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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu