Annemarie, You are absolutely correct. Rockets are a compromise rendering. The rocket itself, the sheet arrow, and the turns are all only approximations of the sort of more exact rendering given by cartoons. I'm very interested in what other users think about your suggestion. (Eric? Frieda?)
Recently Eric Martz pointed out other flaws in Rockets -- the fact that sometime some of the planks comprising the sheet arrows cross collide. In response to that, I created a new class of rendering called "cartoonRockets" that can optionally replace rockets. It seems to me both of you are onto the same thing -- that rockets do not necessarily faithfully represent the secondary structure of proteins. I have just uploaded a modified JmolApplet.jar file that changes cartoonRockets in a way that removes those loops you are referring to. So, what I suggest is that if this bothers you, use cartoonRockets. The way to do this is as follows: set cartoonRockets true; cartoons on; That is, render as cartoons with the special "cartoonRockets" flag set, and do not use the rockets command. Eric, if you are reading this, please check this out and see if it satisfies your needs as well. For testing, please close your browser and reopen it to see the new Jar file at: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/altloc.htm and enter the following in that command area: load 1crn.pdb;set cartoonRockets;cartoons on; then, if you want to compare to the "old" way, do: set testflag1on and back to the new way: set testflag off You can compare with cartoons using: set cartoonRockets off or set cartoonRockets on You can load your own model for testing using the "STOLAF-ANY" link under the applet. Bob Annemarie Honegger wrote: > Dear Bob > > Now that I got the most recent version of Jmol running and am > retesting my pages, > I just noticed this bug in the "rockets" -representation (see > screenshots > at http://www.biochem.unizh.ch/biocinfo/bugReports/Trace.html, the > first two images: rockets (in red): In the turn/coil regions, the > chain overshoots compared to the backbone (blue), trace (gray) or > wireframe (green) representation of the chain, forming kind of > M-shaped structures). In "cartoonrockets", the chain runs correctly in > the regions next to the beta-sheets, but overshoots next to the helices. > > The type of double arches that are produced bay "rockets" suggests > detail that is not present in the actual structure. A more abstract > representation should decrease the level of detail, not introduce > spurious detail. In the example shown, I would not object to the > trace connecting the two secondary structure elements forming a > simpel semicircle, but the double arches suggest structural features > that are not present in the actual structure. You find such double > turns e.g. in CDR-L1 of antibodies, where you have the large > hydrophobic side chain of a residue intercalating between the two > sheets of a beta sandwich, dividing the loop into two beta-turns. > However, in the structure shown (1QYS.pdb) you have canonical > beta-turns represented as double arches. > > As I see it, in the calculation of the trace line connecting the > secondary structure elements in the rockets representation, too much > weight is given to the trace continuing in the direction of the helix/ > sheet axis. There is nothing wrong with the trace coming out sidewise > from the helix cylinder rather than emerging from the center, in the > actual direction of the chain. For the sheets, you would probably > want the trace to go through the tip of the arrow, but not > necessarily in the direction of the arrow > > A suggestion of how an alternative rendering might look is in the > third image, which i generated by > rendering the helix and sheet regions as rocket, > all residues that are not (helix or sheet) and the residues > immediately adjacent in sequence to these residues as trace. > > Annemarie > ________________________________________________________ > > Dr. Annemarie Honegger, Ph.D. > Zürich University, Dept. of Biochemistry > Winterthurerstr.190 > CH-8057 Zürich > Switzerland > > e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > Tel.: 41-44-635 55 62 > Fax: 41-44-635 57 12 > URL: http://www.biochem.unizh.ch/antibody > _______________________________________________________ > > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
