[Chimera-users] Deleting Psubobonds/Connectivity

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 11 09:16:40 PDT 2013

Hi Dylan,
You can do it in a few steps:

(1) text-edit the PDB file to put TER at the start of its own line between the ATOM lines of one chain and the ATOM lines of the next

(2) open the resulting PDB file in Chimera, use Change Chain IDs (under Tools… Structure Editing).  If there were no chain IDs to start with, it would detect the separate chains and list them separately in the dialog.  If the chains already have an ID, e.g. both are "A" (as in your example), it will still show only one listing for that ID, but you can change the ID to " " (one blank space) so that Chimera will detect chains based on connectivity.  In other words,

  (a) change ID of all chain A to blank (you have to actually enter one blank space, rather than not entering anything), Apply
  (b) now the dialog should list two separate chains and you can choose each one in turn and assign its ID as you like, Apply

(Apply and OK will both perform the action, but Apply keeps the dialog up and OK dismisses it)

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 11, 2013, at 6:11 AM, "Dylan J. Bennett" <dylan.john.bennett at gmail.com> wrote:

> Hi,
> I was wondering if there was a way to delete psudobonds and connectivity in Chimera. I use a protein-protein docking software that does not renumber chains, this results in a structure that has 2 chain As for example. When I go to analyze this in Chimera, it automatically creates a psudobond between the two chains with the same ID. Since it thinks they're connected, I can't rename the chain IDs for just one of them. I know I can hide all the psubobonds, but this doesn't really help as I still need some of them and would like to rename the chain IDs uniquely. Thank you.  
> -- 
> -Dylan J. Bennett

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