I spoke too soon. Also tucked into 11.3.14 is the capability to create your own menu, and change the menu on demand using the script command:
load menu "myMenu.mnu" We should probably have a discussion relating to how this works. Then someone needs to write a Wiki piece on this, because it's pretty cool. There is a file not currently in the distribution, but it can be put there -- http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/jmol.mnu (probably not its final home) It's pretty obvious how this works: In Part I, each line is a definition consisting of a menu name followed by a list of submenus or menu items or "-" to indicate a horizontal separator. In Part II, each item is defined in terms of a Jmol command. You only need to include in your file the parts of the menu that you want to change. For example, say I don't want the select menu to include PDB stuff. Then I would put JUST THIS in myMenu.mnu: selectMenu = hideNotSelected;hide(none)Checkbox showSelectionsCheckbox - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYComputedMenu instead of the current line: selectMenu = hideNotSelected;hide(none)Checkbox showSelectionsCheckbox - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYComputedMenu - PDBproteinMenu PDBnucleicMenu PDBheteroMenu PDBcarboMenu PDBnoneOfTheAbove Just that line will do it. The PDB items won't show up on the menu. 11.3.15 will also include an option for the applet -- jmolSetCallback("menuFile","myMenu.mnu") So let's talk about whether this is a good idea or not. Bob ----------------------------------- This will probably be the last set of innovations for a while -- time to get back to teaching... 11.3.14 will fix a few bugs and introduce some valuable functionality in the area of color schemes. It was a rather complicated set of modification; testing appreciated! -- you can map color schemes with customized ranges onto atoms, labels, etc. with the COLOR command. select *; color atoms property partialcharge "rwb" range -0.5 0.5 -- you can define your own color schemes by name, and you can redefine any Jmol color scheme such as "roygb" if you really want to. This means, for example, that you could redefine the atom colors 1-120 as a color scheme and then call that up for atoms or any other reason, using the elemno property for the coloring. select none; color "myscheme=[xFF0000] [xFFFF00] [x00FF00] [x00FFFF] [x0000FF]" select none; color "roygb=[xFF0000] [xFFFF00] [x00FF00] [x00FFFF] [x0000FF]" select none; color "roygb=" # un-define the scheme roygb select *; color atoms property elemno "myscheme" range 1 100 -- you can remap isosurfaces with difference coloring schemes after the fact. isosurface s1 molecular map mep color $s1 "rwb" range -0.3 0.3 color $s1 "bwr" Enjoy! Bob # bug fix: HDO not recognized as "water" # bug fix: rotateSelected MOLECULAR not around {0 0 0} # bug fix: -g ignored on -n option, even if -w is present # bug fix: unknown color palette could cause error # new feature: %l atomic element number # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] # adjustment: setting JPG default quality to 75, not 100 # new feature: {r,g,b} can be used in place of [r,g,b] for indicating color, # allowing programmatic color definition: # # r = 255; g = 255; b = 0; # background [EMAIL PROTECTED],@g,@b} # new feature: expanded color command for properties # # color atoms property partialcharge "rwb" range -1.0 1.0 # # and reverse with range inverted: # # color atoms property partialcharge "rwb" range 1.0 -1.0 # new feature: unlimited user-defined color schemes: # # select none; # color "myname=[xff00ff] [xffff00] [xff00ff]" # # colors must be [xRRGGBB] format for this one # new feature: fully remappable isosurface using COLOR command: # # isosurface s1 molecular map mep # color $s1 "bwr" # color $s1 "rwb" range -0.2 0.2 -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
