I have made an initial implementation of:
colo(u)r hbonds type
The RasMol manual says:
-----
HBond Type Colours
The RasMol 'type' colour scheme applies only to hydrogen bonds, hence is
used in the command 'colour hbonds type'. This scheme colour codes each
hydrogen bond according to the distance along a protein chain between
hydrogen bond donor and acceptor. This schematic representation was
introduced by Belhadj-Mostefa and Milner-White. This representation gives
a good insight into protein secondary structure (hbonds forming alpha
helices appear red, those forming sheets appear yellow and those forming
turns appear magenta).
Offset Colour Triple
+2 white [255,255,255]
+3 magenta [255,0,255]
+4 red [255,0,0]
+5 orange [255,165,0]
-3 cyan [0,255,255]
-4 green [0,255,0]
default yellow [255,255,0]
-----
I have a few questions ...
Q: Is there a literature reference I should read on this? If so, send it.
Q: Under what circumstances do you get bonding with residue -3 or -4? Can
you give me an example pdb file so that I can see this?
Q: These are for proteins. Shouldn't there be another color (or set of
colors) for nucleotide chains? What color should nucleotide hbonds be?
Q: I always feel the need to play with colors ... Are these rgb values good?
Miguel
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