The Jmol molecular visualization system began life as a series of Java applets that could be embedded in web pages. With eventual security concerns about Java, Jmol was re-formulated as JavaScript applets. The reformulated version is named “JSmol” to emphasize the “JavaSscript” nature of the software. However, this convention is not applied consistently; the general term “Jmol” is often used. An example of the Jmol visualization of bucky ball is shown in the frame on the right:
To rotate the molecule, press the mouse button wile the cursor is inside the frame and drag it. To access a pop-up menu press the right mouse button while the cursor is inside the Jmol frame. To measure a bond distance, double-click on two atoms. To measure a bond angle, do double-click, single-click, double-click on three atoms. To measure a torsion angle, do double-click, single-click, single-click, double-click on four atoms. The Penn X-ray Facility uses Jmol in the archiving of completed X-ray structure determinations. As shown in the next link, the webpage displays a graphical index of completed structures for each research group. When a user clicks on a molecular drawing, the user is sent to a Jmol display of the molecule.There is also the capability to download the res file, the PDB file, the CIF and the final report (as a Microsoft WORD document).
The Penn X-ray Facility uses Jmol in the archiving of completed X-ray structure determinations. As shown in the next link, the webpage displays a graphical index of completed structures for each research group. When a user clicks on a molecular drawing, the user is sent to a Jmol display of the molecule.There is also the capability to download the res file, the PDB file, the CIF and the final report (as a Microsoft WORD document).
