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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Remove any typos that occurred while you were designing your model. Editing a History 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.

File formats/3D Objects

Note, however, that the STL format does not support colorsso the whole model will have a single color. Jmol reads mmCIF files. The 2nd is referenced from the 1st, so you should keep them together for loading into any other software.

Use comments to indicate what features you are depicting in each of the blocks of commands. Example by Paul Bourke. File formats for ray tracing images.

V the hmol common is limited to atoms. Jmol links Website Sourceforge. A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames.

In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI. It is somewhat similar to the mol format. Supports multi-model data multi-frame, animations. Jmol reads and writes PQR files. This gives the acronym: Retrieved from ” http: If the materials file is missing your model will be monochrome. This format supports formal charges, and only hydrogen isotopes as D and T ; they are all read by Jmol. Jmol does jmop fully support reading of Alchemy and Alchemy files.


You can see an example. Views Page Discussion View source History.

File formats/Export

There are, however, some problems in implementing this format in Jmol and so in successfully producing PDF files more directly. 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.

If the script doesn’t execute, look in the console for error messages; the console should direct to you the location of your error. Contains atom coordinates, bonds, substructure information. See the sections below on opening and running a script. The vrml or wrl file can then be opened using several programs and browser plugins, and manipulated in 3D using the mouse.

We recommend that you save your designs early and often. Opening a Script in Jmol Once you have your script, run it as follows: Note that you will need to click the step button to execute each individual line.

This format supports partial charges and isotopesbut only partial charges are currrently supported by Jmol. Alternately, you can quickly narrow your search by removing the last half of the script, then running the first half. Scripts allow you to create an exact record of your model design. The same information that would be exported to a file may be put into a variable using this function. 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.


Jmol will read any file and try to determine its format from its content. If the first part doesn’t work, break it down into smaller chunks to isolate the problem.

Jmol Wiki – File formats/3D Objects

Example files supported by Jmol. See also show below, as an alternative. Wxport formats support formal charges and isotopes ; both are read by Jmol.

If you have those details, please contact the developers team. On the Editor Box that pops up, click “script” then click ‘clear’ so you have an empty window. Now, you can easily see the changes that you made in your script.

CIF files may contain an inline script dxport with jmolscript: Naming Conventions As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design. We call these blocks “cassettes”. Save the image in the same folder as the PDB file that accompanies this image. Contains only atom coordinates no bonds and, optionally, charges and vectors e.