This prototype file demonstrates new features in Jmol. Click first on a load command, then go down the list in order (or not).

• ### higher zoom capability ###
• load kinesin.pdb;select not protein and not solvent;spacefill 2.0
• zoom 1000
• zoom 5000
• zoom 10000
• zoom 20000
• zoom 20001 # out of range
• reset;set perspectiveDepth off
• zoom 100
• zoom 400
• zoom 800
• zoom 2000
• # Note how zoom is much more powerful with perspectiveDepth off
• reset;set perspectiveDepth on
• ### HBONDS CALCULATE ###
• load 1crn.pdb
• hbonds on
• # INTENTIONALLY NO LONGER WORKS TO CREATE HYDROGEN BONDS.
• hbonds calculate
• # the exact equivalent of the old "hbonds on"
• load 1crn.pdb
• select 1-20; hbonds calculate
• # as with hbonds on, hbonds calculate takes into consideration the current selection set.
• ### new Label format options ###
• load 1crn.pdb
• set labelOffset 0 10
• select *.CA; label %n
• # the %n format is still the three-character code for amino acid residues
• select *.CA; label %m
• # the new %m format is the single-character code for amino acid residues
• select *.CA and atomno<10; label %5.3x %5.3y %5.3z
• # standard C++ "pformat" formating is available for any numeric label option.
• select atomno=200; label __left:%-8.3x__zero-filled:%08.3y__normal:%8.3z__
• ### new rendering options ###
• # NOTE: SET wireframeRotation ON/OFF has been removed.
• # NOTE: SET oversampleAlways ON/OFF has been removed.
• # NOTE: SET oversampleStopped ON/OFF has been removed.
• load znqukrod.mol
• # optional grey-scale rendering:
• set greyScaleRendering ON
• set greyScaleRendering OFF
• load 1a31.pdb
• set chainCaseSensitive ON
• select *:a; color yellow #none selected
• select *:A; color white #chain A selected
• set chainCaseSensitive OFF #the default
• select *:a; color yellow
• ### miscellaneous options ###
• set hideNameInPopup TRUE
• load 1crn.pdb
• # right-click applet to see no name in menu, no way to view file contents in a pop-up window
• set hideNameInPopup FALSE
• load 1crn.pdb
• # right-click applet to see name in menu and access to file contents
• # note that behavior starts with the NEXT LOADED FILE
• set disablePopupMenu TRUE
• set disablePopupMenu FALSE
• ### SELECT CONNECTED() ###
• load znqukrod.mol
• select connected();color green
• select connected(7);color red
• select connected(zinc);color yellow
• select connected(2,hydrogen);color blue
• select hydrogen and connected(connected(2,hydrogen));color orange
• ### COLOR [element] ###
• load znqukrod.mol
• select(hydrogen); color ATOMS yellow
• # Here we are referring to "all hydrogens in the model"
• color hydrogen purple
• # Here we mean "the default color for the element hydrogen"
• # notice that no change occurs in this case, because these hydrogens have already been given a special color, yellow.
• load caffeine.xyz
• # This use of color is PERSISTENT FOR THE LIFE OF THE APPLET
• # and will only revert when the page is reloaded or we assign hydrogen another color.
• color hydrogen white
• # since we haven't changed their color, these atoms do go back to white.
• load znqukrod.mol
• # and they are white from now on
• ### CONNECT ###
• load nacl.mol
• connect 1.0 3.0 (atomno<100) (atomno>100) SINGLE ModifyOrCreate
• # the full command consists of distances, two atom sets, bond type, and create/modify option
• # options for bond type include SINGLE, DOUBLE, TRIPLE, AROMATIC, PARTIAL, PARTIALDOUBLE, and HBOND
• # options for create/modify include ModifyOrCreate MODIFY CREATE DELETE
• connect (*) (*)
• # don't do this!
• connect
• # by itself, returns to defaults for covalent bonds
• connect; select atomno < 100; connect 3.0 (atomno>100)
• # missing one or both atom set implies (selected)
• connect; select atomno < 100;connect 3.0
• # atom sets can be pre-selected
• load ice.pdb
• connect 1.8 (hydrogen) (oxygen) hbond create
• moveto 3 -962 82 262 72.9;set spin y 10;spin on
• spin off
• load caffeine.xyz
• connect 1.2 1.26 (carbon) (oxygen) DOUBLE
• connect 1.5 (carbon) (connected(2,nitrogen)) DOUBLE
• connect 1.5 (nitrogen and not connected(3)) (connected(1,hydrogen)) DOUBLE
• connect 2.0 (carbon) (connected(2,nitrogen)) AROMATIC
• connect 2.0 (nitrogen and not connected(3)) (connected(1,hydrogen)) AROMATIC
• connect (oxygen) (oxygen) HBOND
• # new hbonds are thin lines
• connect HBOND DELETE
• connect (atomno=9) (atomno=18) PARTIAL
• # partial bonds are standard-radius and have a slightly different pattern
• connect PARTIAL DELETE
• connect AROMATIC DELETE
• connect 2.0 (*) (not hydrogen) AROMATIC CREATE
• select not (connected(3,hydrogen) or hydrogen);color yellow
• connect HBOND MODIFY
• # modified hbonds take previous bond's diameter
• load nacl.mol
• connect 3.0 (chlorine) (sodium)
• # only nearby Na-Cl formed
• connect (chlorine) (sodium) DELETE
• select (chlorine); connect 3.0 (sodium) #same thing
• connect (chlorine) (sodium) DELETE
• connect 3.0 6.0 (chlorine) (sodium) HBOND
• # only distant Na-Cl formed
• connect (chlorine) (sodium) HBOND DELETE
• ### ISOSURFACE ###
• see the Jmol Script Documentation for examples of drawing orbitals and other information as isosurfaces.
• ### PMESH ###
• see the Jmol Script Documentation for examples of drawing orbitals and other information as isosurfaces.
• ### enhanced POLYHEDRA ###
• load nacl.mol
• connect 3.0 (chlorine) (sodium)
• # this is needed for bonding designation in the polyhedra command
• polyhedra 4,6 BONDS (chlorine) collapsed edges; color polyhedra yellow
• # the new "collapsed polyhedra" idea
• polyhedra 6 RADIUS 3.0 (chlorine) to (sodium)
• # only the chlorines that are within 3 Angstroms of exactly 6 sodiums
• select *; wireframe off; spacefill off
• select connected(4); polyhedra OFF
• select connected(6); polyhedra COLLAPSED
• polyhedra EDGES
• color polyhedra yellow
• spacefill 0.5
• # here we use those connections to provide clickable atoms (for distance and angle measurement)
• select connected(6); spacefill 0.005
• # they can be almost inperceptible but still clickable
• load quartz.xyz
• polyhedra 4 BONDS; color polyhedra red
• # the standard look
• polyhedra 4 BONDS EDGES
• # edges are a nice touch
• polyhedra 4 BONDS (silicon) TO (oxygen) COLLAPSED EDGES
• # the "collapsed" look
• load p4o10.mol
• polyhedra 4 COLLAPSED EDGES
• load znqukrod.mol
• select zinc; polyhedra BONDS EDGES
• select zinc; polyhedra BONDS COLLAPSED EDGES
• select carbon; polyhedra BONDS COLLAPSED EDGES
• select carbon; polyhedra BONDS COLLAPSED EDGES faceCenterOffset=0.4
• load tcbewrea.mol
• polyhedra (*) (*) COLLAPSED EDGES
• # notice the effect of faceCenterOffset:
• polyhedra (carbon) DELETE
• polyhedra BONDS (carbon) COLLAPSED EDGES
• # if you look closely, not all the planes have been drawn. This model is quite distorted, so we increase the value of faceNormalMax from its default value of 30 to 50:
• polyhedra BONDS (carbon) COLLAPSED EDGES faceNormalMax=50
• select not nitrogen; polyhedra BONDS COLLAPSED EDGES faceCenterOffset=0.0
• # faceCenterOffset of 0 can result in lighting problems
• select not nitrogen; polyhedra BONDS COLLAPSED EDGES faceCenterOffset=0.25
• select not nitrogen; polyhedra BONDS COLLAPSED EDGES faceCenterOffset=0.5
• see the Jmol Script Documentation for details regarding polyhedra.
• ### STARS ###
• load caffeine.xyz
• select oxygen;stars ON
• stars 50% # of Van der Waals radius
• stars 1.0 # Angstroms
• color stars translucent
• stars OFF
• see the Jmol Script Documentation for additional examples of displaying a thin-lined star at atom positions.