On May 15, 2004, at 01:04 am, Miguel wrote:
Jan wrote:Miguel, You are right. The idea of having the turn/random coil as square is not a good. A cylindrical shape would be a
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.
better representation of the coil.
[snip]The standard secondary structure types are helixes, directional strands, and turns/coils. Hence, I would prefer cartoon models with
I like the rocket alternative
Are you saying that you prefer the rocket over the boxy ribbon for cartoon?
these shapes. Additionally the H-bonds patterns in a helix can be visualized better in the ribbon type shapes than the 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.
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.
Regards Gopalan Vivek PhD student ( Bioinformatics) Department of Biochemistry NUS,Singapore
Miguel
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