[Chimera-users] Error when making Covalent bonds

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 25 09:23:14 PDT 2005

Hi David,
Currently you cannot form a bond between two different models, i.e.  
structures opened from two different files (or separated with MODEL/ 
ENDMDL records in a single file).  You need to first put the  
coordinates for both structures in the same PDB file, without MODEL/ 
ENDMDL records.  There may be an issue of duplicate residue numbers;  
if so, you'd need to renumber to avoid the problem.  For example,
if one structure has residues 1-10 and another has residues 1-50, the  
coordinates should be concatenated into one file and renumbered so  
that no two residues have the same number (1-60 is
one possibility; 1-10, 100-150 is another).
Hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 25, 2005, at 12:31 AM, David Chenoweth wrote:

> Hi!
> I am trying to pull up two molecules in chimera and link them by
> forming a covalent bond between a N and C atom.  I am selecting only
> the N of one molecule and the C of the other.  When I go to command
> line and use the bond sel command I get the following error message.
> Type error: Cannot form covalent bond joining two molecules.
> Does anyone know how to get around this.
> Thanks,
> David C.
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