timothy driscoll wrote:
sorry for perpetuating confusion :-) when I visualize hbonds with 'hbonds 0.1' they are white. if I color hbonds by type, the 'default' color is yellow. I am advocating consistency between these two defaults - and I suggest white since it is the cpk color for hydrogen.
Is that using Chime with a PDB file? My experience is different. With Chime I get half-colored CPK color of donor, half acceptor (blue/red for NH/O) as default. (Aside--I don't know which is properly called the donor--the one with the H or the one with the pair of electrons.)
This is also true with my version of Raswin (2.6).
So from what I can see, the default is a H-bond that has the colors of the two end atoms. This is before or after "hbonds 0.1" then when I type "color hbonds type" I get the expected colors based on the chain offsets between the two end points. Tim, maybe the protein you are looking at has only long-distance (yellow) H bonds.
Bob
and there should be no code-level distinction between protein and nucleic hydrogen bonds - one can easily build selections to tweak those apart.
and in fact, I retract my own statement here. see my recent email to the list responding to Bob's comments.
my day, my life, is a work in progress. please excuse the mess. :-)
regards,
tim
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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