(Several REMARK jmolscript: lines are also supported.) In a PDB file, use REMARK jmolscript: in any line, followed by the script commands in the same line.This must be taken as a comment by the molecular file parser, so its location depends on the file format: Scripts can be included, in a single line, after a jmolscript: tag (case-sensitive the final colon is needed). Script inline within a molecular coordinates file Molecular coordinates inline within a script or script fileĬan be done using the data 'model' command. Molecular coordinates inline within a webpageĬan be done using direct instructions for the applet or, more easily, using functions in the Jmol.js library: jmolAppletInline, jmolLoadInline, jmolLoadInlineScript. For normal needs, they can be avoided in favour of using normal scripting practices. Please, note that these are advanced procedures. To allow for this 'inline' formats, several methods are implemented: In turn, script commands can also be contained in the molecular file. Molecular data are usually contained in an external file and loaded into Jmol using the load command, but they can also be contained within the webpage (or fed into it using JavaScript or PHP, e.g. In older versions of Jmol: File > Export > Export Image or Script and in the Image Type drop-down list, choose SPT, write a filename and click on Save. Or you can use the button in the toolbar. The unsigned applet cannot save files, but can output the data to the console, from where they can be copied and then pasted and saved to a file by the user. The Jmol application and the signed applet can write a script file that will restore the current appearance and state of the model. In both the application and the signed applet, the pop-up menu Load > Script. In the Jmol application, you can also read a script file using the top menu, File > Open. spt is the acknowledged standard).įor details on the scripting language, visit the Interactive Scripting Documentation. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. Jmol reads script files, using not the load command, but the script command. 1.3.3 Script inline within a molecular coordinates fileįile Formats for Scripting Jmol Script input.

1.3.2 Molecular coordinates inline within a script or script file.1.3.1 Molecular coordinates inline within a webpage.