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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A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames.

Two files will be generated: The 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. Feel free to add a subsection with a description of a format you know well. Alternately, you can quickly narrow your search by removing the last half of the script, then running exporrt first half.

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

File formats/Coordinates

An extension of this format supports isotopesand they are read by Jmol. Views Page Discussion View source History. It is also one of the common formats for sending to a 3D printerin order to get a physical model jmop your hands. Jmol reads files output from the computational chemistry package Q-Chem. Description of the format. Scripts allow you to create an exact record of your model design.

Date PDB file name Name of file s containing your model design — and the path to the files folder name, etc. Description of Cube Input and Cube Output formats: A complete specification of these formats would be needed to fully implement the reader. Make sure there are no extra lines or spaces at the end of the script – these will prevent the script from executing properly. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI.


Example files supported by Jmol.

Jmol links Website Sourceforge. 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. Details of HIN format.

This format supports formal charges, and only hydrogen isotopes as D and T ; they are all read by 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:.

Retrieved from ” http: Jmol reads only the output format. Acta Crystallographica A Wikipedia info on Maya. Retrieved from ” http: Remove any “blind alleys” that you took in your model design Contains atom coordinates and bonds.

This is a popular format for sending to a 3D printerin order to get a physical model in your hands.

The most interesting feature of this format is that it can be embedded in pdf filesproviding a 3D experience inside this well established standard for publication. Blank lines are ignored. This information will be wxport if you decide to create an electronic poster or Proteopedia page to accompany a model. Annotating a Script Any line that begins with the symbol is ignored by Jmol, so jmok can add comments to your script.

As a result, atoms are not umol, but polyhedra with many faces visible when zooming in closely. Contains atom coordinates, bonds, substructure information. Insert comments throughout your script. On the Editor Box that pops up, click “script” then click ‘clear’ so you have an empty window.


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

Jmol Wiki – File formats/3D Objects

Copy and paste your script into the editor window. If you need rxport for expoort charges, see the similar PQR format below. These formats support formal charges and isotopes ; both are read by 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. Contents 1 Exporting or saving molecular model files from Jmol 1. The 2nd and 4th are equivalent and contain, packed in a single ezport, a snapshot PNG image, the coordinates file and the state script file.

See VRML for details. File formats for ray tracing images. See the Q-Chem specific section. After you have completed your model design, click “history” on the Jmol Console. After annotating your script, you should always run the script to make sure there aren’t any errors.

File formats/3D Objects

Remove the first three lines or so of your script, starting with zap, jmool file, etc. Due to Java security restraints, only the application and the signed applet can write to files on disk. 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. See the sections below on opening and running a script.