[Chimera-users] Making a new covalent bond

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 27 16:09:35 PST 2006

On Feb 27, 2006, at 3:37 PM, Goel, Manisha wrote:

> Hi,
> I have often come across detailed answers from chimera group for a  
> variety of modelling problems on pdb-l or bioinformatics mailing  
> lists.
> My problem should relatively easy to solve except that I havn't  
> been able to figure it out myslef on chimera.
> I just need to make a covalent bond between a sugar molecule and an  
> aminoacid (aa-COOH + sugar-OH --> H2O + aa-sugar).
> Is there an easy way of doing this manipulation in Chimera ?

The answer is "it depends".  If the sugar and amino acid are in the  
same model, then it's easy.  Just select the two atoms you want to  
bond and in the command line (Favorites->Command Line) type "bond sel".

If the sugar and amino acid are in different models then it's  
trickier, since the definition of "model" is that there are no  
covalent bonds between models, so you need to get the structures into  
the same model.  One way is to edit the original input files together  
(if they were PDB files, make sure to get rid of the END record in  
the middle of the combined files).  Another way, if you have the  
1.2199 release, is to save the two models in Mol2 format (File...Save  
Mol2).  In the Save Mol2 dialog, select both models and make sure the  
"Save multiple models in" menu is set to "a single file [combined  
@MOLECULE section]".  If you read the resulting saved Mol2 file back  
into Chimera, then the two structures will be in one model.  You can  
then use "bond sel" to make the bond.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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