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 format is used e. As a result, atoms are not spheres, but polyhedra with many faces visible when zooming in closely. Naming Conventions As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design.

Features are nearly identical to those of VRML. Jmol does not fully support reading of Alchemy and Alchemy files.

Jmol Wiki – File formats/Export

Copy and paste your script into the editor window. The file extension is not taken into account for identifying the format. A simple Alchemy reader is implemented starting Jmol Jmol links Website Sourceforge. 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. This can be done from script or from the pop-up menu. These formats support formal charges and isotopes ; both are read by Jmol.

File formats/Coordinates

Contains atom coordinates, bonds, substructure information. Copy and paste this history into a word processor or text editor. Scripts allow you to create an exact record of your model design.

The filter option of the load command can be used, as well as a new option to allow selective “first,last,step” loading of coordinate trajectories. On the Jmol Console, click “editor”. Any line that starts with will be taken as a comment and it can contain an inline script. Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms.


Be sure to include the following information in your Word document before saving: Blender is a free, open source, 3D content creation suite, available for all major operating systems under the GNU General Public License. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI.

Description by Paul Bourke. A complete specification of these formats would be needed to fully implement the reader.

The same information that would be exported to a file may be put into a variable using this function. A jjmol MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames.

The vrml or wrl file can then be opened using several programs and browser plugins, and manipulated in 3D using the mouse.

Blank lines are ignored. Save the image in the expor folder as the PDB file that accompanies this image. Remove the first three lines or so of your script, starting with zap, load file, etc.

There are, however, some problems in implementing this format in Jmol and so in successfully producing PDF files more directly. Note that you will need to click the step button to execute each individual line. This gives jmoll acronym: Wikipedia info on Maya. We call these blocks “cassettes”. After you’ve made a change to your script and want to test out the change, run the script on a “fresh” PDB file.


Personal tools Log in. Saving a Script in Jmol 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. Contains only atom coordinates no bonds and, optionally, charges and vectors e. See the Q-Chem specific section. Select the script, then drag and drop into a word processor.

Also, force vectors are read and included as fxport activated by default on file load. If the materials file is missing your model will be monochrome.

V the most common is limited to atoms. See also show below, as an alternative. Details of Xeport format. Testing a Script After annotating your script, you should always run the script to make sure there aren’t any errors. If you can’t find the error, you can click on “step” instead of “run” to execute the script line by line. Remove any typos that occurred while you were designing your model.

Alchemy example and Alchemy description by Paul Bourke.

Saving and Opening your Files in Jmol

Views Page Discussion View source History. Jmol can get files directly from the ligand collection at the Protein Data Bank website. Can also contain temperature factor, formal charge, element symbol, alternate locations. 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. Contents 1 Exporting or saving molecular model files from Jmol 1.

After you have completed your model design, click “history” on the Jmol Console.