Dear Jmol developers and users,
I am always thinking about the question that how does Jmol display the
secondary structures of proteins.
As we know, the secondary structures are related to the hydrogen bonds
between the C=O and H-N groups of the amino acid residues. However, in many
of the PDB files, the H atoms are not included. As a result, it is
impossible to check the hydrogen bond in *original* PDB files. Then how
does Jmol 'know' where is the \alpha-helix and where is the \beta-sheet? (I
understand that there are some tools to add H atoms to the PDB files, but
that is another story).
Another possibility might that Jmol read the information of HELIX and SHEET
sections. However, if I delete all of them, remaining only the ATOM
sections, Jmol is still able to display the secondary structures!
I was wondering how does Jmol 'know' and display the secondary structures
without hydrogen bonds information and without the hints from HELIX and
SHEET sections. Does Jmol calculate all the \phi, \psi dihedral angles when
loading the PDB file? And then make predictions based on those angles?
It would be greatly appreciated if anyone could answer it.
Thank you very much.
Huan
.
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