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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 results from Jmol

This is preliminary and needs testing. 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 can get files directly from the Protein Data Jmkl website. Jmol does not fully support reading of Alchemy and Alchemy files.

Testing a Script After annotating your script, you should always run the script to make sure there aren’t any errors. Jmol can get files directly from the ligand collection at the Protein Data Bank website.

Recent versions of Jmol application and signed applet can export models to several formats that specify three-dimensional objects and can be read by specialized software 3D-world or 3D-scenes. Select the script, then drag and drop into a word processor.

Also, force vectors are read and included as vibrations activated by default on file load. Save the image in the same folder as the PDB file that accompanies this image. This can be done from script or from the pop-up menu, only from the Jmol application and the JSmol-Java modality. After you have completed your model design, click “history” on the Jmol Console.


If you have those details, please contact the developers team. This format is used e.

File formats/Coordinates

Jmol reads only the output format. Insert comments throughout your script. Contains atom coordinates, bonds, substructure information. CIF files may contain an inline script starting with jmolscript: Edport reads files output from the computational chemistry package Q-Chem.

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.

Jmol links Website Sourceforge. Retrieved from ” http: Jmol reads Cube files, original from Gaussian software Gaussian website. This option is not available from either the top menu or the expodt menu; it must be done from the console command line or from a script file. The described objects are handled as isosurfaces in Jmol, so. We call these blocks “cassettes”. This format supports partial charges and isotopesbut only partial charges are currrently supported by Jmol.

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

Date PDB file name Name of file s containing your model design — and the path to the files folder name, etc. Views Page Discussion View source History. Due to Java security restraints, only the application and the signed applet can write to files on disk. If the first part runs fxport problems, you can add additional chunks of script and run again.


Supports multi-model data multi-frame, animations. Correct the script as needed.

Example by Paul Bourke, and other example files. You can see an example. Acta Crystallographica A You’ll only need the final “color backbone” command that has the actual color of your model. As a result, atoms are not spheres, but polyhedra with many faces visible when zooming in closely.

A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames. Retrieved from ” http: Retrieved from ” http: Features are nearly identical to those of VRML.

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. More flexibility is allowed by using the write isosurface command. It is somewhat similar to the mol format.

File formats/3D Objects

ezport If the first part doesn’t work, break it down into smaller chunks to isolate the problem. Jmol reads MOL2 files. Here is a sample script before and after annotating.