Re: [PyMOL] Unwanted bond formed in azetidine ring

[Timofey T. <tyu...@ni...>]

The bonds are initially generated based on proximity between the atoms 
in the structure.

To remove the erroneously generated bonds use command Unbond:

unbond atom1,atom2

04.06.2019 3:46, pym...@li... пишет:
> Message: 1
> Date: Mon, 3 Jun 2019 16:15:33 -0400
> From: Hao Li<hl...@um...>
> To:pym...@li...
> Subject: [PyMOL] Unwanted bond formed in azetidine ring
> Message-ID:
> 	<CAL...@ma...>
> Content-Type: text/plain; charset="utf-8"
>
> 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.