vivek sent (2004.05.15 at 2.12a [+0800gmt]) : >Hi Miguel, > >On May 15, 2004, at 01:04 am, Miguel wrote: > >>Jan wrote: >> >>>>Q: Do you like the fact that turn/random coil is square? >>>> >>>nobody likes this, therefore the application menu command renders >>>this part as trace 100 >>>:-) >> >>Actually, I had no idea that a *menu* even existed :-) >> >>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. >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. >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). >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. It would be great if Jmol supported this visualization. I can provide examples if necessary... regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- 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%62&alloc_ida84&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
