Miguel wrote:
Tim wrote:
It doesn't seem right to me that hbonds between chains are the same color as hbonds within a chain (like beta-sheets).
why not?
When you say:
color hbonds type
You get special colors for hbonds that are part of alpha-helices and part of turns. I assume that is because those hbonds are responsible (in large part) for creating/stabilizing those structures.
It seems to me that the same thing should apply to beta sheets. And that the hbonds that are part of beta-sheets should be colored specially.
But instead, 'color hbonds type' colors beta sheet hbonds the same color as other random hbonds.
right. It was apparently just an easy-to-implement clever coloring scheme. Really very clever, except, as you say, it doesn't really highlight beta pleated sheets.
It also seems to me that sidechain hbonds should be different from mainchain hbonds.
it's kind of like saying covalent bonds are different - they are, but we generally treat them as a group anyway.
Q: Why do we have this special command 'color hbonds type'?
because it does in fact highlight interesting secondary structure, though not beta-pleated sheets, really.
it would be very useful to have a way to access different sub-categories of hydrogen bonds, though:
select hbonds interchain select hbonds sidechain select hbonds mainchain
That is a subject for another day.
but I think the default should be to color all hbonds white, inheriting the CPK color for hydrogen.
You realize that this is a change from the RasMol/Chime behavior.
And under 'color hbonds type' the default color is yellow.
Q: What are you advocating?
For compatibility I would recommend going with the Rasmol default. One can always say
color hbonds white
if that is what is desired instead.
and there should be no code-level distinction between protein and nucleic hydrogen bonds - one can easily build selections to tweak those apart.
Miguel
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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
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