Apologies if you receive two copies of this...my email client is acting up.
First, hearty thanks and kudos to Bob, et al. for all the great improvements and additions to Jmol since the 10.2 full release. I've been happily exploring the use of jvxl files in web-based macromolecular tutorial construction using some of the new pre-release versions. However, I've noticed some curious behavior with respect to spacefill commands when I run scripts that previously work fine in 10.2 (and older versions). Specifically, it seems that in some cases preceding move commands, spacefill is ignored until after the move when using newer pre-release versions of Jmol. If you are interested in helping with this, please compare the following two illustrations, the first uses 10.2, the second 10x38b. To see the effect, click on the 5th radio button, the one before "The connection between nucleotides in a DNA strand is thus referred to as a phosphodiester linkage.": http://www.callutheran.edu/Academic_Programs/Departments/BioDev/marcey/jmol_test/dna_intro_10_2/intro/start.html http://www.callutheran.edu/Academic_Programs/Departments/BioDev/marcey/jmol_test/dna_intro_10x_38b/intro/start.html Note that the spacefill on the phosphate groups disappears until the move is completed using v10x_38b. These tutorials are identical, except that the first calls 10.2 and the second uses 10x.38b. I get this with ALL post 10.2 versions, however. I'd be very interested to know if others are seeing seeing this in the above examples and if anyone else has run into this in their own work (I get it with both Firefox and IE6 in Windows). I also see the difference using Jmol.jar independently of a browser. The effect occurs with any pdb file. The effect dissapears if the move commands (move 5 15 2 -100 0 0 0 0 4; move 0 0 0 0 0 25 0 0 1) are removed. In this case, the effect is trivial, but for other illustrations, it would be really nice to get rid of this potential bug, if it is real. The full script is: "load atcg.pdb; background white; set frank off; select all; wireframe off; spacefill off; trace off; ribbons off; cartoons off; label off; monitor off; zoom 85; rotate x 180; rotate y -70; rotate x 30; move -5 -10 -2 100 0 0 0 0 .1; move 0 20 0 0 0 -25 0 0 .1; move 0 -25 0 0 0 0 0 0 .1; select all; wireframe 25; spacefill 75; select a; color [x5050ff]; select t; color [xe6e600]; select c; color [xe00000]; select g; color [x00c000]; select c; color cpk; define cbase atomno=50, atomno=51, atomno=52, atomno=53, atomno=54, atomno=55, atomno=56, atomno=57; select cbase; color [xe00000]; define csugar atomno=46, atomno=47, atomno=48, atomno=49, atomno=58, atomno=59, atomno=60; select csugar; color [x33CCFF]; define cphosphate atomno=42, atomno=43, atomno=44, atomno=45; select cphosphate; color cpk; select atomno=46; color [x999999]; delay 1; select all; color cpk; set specular on; set ambient 50; delay 1; select atomno=61, atomno=42, atomno=22, atomno=64, atomno=62, atomno=63, atomno=60, atomno=45, atomno=43, atomno=44, atomno=41, atomno=25, atomno=23, atomno=24, atomno=11, atomno=1, atomno=2, atomno=3, atomno=4; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; wireframe 25; spacefill 75; move 5 15 2 -100 0 0 0 0 4; move 0 0 0 0 0 25 0 0 1; delay .5; select atomno=61, atomno=42, atomno=22, atomno=64, atomno=62, atomno=63, atomno=60, atomno=45, atomno=43, atomno=44, atomno=41, atomno=25, atomno=23, atomno=24, atomno=11, atomno=1, atomno=2, atomno=3, atomno=4; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25; delay .5; spacefill off; wireframe off; delay .5; spacefill 75; wireframe 25" Attached is the pdb used in the above examples if you want to try it with your applet. Cheers, and advance thanks, David -- <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology Chair, CLU Biology Department 60 W. Olsen Rd., MC3700 Thousand Oaks, CA 91360 (805)-493-3263, 3590 [EMAIL PROTECTED] <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> ------------------------------------------------------------------------- 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
