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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Example by Paul Bourke.

File formats/3D Objects

Contains only atom coordinates no bonds and, optionally, charges and vectors e. Expirt the dropdown menu, select “Export” and then “Export Image”. Alternately, you can quickly narrow your search by removing the last half of the script, then running the first half.

Jmol interprets the charge values property partialcharge and the radii property vanderwaalsand can hence use them e.

If the materials file is missing your model will be monochrome. Be sure you save your final revised script into a text editor or word processor. Details of HIN format. 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 eexport or not.

File formats/Export

Jmol reads mmCIF files. The 2nd and 4th are equivalent and exxport, packed in a single file, a snapshot PNG image, the coordinates file and the state script file. Note that you will need to click the step button to execute each individual line.


This can be done from script or from the pop-up menu, only from the Jmol application and the JSmol-Java modality.

Saving and Opening your Files in Jmol

Jmol can export, with limited features, the current view of jmll model into Maya ascii format. On the Jmol Console, click “editor”. Jmol links Website Sourceforge.

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Jmol Wiki – File formats/3D Objects

Can exoprt contain temperature factor, formal charge, element symbol, alternate locations. An extension of this format supports isotopesand they are read by Jmol. You can make changes to your script in the “script” box of Jmol, and rerun the script to view the change, rather than typing it into the Jmol Console. Annotating a Script Any line that begins with the symbol is ignored by Jmol, so you can add comments to your script.

Jmol reads Cube files, original from Gaussian software Gaussian website. See the Q-Chem specific section. After you’ve made a change to your script and want to test out the change, run the script on a “fresh” PDB file.

See VRML for details. Jmol can get files directly from the ligand collection at the Protein Data Bank website. 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. This is preliminary and needs testing.


On the Editor Box that pops up, click “script” then click ‘clear’ so you have an empty window. Save the image in the same folder as the PDB file that accompanies this image. Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors. Jmol can export an image of the model into a pdf document single page, just the image in the center. Once you are satisfied with your final designs, you may wish to delete the unnecessary files.

Crystallographic Information File, the official format from the International Union of Crystallography:.

Supports multi-model data multi-frame, animations. Jol recommend that you save your designs early and often. Also, force vectors are read and included as vibrations activated by default on file load. 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.