Re: [PyMOL] extra bonds

[Thomas H. <tho...@sc...>]

Hi Jianghai,

by default PyMOL does a distance based bonding (basically when the VDW
radii of two atoms overlap, they get connected). To prevent that, you
need two settings:

# before saving the correctly bonded but distorted structure
set pdb_conect_all

# before loading
set connect_mode, 1

http://pymolwiki.org/index.php/connect_mode

Cheers,
  Thomas

Jianghai Zhu wrote, On 04/30/13 02:39:
> Hi,
> 
> In my trajectory movie, there are some minor distortions of some of
> the residues, but the sticks presentation in pymol seems fine.
> However, after I loaded the trajectory pdb file use discrete=1, extra
> bonds would be shown in sticks in those slightly distorted residues.
> Is there is way to avoid those extra bonds?  Thanks a lot.
> 
> --Jianghai

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor