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 can export an image expodt the model into a pdf document single page, just the image in the center. There are example files of Gaussian input, output and log.

The 2nd is referenced from the 1st, so you should keep them together for loading into any other software. Insert comments throughout your script.

We recommend that you save your designs early and often. Jmol links Website Sourceforge. Example files supported by Jmol. Crystallographic Information File, the official format from the International Union of Crystallography:.

Saving a Script in Jmol Saving a JPEG of your model design is useful, but it doesn’t exporrt a record kmol the commands you used to obtain the design. Jmol reads and writes PQR files. It is somewhat similar to the mol format. Jmol can get files directly from the Protein Data Bank website. The same information that would be exported to a file may be put into a variable using this function.

Remove any “blind alleys” that you took in your model design Jmol reads CIF files.

File formats/Export

If the first part doesn’t work, break it down into smaller chunks to isolate the problem. These formats support formal charges and isotopes ; both are read by Jmol. Jmol reads mmCIF files. The described objects are handled as isosurfaces in Jmol, so. Supports multi-model data multi-frame, animations. Once you are satisfied with your final designs, you may wish to delete the unnecessary files. It is also one of the common formats for sending to a 3D printerin order to get a physical model in your hands.


V the most common is limited to atoms. Can also contain temperature factor, formal charge, element symbol, alternate locations. Remove any typos that occurred while you were designing your model.

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.

File formats/3D Objects

Contains atom coordinates, bonds, substructure information. If the materials file is missing your model will be monochrome.

Personal tools Log in. Date PDB file name Name of file s containing your model design — and the path to the files folder name, etc. Jmol can export, with limited features, the current jmmol of a model into Maya ascii format.

Saving and Opening your Files in Jmol

Testing a Script After annotating your script, you should always run the script to make sure there aren’t any errors. Either reload the PDB file in Jmol, expott simply click “undo” on the Jmol Console to revert your model to its original form in the cartoon formatand then run the script again.

Use comments to indicate what features you expory depicting in each of the blocks of commands. This would allow future web browsers to display 3D content natively, without any plugins or applets.

This is a popular format for sending to a 3D printerin order to get a physical model in your hands. This format is used e. Recent versions of Jmol application can also export to files in Gaussian input format.


Any line that starts with will be taken as a comment and it can contain an inline script. This can be done from script or from the pop-up menu. Fxport vrml or wrl file can then be opened using several programs and browser plugins, and manipulated in 3D using the mouse. Personal tools Log in. More flexibility is allowed by using the write isosurface command. Save the image in the same folder as the PDB file that accompanies this image.

Here is a sample script before and after annotating. This syntax is enough:. The file extension is not taken into account for identifying the format. This option is not available from either the top menu or the popup menu; it expkrt be done from the console command line or from a script file. After annotating your script, you should always run the script to make sure there aren’t any errors. Features are nearly identical to those of VRML.

You’ll only need the final “color backbone” command that has the actual color of your model. Due to Java security restraints, only the application and the signed applet can write to files on disk. After you’ve made a change to your script and want to test out the change, run the script on a “fresh” PDB file.

Jmol reads MOL2 files. Feel free to add a subsection with a description of a format you know well. 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.