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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This option is not available from either the top menu or the popup menu; it must be done from the console command line or from a script file. Details of HIN format. Personal tools Log in. Save expogt image in the same folder as the PDB file that accompanies this image. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI.

Jmol can export, with limited features, the current view of a model into Maya ascii format.

See the sections below on opening and running a script. You can make changes to your script in the “script” box of Jmol, and rerun the script to view the change, rather than typing it into the Jmol Console. If the first part runs without problems, you can add additional chunks of script and run again. V the most common is limited to atoms. Here is a list of expory values. We call these blocks “cassettes”.


You can instruct Jmol as to which format to assume using this special explrt syntax:. If you want to create a JPEG image of jmoll molecule from Jmol to use in a poster, for exampleclick the “File” menu located on the top left of the Display Window.

Saving and Opening your Files in Jmol

Example by Paul Bourke, and other example files. Retrieved from ” http: The result text string as the value of the variable may then be displayed, processed, or even may be written to a file using write var d myFile. The fileset must have a structure like:. For example, if you changed your backbone color multiple times, you no longer need the previous “color backbone” commands for the colors you didn’t like.

Be sure to include the following information in your Word document before saving: This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file. Jmol reads and writes PQR files. This format supports formal charges, and only hydrogen isotopes as D and T ; they are all read by Jmol. Recent versions of Jmol application can also export to files in Gaussian input format. Due to Java security restraints, only the application and the signed applet can write to files on disk.

Also, force vectors are read and included as vibrations activated by default on file load. Jmol will read any file and try to determine its format from its content.

File formats/3D Objects

If the materials file jmo, missing your model will be monochrome. After you have completed your model design, click “history” on the Jmol Console.


Scripts allow you to create an exact record of your model design. Any line that starts with will be taken as a comment and it can contain an inline script. Jmol does not fully support reading of Alchemy and Alchemy files.

Just use the methods for exporting images and choose pdf format in the drop-down list. A complete specification of these formats would be needed to fully implement the reader. After annotating your script, you should always run the script to make sure there aren’t any errors. Saving a JPEG of your model design is useful, but it doesn’t save a record of the commands you used to obtain the design. Copy and paste ex;ort history into a word processor or text editor.

Jmol Wiki – File formats/Export

This can be done from script or from the pop-up menu, only from the Jmol application and the JSmol-Java modality. Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms. Contains atom coordinates, bonds, substructure information.

This format was originally from the XMol package, but has been widely adopted by many other programs. The 2nd is referenced from the 1st, so you should keep them together for loading into any other software.