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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Copy and paste your script into the editor window. 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. More flexibility is allowed by using the write exoprt command. Insert comments throughout your script. The described objects are handled as isosurfaces in Jmol, so.

Jmol will read any file and try to determine its wxport from its content.

Jmol Wiki – File formats/3D Objects

Now, you can easily see the changes that you made in your script. 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.

This would allow future web browsers to display 3D content natively, without any plugins or applets. The data can later be loaded using load var a. 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. Acta Crystallographica A Macromolecular Crystallographic Information File, an expanded format to cope with macromolecules. Example by Paul Bourke. If you want to create a JPEG image of your molecule from Jmol to use in a poster, for exampleclick the “File” menu located on the top left of the Display Window.


If the script doesn’t execute, look in the console for error messages; the console should direct to you the location of your error.

File formats/Export

Note, however, that the STL format does not support colorsso the whole model will have a single color. 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 expirt.

All of the above commands will save the original cooordinates of each atom as they were in the input file. See the sections below on opening and running a script. Views Page Discussion View source History. Description of Cube Input and Cube Output formats: Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms.

If you have those details, please contact the developers team. Retrieved from ” http: There are example files of Gaussian input, output and log. The unsigned applet can however display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file. These next steps “clean up” your script and make it easier for you and others to interpret your script.

An extension of this format supports isotopesand they are read by Jmol.

In the dropdown menu, select “Export” and then “Export Image”. Expot can be done from script or from the pop-up menu, only from the Jmol application and the JSmol-Java modality.


Can also contain temperature factor, formal charge, element symbol, alternate locations. Scripts allow you to create an exact record of your model design. Description of the format.

Saving and Opening your Files in Jmol

There is also the choice only in MOL format of saving the transformed coordinates as they are in the current state of the model:. The 2nd and 4th are equivalent and contain, packed in a single file, a snapshot PNG image, the coordinates file and the state script file.

The fileset must have a structure like:. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI. Views Page Discussion View source History. Jmol reads only the output format.

File formats/Coordinates

Naming Conventions As you are exploring your molecule and developing your molecular story, you will probably go through several iterations of your model design. Jmol can export, with limited features, the current view of a model into Maya ascii format. Jmol does not fully support reading of Alchemy and Alchemy files.

Jmol links Website Sourceforge. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically exlort sites, cofactors. If the first hmol doesn’t work, break it down into smaller chunks to isolate the problem.

You can instruct Jmol as to which format to assume using this special command syntax:. Save the image in the same folder as the PDB file that accompanies this image.