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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Saving and Opening your Files in Jmol

After you have completed your model design, click “history” on the Jmol Console. It is also one of the common formats for sending to a 3D printerin order to get a physical model in your hands.

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

Testing a Script After annotating your script, you should always run the script to make sure there aren’t any errors.

This format is used e. Here is a sample script before and after annotating. Once you are satisfied with your final designs, you may wish to delete the unnecessary files.

Jmol Wiki – File formats/Export

Example files supported by Jmol. The pop-up menu entry will svae the last isosurface selected or generated.

Retrieved from ” http: This can be done from script or from the pop-up menu, only from the Jmol application and the JSmol-Java modality. Taking a few minutes to edit your history immediately after completing a design will make it much easier to “read” the script at a later date. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors.


This syntax is enough:. 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.

Jmol links Website Sourceforge. Crystallographic Information File, the official format from the International Union of Crystallography:.

Jmol does not fully support reading of Alchemy and Alchemy files. This can be done from script or from the pop-up menu. The defining tag 2D or 3D must be located in line 2, columnsbut is ignored by Jmol, which just uses the Z coordinates sxport, be they zero or not. If the first part doesn’t work, break it down into smaller chunks jmoo isolate the jmop.

Saving a JPEG of your model design kmol useful, but it doesn’t save a record of the commands you used to obtain the design. This is preliminary and needs testing.

The file extension is not taken into account for identifying the format. Retrieved from ” http: If expoft have those details, please contact the developers team. Contains only atom coordinates no bonds and, optionally, charges and vectors e.

This format supports formal charges, and only hydrogen isotopes as D and T ; they are all read by Jmol. Annotating a Script Any line that begins with the symbol is ignored by Jmol, so you can exporg comments to your script. See VRML for details. Information about the features that are displayed in this particular model Editing a Script in Jmol These next steps “clean up” your script and make it easier for expoft and others expotr interpret your script.


There are, however, some problems in implementing this format in Jmol and so in successfully producing PDF files more directly. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI.

File formats/Coordinates

The same information that would be exported to a file may be put into a variable using this function. However, since they are very similar to pdb files, they may be misread. Supports multi-model data multi-frame, animations. If the script doesn’t execute, look in the console for error messages; the console should direct to you the location of your error. Remove the first three lines or so of your script, starting with zap, load file, etc.

Any line that starts with will be taken as a comment and it can contain an inline script. See also show below, as an alternative. Jmol reads CIF files. You can see an example. This would allow future web browsers to display 3D content natively, without any plugins or applets. There are example files of Gaussian input, output and log. Example by Paul Bourke, and other example files. If the materials file is missing your model will be monochrome.

Jmol links Website Sourceforge. Just use the methods for exporting images and choose pdf format in the drop-down list.

If you need support for partial charges, see the similar PQR format below.