[Chimera-users] how could u know the order of atoms?

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 23 14:22:31 PDT 2008

On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote:

> Dear Sir/Madam,
> I am using Chimera viewer..and it is a great viewer ever...

Thanks!  I'm glad you like it.

>  I kindly have a question... how could you know (from PDB file) the  
> coorect bonding between atoms? I mean that how could you know that  
> this atom is connected with CA not N nor C.....do u have all these  
> bonds stored already in a database? or you use atom positions to  
> determine that?

For standard amino and nucleic acids, Chimera has templates  
containing the correct connectivity.  For non-standard residues it  
bases the connectivity on inter-atomic distances, with a few added  
heuristics (e.g. hydrogens can only have one bond).

The templates are accessible in the Python layer with the  
chimera.restmplFindResidue() function.  You can look in the Rotamers  
extension for examples of its use.  The distance-based connectivity  
function is also available for an entire molecule as  
chimera.connectMolecule().  It takes the molecule as its only  
argument and adds bonds to it.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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