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, pymol-users-requ...@lists.sourceforge.net пишет:
Message: 1
Date: Mon, 3 Jun 2019 16:15:33 -0400
From: Hao Li<hlum...@umich.edu>
To:pymol-users@lists.sourceforge.net
Subject: [PyMOL] Unwanted bond formed in azetidine ring
Message-ID:
<calomrhqlgx3wn8jdzz09vt2n+x2j0o7hmfa1_jv_t9ogp2e...@mail.gmail.com>
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.
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