[Chimera-users] managing CONECT table

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 27 13:52:46 PDT 2011

Hi Francesco,
Chimera only shows the bonds to metal ions that are in the input PDB file, and treats them as "pseudobonds" (dashed purple line by default).  

If it is just a display issue you could hide pseudobonds near metal ions with a command, for example:

setattr g display false ions z<4

If you really don't want the pseudobonds to exist in Chimera, however, I believe you would need to text-edit the input PDB file to remove the corresponding CONECT records.  Look at the HETATM line for the metal ion to get its atom serial number, then remove CONECT records that include that serial number.

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 Oct 27, 2011, at 12:44 PM, Francesco Pietra wrote:

> Hello:
> In preparing a model comprising various fragments I would like to
> suppress from the PDB CONECT table two connections to the central
> transition metal. I wonder whether there are rules for such
> manipulations. Chimera detects (as a bond) only one of these two
> connections.
> thanks
> francesco pietra

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