Nico's away, and I don't know how to put together the SourceForge files, so for now you will find the latest in Jmol in
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ Recent modifications in 10.9.76-10.9.79 include: redesigned pop-up menu ---------------------- # Jmol 10.9.79 adds a much more dynamic and useful pop-up menu. Check out the new "View" submenu. Also, for crystals, all symmetry operations are listed and selectable, and basic polyhedra are available from the popup menu. I've augmented the "Scheme" and "Structure" submenus for nicer display. The popup menu now displays counts of amino-acid, nucleic-acid, and carbohydrate residues, names of hetero atoms, and lots of graying out of unavaialable options. symop nijk CHANGE ----------------- Because we need to be able to identify symmetry operations in cells for which the origin has a negative fractional coordinate, I have revised the definition of "nijk". n is the number of the symmetry operation, starting with 1. ijk now correspond roughly to the common "555" number -- 1555 is the identity operator for the file atoms. 1666 is the same operation displaced by {1 1 1}. if;else;endif ------------- Jmol 10.9.79 adds rudimentary if;else;endif capability using the "set" options. IF commands can be nested up to 10 deep. The syntax is minimal; only one test is allowed, optionally preceded by NOT, as in "if (NOT showBoundBox);...;endif;". We'll see if this is any use. if (showBoundBox); set showBoundBox off;set showUnitCell; else; set showUnitCell off;set showBoundBox; endif; The tests are all taken from the "set" command. expanded moveTo command ----------------------- You can now include a new center point with a moveTo command. Just add it as (atom expression) or {x y z} at the end of the moveTo command. Fractional coordinates are allowed. moveTo, by the way, allows for braces to provide a bit more readability and the possibility for dispensing with unnecessary default parameters: moveTo 3.5 {0 1 0 90} 300 10 20 (atomno=3) says, "Over the course of 3.5 seconds, rotate 90 degrees CCW around the Y axis, zoom up to 300%, move the center 10% in x and 20% in y, with the center at atom 3. moveTo {0 1 0 90} {2.0 3.0 5.0} says, "Do a 1-second rotation around y, bringing the point {2.0 3.0 5.0} to the center at the same time. It works with or without set windowCentered true. I can hardly wait to see what Frieda, Eric, and Tim do with this! new hide/display option ----------------------- set showHiddenSelectionHalos ON tells Jmol to show selection halos even if their atoms are hidden. I can't quite figure out if people wanted this or not, but it seems like a reasonable option. The default for Jmol is OFF (don't show hidden selections). all user operations funneled through the script command processor ----------------------------------------------------------------- This means that if you use the pop-up menu or select atoms using set picking select group, for example, those operations will be reflected in the command history. [Or, if you wish, you can use applet.jmolScript("show history") to see what the user has been doing. And even send it to yourself, of course.] Where this is going, by the way, is a crazy idea I have for synchronous distant multiuser access to web pages. Sort of like you are both/all at the same computer, but not quite. OK, who wants to drive? special frank-based pop-up menu ------------------------------- # Jmol 10.9.79 adds a new pop-up menu that is accessed by clicking on the Jmol frank. This menu is a quick route to any submenu that you have recently accessed. Try coloring something using the pop-up menu. Now color it another color. Notice how long it take to find the right menu the second time. Now click on the frank and see that your menu is just a mouse jiggle away. select n - ---------- # Jmol 10.9.79 adds open-ended PDB residue selecting. Chem3D reader ------------- # Jmol 10.9.77 adds a c3xml file reader. load {ijk i'j'k' 1|0} --------------------- # Jmol 10.9.77 adds the capability to load a wider range of unit cell blocks. The range should include 555 (the base unit cell). The third parameter, 0 or 1, indicates whether(1) or not(0) to "normalize" the symmetry operations by moving the geometric center of the generated set of atoms back into unit cell 555. hide/display ------------ # Jmol 10.9.76 adds two new commands, hide and display, and two new selectabled terms, hidden and displayed. They are exact opposites of each other, provided for convenience only. display is similar to restrict except it is fully reversible. Like restrict, display hides unselected atoms, but unlike restrict, you can display all later and see everything come back as it was before. Examples: load 1mbo.cif;display HEM;center (displayed);moveto 1.0 -772 -621 -135 158.1 309; display within(group, within(3.0, hem));select displayed and *.ca;label %n %r;color labels yellow select within(group, within(4.0, hem)) and not displayed and *.ca;label %n %r;color labels red;display within(group, within(4.0, hem)); display within(group, within(3.0, hem)) #back to the other display; load quartz.cif {444 676 1};display cell=555 or cell=565;polyhedra 4 collapsed yellow;center displayed;moveto 1.0 -200 863 -464 45.0 252;spin y 10 Bug fixes --------- -preliminary test of solution for translations interfering with message callback -fix for "hide" not properly hiding halos, traces, and dots -fix for symops at small ijk. -fix for popup menus too wide. -fix for popup menu lists being too long. -isosurface fix for multistructure files. -fixed definition of "visible" as a subset of "displayed" ------------------------------------------------------------------------- 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 Bob ------------------------------------------------------------------------- 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
