This prototype file demonstrates new features in Jmol. Click first on a load command, then go down the list in order (or not).
- 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
- 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.
- 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__
- # 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
- 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
- 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
- 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
- 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
- see the Jmol Script Documentation for examples of drawing orbitals and other information as isosurfaces.
- see the Jmol Script Documentation for examples of drawing orbitals and other information as isosurfaces.
- 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.
- 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.
|
