[Chimera-users] pseudobond problem while writing mol2 format

Palani, Kirubakaran Kirubakaran.Palani at fccc.edu
Fri Dec 6 12:03:14 PST 2019

Hi Eric,

That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes.

Best regards,

From: Eric Pettersen <pett at cgl.ucsf.edu>
Reply-To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date: Friday, December 6, 2019 at 2:28 PM
To: "Palani, Kirubakaran" <Kirubakaran.Palani at fccc.edu>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] pseudobond problem while writing mol2 format

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Hi Kiruba,
For each of those pseudobonds, there is a hidden “real” bond.  To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted.  I have attached a simple Python script that does that.  So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2.
Keep in mind that deleting those hidden bonds will change the corresponding atom types.  So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).


Eric Pettersen
UCSF Computer Graphics Lab


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