Feature Requests item #1539252, was opened at 2006-08-12 12:10 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1539252&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: v10 Status: Open Priority: 5 Submitted By: Eric Martz (emartz) >Assigned to: Bob Hanson (hansonr) Summary: Need better cartoon renderings Initial Comment: I would like to request that Jmol's rendering of secondary structure cartoons be improved. In my opinion, its 'cartoon' rendering is very important but unsatisfactory. With increased exposure (Nature is working on installation of FirstGlance in Jmol), the present rendering may diminish Jmol's acceptance/reputation. Presently, Jmol draws beta planks as absolutely straight. In reality, beta strands are often curved and usually somewhat twisted. In some cases, Jmol's beta strand planks not only largely miss the correct positions, but end up crossing through each other. This happens for 1APM (restrict 42-75 to see the relevant portion). Similarly, many alpha helices are curved, and Jmol's rockets need to reflect this. Also, the cone-heads of Jmol's rockets (very nice) sometimes "flap" annoyingly when the molecule is rotating. Though less important, it would be great if this could be fixed. I have put an MS Word 2002 file, ss-cartoon.doc, containing snapshots of some cases where Jmol's rendering is unsatisfactory at: http://www.umass.edu/microbio/chime/beta/jmol/ and I have also uploaded it here as an attachment. Snapshots there compare the renderings of Jmol, Chime, and Protein Workshop. (If anyone has trouble displaying the .doc file, let me know.) ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-08-14 22:59 Message: Logged In: YES user_id=1082841 10.x.42c This is pretty much complete. See http://www.stolaf.edu/people/hansonr/jmol/test/proto Arrow head wiggling is fixed. It was really a problem with all parts of all cylinders. It's still not absolutely perfect, but it's pretty close. I'll leave this open for additional comments/suggestions. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-08-14 04:25 Message: Logged In: YES user_id=1082841 A first attempt is at http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm 10.x.42 includes the command set cartoonRockets on|off A hybrid of cartoons and rockets. I'm dissatisfied with the renderings, though, and have tracked this down to a bug in the line drawing rasterizer. I will look at it when I have more time. Basically, the beta sheets are fine; the alpha helix rockets show undesireable characteristics, though, including flapping cones and undesireable line breaks. This has been a problem since the inception of rockets; I will see what I can do. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1539252&group_id=23629 ------------------------------------------------------------------------- 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-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
