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 has a limited capability for writing molecular coordinates, including only the currently selected set of atoms. A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames. 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. Information about the features that are displayed in this particular model Editing a Script in Jmol These next steps “clean up” your script and make it exporrt for you and others to interpret your script.

All of the above commands will save the original cooordinates of each atom as they were in the input file. This information will be helpful if you decide to create an electronic poster or Proteopedia page to accompany a model.

On the Jmol Console, click “editor”. This is preliminary and needs testing. Two files will be generated: 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.


Here is a list of format values. Features are nearly identical to those of VRML.

Jmol Wiki – File formats/Export

Jmol can export, with limited features, the current view of a model into Maya ascii format. This can be done from script or from the pop-up menu. Example files supported by Jmol.

After you’ve made a change to your script and want to test out the change, run the script on a “fresh” PDB file. An extension of this format supports isotopesand they are read by Jmol.

This option is not available from either the top menu or the popup menu; it must be done from the console command line or from a script file. Contains atom coordinates and bonds. Retrieved from ” http: Example by Paul Bourke.

File formats/3D Objects

Due to Java security restraints, only the application and the signed applet can write to files on disk. Either reload the PDB file in Jmol, or simply click “undo” on the Jmol Console to revert your model to its original form in the cartoon formatand then run the script again. A simple Alchemy reader is implemented starting Jmol Select the script, then drag and drop into a word processor.

Exoprt PDB file name Name of file s containing your model design — and the path to the files folder name, etc. Description of the format. We recommend that you save your designs early and often.

This can be done from script or from the j,ol menu, only from the Jmol application and the JSmol-Java modality. This would allow future web browsers to display 3D content natively, without any plugins or applets.


Jmol links Website Sourceforge.

Insert comments throughout your script. Acta Crystallographica A These next steps “clean up” your script and make it easier for you and others to interpret your script. This format supports partial charges and isotopesbut only partial charges are currrently supported by Jmol.

What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported. Jmol can export an image of the model into a pdf document single page, just the image in the center.

More flexibility is allowed by using the write isosurface command. Personal tools Log in.

Jmol Wiki – File formats/3D Objects

You’ll only need the final “color backbone” command that has the actual color of your model. Jmol reads CIF files. Annotating a Script Any line that begins with the symbol is ignored by Jmol, so you can add comments to your script. Views Page Discussion View source History.

File formats/Coordinates

Once you are satisfied with your final designs, you may wish to delete the unnecessary files. Remove any “blind alleys” that you took in your model design After you have jnol your model design, click “history” on the Jmol Console. Jmol reads only the output format. Any line that starts with will be taken as a comment and it can contain an inline script.