at 1.07p EDT on 2003 December 12 Friday Miguel Howard said:the problem arises because we can't bent rocked helix representations and moving start and end away from the spline would create as much conflicts as the fit result.
Jan,
I do not agree.they should end and start on the same point of the spline, no rope isAnd the two cylinders/helices do not join because each of them is in an idealized position.
needed,
The axis of the cylinders should be fit to all of the atoms that
participate in the helix.
you my use a strait line, with properties as used for backbone representation, while using a spline for loops and turns.
may be, rocket tips and arrow heads could be used as joining elements without extension on an own residue?
should the fit better be done from the second to the before last residue?We should not just draw the cylinder from the first residue spline point to the last residue spline point. This would put the cylinder out of position. Particularly since the two ends of the helix are almost always out of alignment with the rest of the helix.
I don't think so.Let me know what you think.
if I can jump in:
1. modify the cartoon calculation - if the cartoon being drawn is immediately
adjacent to another, draw both as a single object.
you could have two helix structures perpendicular to each other http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?CHIME=y&JMOL=1kyz px73317
2. add a rope from the last CA in cartoon 1 to the first CA in cartoon 2.no to better distinguish from loops a strait line from structure element representation n to structure element n+1
is there a specific pdb file that shows this problem?
e.g. 1kyz regards, Jan
regards,
:tim
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