>>>So Jmol will certainly *not* draw turn/random coil as square. >>> >>Miguel, You are right. The idea of having the turn/random coil as >>square is not a good. A cylindrical shape would be a better >>representation of the coil. > > I agree.
Resolved >>The standard secondary structure types are helixes, directional >>strands, and turns/coils. Hence, I would prefer cartoon models with >>these shapes. Additionally the H-bonds patterns in a helix can be >>visualized better in the ribbon type shapes than the cylinder. >> > I agree with this, too - one can visualize internal helix components > (like hbonds) in the twisted ribbon shape, but not the solid cylinder. Good point. We will use a twisted ribbon of some sort for 'cartoons' >>Usually the only directionality of the strands are useful for >>identifying beta-sheet(parallel or anti-parallel) formation and >>domain/motif classifications. It may not be required to add >>directionality to the helices. hence my suggestion would be a >>cylindrical representation of helices without caps. >> > I like directionality for helices merely as a visual cue to indicate > N->C, especially in structures that lack any beta strands (1d66, for > example). As a complete novice, I am inclined to think that the arrow heads are useful. That is why we have 'rockets' instead of 'dynamite' >>It may be also a good idea of having cylindrical representation as a >>separate type of structure model named 'cylinder' in addition to the >>cartoon model. >> > I called them Richardson diagrams in an earlier email; I believe the > correct term is 'topology diagrams'. (sorry.) these are commonplace in > print and use solid cylinders for helices. OK > It would be great if Jmol > supported this visualization. I can provide examples if necessary... Yes, a couple of examples (or URLs) of this would be very useful for me. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
