HI Using the set addPdbHydrogens functionality I am finding that sometimes the hydrogens are associated with more than one amino acid. Are you making the hydrogen selection based on the label of the hydrogen or based on its distance from the surrounding atoms? Is there any way to have control over this?
Example: set addPdbHydrogens; load=1H6I; select [ALA]232:A; spacefill 100%; select [TYR]227:A; spacefill 50%; Note how the hydrogen atom labeled [ALA]232:A.H #3348 changes in size for both selections. This becomes relevant for me as I am sorting hydrogen bonds according to the structures they apply to. From the example given about, according to the label on the hydrogen this should be a tertiary hbond between the oxygen in 227 and the hydrogen in 232 and that part works fine. The problem comes in when this same hbond is added to the secondary hbonds. Because both the O and H atoms are considered to be in the same amino acid bondMode AND doesn't help. Thanks Sara
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