Some examples of Jmol surfaces

• Molecular and Solvent Surfaces
• Planar Slices Through Molecular Surfaces
• Crystallographic Planes
• Molecular Electrostatic Potentials
• Atomic and Molecular Orbitals
• Other Surface Objects

Molecular and Solvent Surfaces

1 A simple solvent-accessible surface. These surfaces are very quick to calculate and display. They represent the trace of the center of a spherical solvent probe as it rolls around the molecule. load 2ptn.cif;moveto 1.0 245 959 140 66.2 isosurface ignore(solvent) sasurface 1.2

2 A simple solvent-excluded or "molecular" surface. These surfaces take considerably more time to calculate, since they involve the creation of rounded troughs. load 2ptn.cif;moveto 1.0 245 959 140 66.2 select resno <= 25 isosurface ignore(solvent) molecular

3 Jmol can depict the cavities around a ligand or substrate. load 2by9.pdb;moveto 1.0 { -876 -280 393 130.71} 210.14 -31.4 14.8 {23.699003 21.285 22.801003} 29.576609 {0.0 0.0 0.0} -25.99526 106.25879 50.0 select BAM color white;refresh select within(5.0, BAM);moveto 1.0 { -876 -280 393 130.71} 210.14 -31.4 14.8 {23.699003 21.285 22.801003} 29.576609 {0.0 0.0 0.0} -25.99526 106.25879 50.0 select within(5.0, BAM) isosurface cav1 ignore(bam or solvent) cavity molecular colorscheme sets translucent 0.3

Planar Slices Through Molecular Surfaces

4 Jmol uses a unique algorithm to calculate surfaces. Each position in space is given a value that is its distance from the nearest surface point. What this means is that a "surface" is really an "isosurface with cutoff 0". And what that means is that a surface is no different in terms of visualization from a molecular orbital or other atom-based spacial property. load 2ptn.cif isosurface plane {1 0 10} {0 1 10} {1 1 10} ignore(solvent) sasurface 0.5 moveto 1.0 { -822 -490 -290 168.25};

5 A molecular "slice" generated from a JVXL file. load 2ptn.cif isosurface "2ptn-molecular_slice1.jvxl" moveto 3.0 -308 401 863 108.1;

Crystallographic Planes

6 The "hkl" keyword indicates that the next three numbers in braces are Miller indices. Note that all coordinates are implicitly fractional. A faster alternative is to use "solvent 0" instead of "molecular". load nacl.cif {2 2 2} unitcell off;axes 0.2;boundbox on select * isosurface hkl {1 1 1} resolution 4 moveto 1.0 268 -953 -141 88.0;

7 While both "molecular" and "solvent 0" give an electron-density-like depiction, "solvent 0" is faster. load nacl.cif {2 2 2} unitcell off;axes 0.2;boundbox on select * isosurface hkl {1 1 1} resolution 4 solvent 0 moveto 1.0 268 -953 -141 88.0 delay 3;restrict none;

Molecular Electrostatic Potentials

8 Molecular electrostatic potentials are calculated from partial charge data present in a file; Jmol cannot calculate these charges. Generally MEP data would be mapped onto a molecular surface, as shown here. load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81} isosurface resolution 6 molecular map mep

9 MEP data can also be rendered directly... load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81} isosurface resolution 6 mep

10 ...or mapped onto a plane. load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81} isosurface resolution 6 contour 41 plane xy map mep

Atomic and Molecular Orbitals

11 Simple atomic orbitals can be placed on any atom or, for that matter, anywhere in space. One simply specifies the values of n, l, and m. isosurface phase atomicOrbital 3 2 1 set axesMolecular;set axesScale 0.5;axes on moveto 1.0 { 462 -868 -180 47.18} 141

12 Jmol can render many standard calculated molecular orbitals without the need for CUBE files. Most ab initio (STO-3G, 3-21G*, 6-31++G**, etc.) and semi-empirical (AM1, PM3) basis sets can be rendered. For GAUSSIAN, use keywords pop=full gfprint; the orbitals will be in frame 2. load ch2o_homo.mo;wireframe 0.05;spacefill off;moveto 1.0 940 -340 -34 67.0 mo 1

13 For files specifying orbital occupancy, the keywords "homo" and "lumo" can be used. Several other options are available with the MO command. load C6H6.smol;moveto 1.0 -821 -377 -430 69.2 mo cutoff 0.008 mo resolution 8 mo homo -1;

14 The isosurface command can also be used with molecular orbitals in order to create special effects. load ch2o_homo.mo;wireframe 0.05;spacefill off;moveto 1.0 940 -340 -34 67.0 isosurface color yellow purple mo 1 translucent

15 Planar slices through molecular orbitals can be made using the isosurface command (Jmol 11.3.2). load ch2o_homo.mo;wireframe 0.05;spacefill off;moveto 1.0 940 -340 -34 67.0 isosurface color absolute -0.1 0.1 plane xz mo 1

Other Surface Objects

16 Spheres and ellipsoids can be created using the isosurface command. load caffeine.xyz;moveto { -960 -278 -23 85.64} isosurface i1 center {substructure( "[C]1[C][C][N][C][N]1")} sphere 1.0 translucent blue co_xyz = ({atomno=11}.xyz - {atomno=5}.xyz) * 0.7 x = co_xyz.x;y = co_xyz.y;z = co_xyz.z isosurface i2 center {atomno=11} ellipsoid {@x @y @z 0.5} translucent yellow;

17 Planes can be created using the draw command. load caffeine.xyz;moveto { -960 -278 -23 85.64} draw d1 PERP 150 PLANE (atomno=3) (atomno=5) "red" opaque red draw t2 (atomno=9) (atomno=10) (atomno=11) scale 1.5 translucent moveto 1.0 { -996 -84 -15 61.39}