Hi All
I've recently started using JMol for visualization in my research on
proteins and am coming up against a wall: I need to find out how JMol
determines the intra-residue atom bond connectivities in standard amino
acids? I've scoured the PDB documentation and found that this information is
not contained in the CONECT or LINK records. The PDC docs refer to a
mysterious "standard residue connectivity table" that I've been unable to
locate.
I understand that absolute coordinate information is available within PDB
structures but I need to know which atoms are connected to which. This is
not a problem for the alpha carbons (.ca) but is for the residues that
branch out.
Sorry for the newbiw question.
I'm looking forward to using JMol more since it seems like a very
well-developed tool.
Thanks!
Ansari
--
Graduate Student
Dept. of Computer Sciences
University of Wisconsin-Madison
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