Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Jmol is cross-platform, running on Linux/Unix, Mac OS X, and Windows systems.
� The JmolApplet is a web browser applet that can be integrated into web pages.
� The Jmol application is a standalone Java application that runs on the desktop.
� The JmolViewer is a development tool kit that can be integrated into other Java applications.
Jmol v10 is a complete rearchitecture and rewrite of Jmol, undertaken in the Spring of 2003, with the specific goal of developing Jmol into a replacement for the Chime Plug-in.
Jmol v10 retains most of the features and functionality of the previous Jmol releases while offering significant enhancments in the following areas:
� true 3D graphics engine that requires no special hardware
� 24 bit color with accurate lighting and shading
� substantially higher rendering performance
� handles large macromolecules with excellent performance
� protein/nucleic acid secondary structure graphics
� RasMol/Chime script compatibility
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Here are some key features of "Jmol":
· Free, open-source software licensed under the GNU Lesser General Public License
· Applet, Application, and Systems Integration Component
· Cross-platform
· Supports all major web browsers
· High-performance 3D rendering with no hardware requirements
· File formats
· Animations
· Vibrations
· basic unit-cell support
· schematic shapes for secondary structures
· measurements
· RasMol/Chime scripting language support
· JavaScript support library
· Exports to .jpg, .pdf, and PovRay
What's New in This Release: [ read full changelog ]
· FEATURE CHANGE: "ligand" definition changed to
· !(protein,nucleic,water,UREA)"
· instead of "hetero and not solvent"
· FEATURE CHANGE: default zShadePower set to 3
· FEATURE CHANGE: undocumented a[13] = 3 (where a is a matrix, for a[1][3]) removed
· FEATURE CHANGE: DSSP default for "calculate structure"
· -- old way is now "calculate structure RAMACHANDRAN"
· FEATURE CHANGE: DSSP default for LOAD of PDB file with no header.
· in previous versions, Jmol used a ramachandran-angle-based calculation
· for secondary structure determination when a PDB file had no HELIX or SHEET records.
· It just seems reasonable to use the industry-standard DSSP method instead.
· new feature: JmolSmilesApplet method (smiles1)
· new feature: JmolSmilesApplet method getRelationship(smiles1, smiles2)
· new feature: The Jmol application can now communicate via sockets
· with other Jmol applications or specialized servers.
The SYNC command has been expanded to make this very easy:
· sync -nnnn starts a server on local port nnnn accepting only local connections
· sync nnnn "background white" (from another app, generally) would execute that
· command on the app acting as a server
· You can also do this from one app frame to another, because they are independent
· instances of Jmol.
Jmol can provide server service to other apps using:
· sync -3000
· [start other app, connecting on 3000]
· sync 3000 .....
· Because once the server is started and another app has connected,
· Jmol will send messages to that other app, not itself.
· To test the service within one application, just create the server and send
commands to itself using a negative port number:
· sync -3000;sync -3000 'Mouse: rotateZBy 30'
· Note that in this context the "server" is the one getting commands from the "client"
· But the server can also send commands to the client provided the client has given the
· appropriate handshake: {"magic":"JmolApp","event":"out"}
Sent from Jmol (via outSocket):
· {"magic" : "JmolApp", "role" : "out"} (socket initialization for messages TO jmol)
· {"magic" : "JmolApp", "role" : "in"} (socket initialization for messages FROM jmol)
· {"type" : "script", "event" : "done"} (script completed)
Sent to Jmol (via inSocket):
· {"type" : "banner", "visibility" : "ON" or "OFF" } (set banner for kiosk)
· {"type" : "banner", "text" : bannerText } (set banner for kiosk)
· {"type" : "command", "command" : command } (script command request)
· {"type" : "content", "id" : id } (load content request)
· {"type" : "move", "style" : (see below) } (mouse command request)
· {"type" : "quit" } (shut down request)
· {"type" : "sync", "sync" : (see below) } (sync command request)
· {"type" : "touch", (a raw touch event)
· "eventType" : eventType,
· "touchID" : touchID,
· "iData" : idata,
· "time" : time,
· "x" : x, "y" : y, "z" : z }
· For details on the "touch" type, see org.jmol.viewer.ActionManagerMT::processEvent
· Content is assumed to be in a location determined by the Jmol variable
· nioContentPath, with %ID% being replaced by some sort of ID number of tag provided by
the other half of the system. That file contains more JSON code:
· {"startup_script" : scriptFileName, "banner_text" : text }
· An additional option "banner" : "off" turns off the title banner.
· The startup script must be in the same directory as the .json file, typically as a .spt file
Move/sync commands include:
· {"type" : "move", "style" : "rotate", "x" : deltaX, "y", deltaY }
· {"type" : "move", "style" : "translate", "x" : deltaX, "y", deltaY }
· {"type" : "move", "style" : "zoom", "scale" : scale } (1.0 = 100%)
· {"type" : "sync", "sync" : syncText }
· Note that all these moves utilize the Jmol sync functionality originally intended for
· applets. So any valid sync command may be used with the "sync" style. These include
· essentially all the actions that a user can make with a mouse, including the
· following, where the notation represents a number of a given type. These
· events interrupt any currently running script, just as with typical mouse actions.
· "centerAt "
· -- set {ptx,pty,ptz} at screen (x,y)
· "rotateMolecule "
· "rotateXYBy "
· "rotateZBy "
· "rotateZBy " (with center reset)
· "rotateArcBall "
· "spinXYBy "
· -- a "flick" gesture
· "translateXYBy "
· "zoomBy "
· "zoomByFactor "
· "zoomByFactor " (with center reset)
· new feature: preliminary QuantumEspresso XML reader
· new feature: Jmol Application flags -k and -P
· -- -k kiosk mode: like applet, but with a banner across the top
· -- -P JSON NIO client mode over port
· -- for JSON NIO, use -J or -j to set nioContentPath and nioTerminatorMessage
to the desired values. For example:
· Jmol -k -P 31461 -j "nioContentPath='./%ID%/%ID%.json';nioTerminatorMessage='SCRIPT_DONE'"
· new feature: Jmol.js adds jmolSwitchToSignedApplet().
· This needed a new tag that is now inserted around the applet.
· new feature: filter "_Xx" for filtering element Xx
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