they should end and start on the same point of the spline, no rope is needed,in RasMol, backbone is like you described it but cartoon is like tracethat is not the case with cartoons. with cartoons, the alpha carbon atoms are in the center of the residue. so the residue extends from one side of the alpha carbon to the other side.
(ribbons, strands) a spline based on C-alpha, may be you should
interpolate the end and start of the residues by simply dividing the
curve between CA n -- CA n+1 and associate this with the cartoon
representation start and end points.
That is exactly what I am doing. Calculating the mid-points between the alpha carbon atoms.
until C n its part of helix 1 and from N n+1 it is part of helix 2Q: In the case of two fused helixes, in cartoon representation, how do you describe the segment that runs between the end of one alpha carbon and the beginning of the next?
That is waht I am doing.
Q: How would you pick/specify a size for this segment of 'rope'?I would expect that picking would select C-alpha
If I understand you correctly, that is what I am doing ... and that is why it doesn't work. I am not doing a good job of explaining the problem.
Let me try asking the question a different way:
A 'cartoon' representation is an idealized view of the protein. a helix is represented by a helix a sheet is represented by an arrow other residues are represented by a rope
When you have two adjacent helices there are no intervening residues. Therefore there is no rope.
And the two cylinders/helices do not join because each of them is in an
idealized position.
regards, Jan
So, we can (and should) put a 'false' rope between adjoining helices.
But, how do I determine the size of that 'false' rope? How does the user specify the size of that 'false' rope?
Miguel
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