon atoms in the azetidine ring. > > The pdb file of this ligand was generated by Chem3D and the restraint cif > file was generated by eLBOW in Phenix. I tried to edit both pdb and cif files > of the ligand but it did not work very well. I was able to remove certain > atoms but not the bond. > > I am kindly asking if there is a way to remove this unnecessary bond? Thank > you. > > Regards, > Hao > > > > <20190603160708.png>_______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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