[Chimera-users] Error when making Covalent bonds

[Elaine Meng]

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


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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