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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Jmol links Website Sourceforge. This is a popular format for sending to a 3D printerin order to get a physical model in your hands.

The pop-up menu entry will svae the last isosurface selected or generated. After annotating your script, you should always run the script to make sure there aren’t any errors. A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames. Description by Paul Bourke.

Here is a list of format values. If the script doesn’t execute, look in the eport for error messages; the console should direct to you the location of your error. See also show below, as an alternative. Views Page Jmmol View source History.

Saving and Opening your Files in Jmol

Remove any “blind alleys” that you took in your model design The data can later be loaded using load var a. Insert comments throughout your script.

Contents 1 Exporting or saving molecular model files from Jmol 1. We recommend that you save your designs early and often.

File formats/Export

Also, force vectors are read and included as vibrations activated by default on file load. Remove the first three lines or so of your script, starting with zap, load file, etc. This can be done from script or from the pop-up menu. You’ll only need the final “color backbone” command that has the actual color of your model. There are, however, some problems in implementing this format in Jmol and so in successfully producing PDF files more directly.


Copy and paste this history into a word processor or text editor. Contains only atom coordinates no bonds and, optionally, charges and vectors e. The unsigned applet can however display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file. Jmol can get files directly from the Protein Data Bank website. It is also one of the common formats for sending to a 3D printerin order to get a physical model in your hands.

Now, you can easily see the changes that you made in your script. Views Page Discussion View source History.

Views Page Discussion View source History. This will bring your saved work back up in Jmol. What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported. Description of Cube Input and Cube Output formats: We suggest that you save each design as a new file, and that you number the designs consecutively. Personal tools Log in. Alternately, you can quickly narrow your search by removing the last half of the script, then running the first half.

Opening a Script in Jmol Once you have your script, run it as follows: As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design.


Alchemy example and Alchemy description by Paul Bourke. Example files supported by Jmol.

See the sections exporh on opening and running a script. Jmol can export an image of the model into a pdf document single page, just the image in the center. A simple Alchemy reader is implemented starting Jmol In the dropdown menu, select “Export” and then “Export Image”. Correct the script as needed.

Saving results from Jmol

Contains atom coordinates, bonds, substructure information. After you have completed your model design, click “history” on the Jmol Console.

The 2nd and 4th are equivalent and contain, packed in a single file, a snapshot PNG image, the coordinates file and the state script file. Jmol does not fully support reading of Alchemy and Alchemy files. Naming Conventions As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design.

We call these blocks “cassettes”. More flexibility is allowed by using the write isosurface command. On the Jmol Console, click “editor”. Recent versions of Jmol application exort signed applet can export models to several formats that specify three-dimensional jmil and can be read by specialized software 3D-world or jol. The same information that would be exported to a file may be put into a variable using this function.