# new feature: spacefill/ dots/geosurface /cartoon/ trace/etc. This exhibit provides example Jmol scripts that can be copied and pasted into the javascript tags for buttons. These scripts are used to change the rendering of the molecule to illustrate important structural features. # new feature: signed applet/application load ?xxx uses load dialog Jmol, a Java applet used to view molecules in web pages, can read scripts that are contained in Jmol buttons. Set-logic operators like and, or, and notcan be used to specify multiple atoms. To select a few atoms, use select atomnoX. Think about what kind of object you'd like to select when deciding on what selector to use. # new feature: signed applet shows frank "Jmol-S" which is NOT removable. Selecting an atom or group of atoms is almost always the first step in entering Jmol commands. # new feature: signed applet may write file, images, scripts, variables to disk. # new feature: signed applet allows "load ?" and includes previewer Getting Started in Jmol (Downloading Jmol, PDB Files, Setting Up Your Workspace, Moving a Jmol Image) Altering the Jmol Display (Command Line, Display Formats. # new feature: show vdw shows a listing of the currently set VDW radii # new feature: show translation aka show orientation translation # new feature: show rotation aka show orientation rotation Below is the simple PBS script which run the above calculation on 4 cores on. # new feature: show orientation moveto # just the moveTo no comments # new feature: _signedApplet boolean is available: I would like to add a button to my page that can run this script instantly. # new feature: /*SPLIT*/ in a command string allows it to be processed by Afternoon Jmol friends, I have a Jmol script running in a webpage that includes a few time-based commands, such as the 'delay' and 'move to' commands (see example script below in green). # new feature: (popup menu) Biomolecules submenu added within title menu # new feature: $"xxx" quotations or allows variable definition of object id reference # new feature: "quaternion derivative" -> "quaternion difference", which is more # new feature: "load" of Jmol state scripts works same as "script" command make a small window appear, allowing the entering of Jmol script commands. # new feature: "%T" label format for straightness Using a Jmol script, we can alter the view so only certain amino acids are. 8, new feature: // at beginning of a line marks comments htm.ĭocumentation for Jmol 11.6 is available at chemapps. Jmol provides a very rich set of scripting commands to select individual atoms or groups of atoms. One of the most significant upgrades of Jmol to date, Jmol 11.6 includes over 200 new features introduced between January and October of 2008, including several totally new capabilities, such as point group identification and drawing of point group symmetry elements, thermal ellipsoid rendering, the capability to delete specific models from a set, 2D to 3D conversion and 3D minimization using the Universal Force Field (UFF), 3D Ramachandran plotting, quaternion maps for peptides and nucleic acids, and upgrading of the signed applet to enable file writing.
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