Some examples of Jmol 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.;
theimg = "../img/demo_sasurface.jpg";load 2ptn.cif;moveto 1.0 245 959 140 66.2; isosurface ignore(solvent) sasurface 1.2;write image 250 250 @theimg;
 

# 2 A simple solvent-excluded or "molecular" surface. These surfaces take considerably more time to calculate, since they involve the creation of rounded troughs.;
theimg = "../img/demo_molecular.jpg";load 2ptn.cif;moveto 1.0 245 959 140 66.2; select resno <= 25; isosurface ignore(solvent) molecular;write image 250 250 @theimg;
 

# 3 Jmol can depict the cavities around a ligand or substrate. ;
theimg = "../img/demo_cavity.jpg";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;write image 250 250 @theimg;
 

# 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.;
theimg = "../img/demo_molecularslice.jpg";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};;write image 250 250 @theimg;
 

# 5 A molecular "slice" generated from a JVXL file.;
theimg = "../img/demo_jvxlplanarslice.jpg";load 2ptn.cif; isosurface "2ptn-molecular_slice1.jvxl"; moveto 3.0 -308 401 863 108.1;;write image 250 250 @theimg;
 

# 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".;
theimg = "../img/demo_millerplane1.jpg";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;;write image 250 250 @theimg;
 

# 7 While both "molecular" and "solvent 0" give an electron-density-like depiction, "solvent 0" is faster.;
theimg = "../img/demo_millerplane.jpg";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;;write image 250 250 @theimg;
 

# 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.;
theimg = "../img/demo_c6h6mepmap.jpg";load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81}; isosurface resolution 6 molecular map mep;write image 250 250 @theimg;
 

# 9 MEP data can also be rendered directly...;
theimg = "../img/demo_c6h6mep.jpg";load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81}; isosurface resolution 6 mep;write image 250 250 @theimg;
 

# 10 ...or mapped onto a plane.;
theimg = "../img/demo_c6h6mepplane.jpg";load C6H6.smol;moveto 1.0 { -962 -235 -141 56.81}; isosurface resolution 6 contour 41 plane xy map mep;write image 250 250 @theimg;
 

# 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.;
theimg = "../img/demo_atomicorbitals.jpg";isosurface phase atomicOrbital 3 2 1; set axesMolecular;set axesScale 0.5;axes on; moveto 1.0 { 462 -868 -180 47.18} 141;write image 250 250 @theimg;
 

# 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.;
theimg = "../img/demo_mo.jpg";load ch2o_homo.mo;wireframe 0.05;spacefill off;moveto 1.0 940 -340 -34 67.0; mo 1;write image 250 250 @theimg;
 

# 13 For files specifying orbital occupancy, the keywords "homo" and "lumo" can be used. Several other options are available with the MO command.;
theimg = "../img/demo_mohomo.jpg";load C6H6.smol;moveto 1.0 -821 -377 -430 69.2; mo cutoff 0.008; mo resolution 8; mo homo -1;;write image 250 250 @theimg;
 

# 14 The isosurface command can also be used with molecular orbitals in order to create special effects.;
theimg = "../img/demo_isomo.jpg";load ch2o_homo.mo;wireframe 0.05;spacefill off;moveto 1.0 940 -340 -34 67.0; isosurface color yellow purple mo 1 translucent;write image 250 250 @theimg;
 

# 15 Planar slices through molecular orbitals can be made using the isosurface command (Jmol 11.3.2).;
theimg = "../img/demo_moslice.jpg";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;write image 250 250 @theimg;
 

# 16 Spheres and ellipsoids can be created using the isosurface command.;
theimg = "../img/demo_sphere.jpg";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;;write image 250 250 @theimg;
 

# 17 Planes can be created using the draw command. ;
theimg = "../img/demo_plane.jpg";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};write image 250 250 @theimg;