This prototype page illustrates the new capabilities of Jmol to calculate and display dipoles and simple arrows.
displaying user-defined dipoles
load water.xyz;moveto 1.0 727 -680 95 37.4
dipole (atomno=1) (atomno=3)
dipole (atomno=2) (atomno=3)
set dipoleScale 2.0
set dipoleScale -2.0
set dipoleScale -1.0
set dipoleScale 1.0 6. calculating dipoles from charge data in selected file types
load CH3F.smol;moveto 1.0 223 973 -64 51.1 96 -13 -9; the file readers will be updated; so far only the SMOL file type is read for molecular dipole and partial charges.
dipole calculate molecular offset 2.0 the calculation for bond dipoles is just a simple qualitative approximation: (distance12) * (charge1 - charge2) / 2
dipole calculate bonds this calculation is done ONCE per file, unless all the bond dipoles are deleted, in which case, the next command involving bonds recreates them
dipole bonds delete
dipole bonds 5. offsets, widths, cross options you can adjust the offset (along the axis of the arrow), the side offset (perpendicular to that), the width, and the presence of the cross
load CH3F.smol;moveto 1.0 223 973 -64 51.1 96 -13 -9; dipole molecular offset 2.0; dipole calculate bonds the default origin for the molecular dipole is {0 0 0} in the molecular coordinate system.
set axesMolecular; axes on; dipole molecular offset 0.0
axes off; dipole molecular offset 2.0 bond dipoles -- defined as any dipoles between two atoms -- are by default centered between those atoms. these dipoles take a side offset, which is by default 0.4 Angstroms.
dipole bonds offsetSide 0.2
dipole bonds offsetSide 0.6
dipole bonds width 0.1
dipole bonds noCross 4. specifying dipoles
load CH3F.smol;moveto 1.0 223 973 -64 51.1 96 -13 -9; dipole molecular offset 2.0; dipole bonds you can select a bond dipole either by specifying the two atoms or using its identifier
dipole dipole2 width 0.15 offsetSide 0.3
dipole (atomno=1) (atomno=2) width 0.1 offsetSide 0.5 the order of listed atoms is not significant when referring to an already-defined dipole
dipole (atomno=2) (atomno=1) width 0.05 offsetSide 0.5 "dipole" by itself just selects all dipoles
dipole turn off wireframe and spacefill and set offsetSide 0 for the "additive" effect
dipole;dipole offsetSide 0 width 0.1; wireframe 0; spacefill 0; 3. dipole color options
load CH3F.smol;moveto 1.0 223 973 -64 51.1 96 -13 -9; dipole molecular offset 2.0; dipole bonds dipoles inherit their color from bonds, which inherit THEIR color from atoms
color atoms blue
color bonds green
dipole bonds;color dipoles translucent yellow
color dipoles opaque white
dipole molecular; color dipole translucent red
dipole bond; color dipoles none
color bonds none
color atoms none 2. set dipoleScale x.xxx
load CH3F.smol;moveto 1.0 223 973 -64 51.1 96 -13 -9; dipole molecular offset 2.0; dipole bonds you can adjust the overall magnitude of all the dipoles using set dipolescale x.xxx
set dipoleScale 0.5
set dipoleScale 1.0 set dipoleScale negative if you want the arrows pointing the opposite direction
set dipoleScale -1.0 1. user-defined dipoles
load water.xyz;moveto 1.0 145 984 100 51.3 75 7 -9; set axesMolecular;axes on; You can define dipoles yourself using a number of conventions, and you can refer to them using the $name method.
dipole mydipole1 (atomno=1) (atomno=2) offsetSide 0
color $mydipole1 red
dipole mydipole1 {0 0 0} (atomno=2) dipoles can serve as simple arrows
dipole arrow1 {0 0 0} (atomno=3) noCross;color $arrow1 white an initial decimal number specifies the distance from the first point in the direction of the second point
dipole arrow1 0.5 {0 0 0} (atomno=3) noCross;color $arrow1 white
dipole arrow1 1.0 {0 0 0} (atomno=3) noCross;color $arrow1 white
dipole arrow1 1.3 {0 0 0} (atomno=3) noCross;color $arrow1 white
dipole arrow2 {0 0 0} {1 -1 1} noCross; color $arrow2 yellow [appletInfo] [animationInfo] [fileName] [fileHeader] [fileContents] [atomList] [atomInfo] [bondInfo] [extractModel] [orientationInfo] [transformInfo] [centerInfo] [boundboxInfo] [zoomInfo] [modelInfo] [polymerInfo] [chainInfo] [shapeInfo] [stateInfo] [reload THIS orientation]
Decoded: new window