pymol-users

[PyMOL] extra bonds

[Nat E. <ec...@uc...>]

I know this has come up before and I can't remember what the solution was.
PyMOL is drawing bonds between the protein I'm interested in, the ATP
analog, and the bound metal ions, presumably because the metals are close
enough to the protein and analog for bonds to be autodetected.  Is there a
way to turn off this behavior, other than writing a script to do it each
time?  In my case "unbond resnam mg, not resnam mg" does the trick, but
I've had different protein chains or substrates bound together in the
past.

thanks,
Nat

[PyMOL] extra bonds

[Jianghai Z. <jz...@id...>]

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

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