From Jmol

1. Jmol Website
2. Jmolly
3. Jmol Download

Jmol is a cross-platform Java-based program which lets you look at three-dimensional views of chemical structures. With it, the atoms that make up chemical compounds can be seen from almost any angle. Jmol is a molecular structure viewer. It is from an open-source project which can be found at jmol.sourceforge.net. It is used in geWorkbench to view PDB format files. In the figure below, it has been used to open the file for transposase complexed with DNA (1muh.pdb), available from the Protein Data bank at PDB:1muh. The script console is Jmol's command line interface. In the application version type your command after the '$' prompt. The command will appear red until you have typed a complete command. In the applet type the command in the bottom part of the window. There is no syntax checking in the applet. Hit the key to activate the command.

• A list of Jmol Tutorials written by users.
• Using the mouse (English · Español · Français · Japanese).
• Scripting quickstart: rendering options · selecting atoms.
• Various ways to create surfaces and more documentation on surfaces.
• Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
• Creating movies.
• Customizing Jmol: macros · menus.
• Web pages without writing code by using the Jmol 'export to web..' function ( Español ).

Manual for manipulating the molecules using the mouse in Jmol (also called 'mouse gestures')

Notes:

1. In the usual configuration, 'main button' is the left button, and 'secondary button' is the right button.
2. Reportedly, on single-button mice Alt drag may be equivalent to drag with middle button.

How to select

• Use the appropriate picking command, e.g.

set picking group

to toggle selection for an entire amino acid by clicking on one of its atoms,

• Click on an atom will toggle selection status.
• Most useful while

set display selected

is set to monitor the selection status.

To toggle the selection status of individula atoms:
Using the menus:

1. Jmol->Main Menu->Select->Selection Halos (This is optional but very helpful. It shows you which atoms are selected by plaing a golden ring around it.)
2. Jmol->Main Menu->Select->None (Needed because 'select all' is the default at load time. Notice the non-zero number in parenthesis after the word select in the main menu. That is the number of items currently selected.
3. Jmol->Main Menu->Set picking->Select Atom

Now click an atom once to select, click again to deselect. The halos let me know the current selection state of each atom and the count in parenthesis after the Select in Jmol->Main Menu gives me a count of the number of atoms selected.

How to make measurements

• Distance (2 atoms):
  1. double-click on the starting atom
  2. to fix a distance measurement, double-click on second atom
• Angle (3 atoms):
  1. double-click on the starting atom
  2. click on the second atom (central atom in angle)
  3. to fix an angle measurement, double-click on third atom
• Torsion angle or dihedral (4 atoms)
  1. double-click on the starting atom
  2. click on the second atom
  3. click on the third atom
  4. to fix a dihedral angle measurement, double-click on fourth atom
• In all cases:
  • move pointer over destination atom in order to see measurement results without leaving a permanent measurement
  • move outside the window in order to cancel the measurement
  • make the same measurement again in order to delete the measurement

• Description of files in Jmol+JSmol distribution
• File formats read or written by Jmol
• The Jmol scripting interface
  • Scripting as a programming language
  • Complete reference of scripting commands:
    • at St Olaf (primary site)
    • at Jena3D (mirror)
• Loading models directly from databases
• Default colors used by Jmol
• Atom sets predefined in Jmol
• Support for bond orders · isotopes · stereochemistry · hydrogen bonds
• Copying and pasting state scripts between applets.
• Backward compatibility (changes of behavior across versions)
• Users mailing list (and a mirror)

• 3Comments/Discussion

Linux

Jmol runs without problems on Linux machines using Sun's java virtual machines, both as Applet as well as Application. Running the application has not been tried with other virtual machines or compilers, like Kaffe.

Binary Jmol Packages

Binary package are available for Debian, see Debian. Crash drive 2 download mac.

Comments/Discussion

• What I would very much like to see, is a KDE GUI for Jmol. That is, a GUI that is completely independant of Swing and thus runs with free virtual machines, e.g. Kaffe. -- Egon Willighagen

SUSE 10.2 Linux i686 (x86_64)

Couldn't get Jmol to launch with memory overflow messages from script when I've had no problems from SUSE other distros on 32 bit. The message log file showed ALERT - script tried to increase memory-limit to 20971520 bytes which is above the allowed value

Jmol Website

Solution that worked for me after debugging as root was to launch current java binary calling jar file with user permissions in user home subdirectory:eg

/usr/lib/jvm/java-1.5.0-sun-1.5.0_update12/jre/bin/java -jar {HOME}/jmol-11.2.9/Jmol.jar Aerofly rc7 mac free download.

Jmolly

with {HOME} being your own home directory fully specified, eg /home/anuser.

I disabled launch feedback with KDE menu editor options.

Presumably the symbolic links are not where Jmol expects them in jmol.sh with jvm so there will be other solutions. ChaseKiwi

Jmol Download