Tutorial on how to use the Jmol export to web function. Either you do not have Java applets enabled in your web browser or your browser is blocking this applet. Check the warning message from your browser and/or. Another choice is to save from Jmol both the model data and the current orientation, rendering, color, etc. For that, you use the pop-up menu and File > Export.

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Description of Cube Input and Cube Output formats: Jmol reads only the output format. Blank lines are ignored. This format is used e. Jmol will read any file and try to determine its format from its content.

Copy and paste this history into a word processor or text editor. Naming Conventions As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design.

File formats/3D Objects

Be sure to include the following information in your Word document before saving: Supports multi-model data multi-frame, animations. The pop-up menu entry will svae the last isosurface selected or generated. For example, if you changed your backbone color multiple times, you no longer need the previous “color xeport commands for the colors you didn’t like.


See the sections below on opening and running a script.

Jmol Export to Web Tutorial

Alternately, you can quickly narrow your search by removing the last half of the script, then running the first half. Select the script, then drag and drop into a word processor.

The same information that would be exported to a file may be put into a variable using this function. Although Jmol was designed as a viewer, it has now capabilities to save files for the displayed molecular model or a subset of it.

CIF files may contain an inline script starting with jmolscript: What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported. Retrieved from ” http: If you can’t find the error, you can click on “step” instead of “run” to execute the script line by line.

Jmol reads mmCIF files. These next steps “clean up” your script and make it easier for you and others to interpret your script.

The defining tag 2D or 3D must be located in line 2, columnsbut is ignored by Jmol, which just uses the Z coordinates provided, be they zero or not. This will bring your expprt work back up in Jmol. Retrieved from ” http: After you’ve made a change to your script and want to test out the change, jmll the script on a “fresh” PDB file. If you have those details, please contact the developers team. This format was originally from the XMol package, but has been widely adopted by many other programs.


This gives the acronym: This is a popular format for sending to a 3D printerin order to get a physical model in your hands. See the Q-Chem specific section. Testing a Script After annotating your script, you should always run the script to make sure there aren’t any errors. Drag and drop your PDB file into Jmol. After you have completed your model design, click “history” on the Jmol Console. A complete specification of these formats would be needed to fully implement the reader.