Re: [Jmol-users] feature request- alpha carbon trace, and documentation correction

[Frieda Reichsman]

On Oct 8, 2006, at 10:47 PM, Bob Hanson wrote: Frieda Reichsman wrote: None of Jmol's smooth-style backbone representations (cartoon, trace,  ribbon, etc.) is a trace of the alpha carbons of a protein. Would it  be possible to add to Jmol a smooth representation that follows the  alpha carbons quite faithfully? It would be somewhat involved. For the reason that....? Often in my experience one wants to show most of a protein in a cartoon or ribbon, with certain side chains in wireframe-- say, in a close-up of an active site. If the rendering does not go through the alpha carbons, then the wireframe side chains can appear to be unattached to the ribbon. They get close to it but never reach it, because the ribbon does not pass through the alpha carbon. (If you then include in wireframe the other backbone atoms to make the bonds actually reach some part of the cartoon, it complicates the image, so it is less desirable). Further, the current trajectory of these smooth renderings flattens them considerably compared to the actual path of the backbone. An alpha carbon trajectory would show the undulating nature of the backbone more clearly. (This is currently possible with the "backbone" representation, but that is not a smooth curve.) In addition, responding to a comment of Angel's: What I have understood or assumed is that these renderings are drawn as inherited from Rasmol, and all use the same trajectory: I agree that cartoon, ribbon, and trace all use the same trajectory, but I do not think the trajectory itself is inherited from Rasmol/Chime. In Chime, which I assume was the same in this as Rasmol, the  renderings went right through the alpha carbons. At present, Chime presentations that get converted to Jmol will differ in this respect, and side chains that in Chime presentations are attached to a smooth backbone rendering will be hanging in space, albeit nearby. So I think it would be useful to have an option for an alpha carbon trace/cartoon/ribbon perhaps named cartoonAlpha, ribbonAlpha, etc. Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com ///////////////////////////////////////////

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys -- and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users