Click on a link below to see what it does. You can also type a command in the box below the model to see its effect. The script run in this case was ;set echo top left;echo loading quartz.cif...;delay 1;load "quartz.cif" {1 1 1};message done.
This page lists all new features introduced between Jmol 10.2 and Jmol 11.0. Another file lists recent "bleeding edge" developments planned for Jmol 11.2
Jmol 11.1.20 enables differential coloring of axes. In addition, a change relative to Jmol 11.0 is that these colorations persist past file loading -- they are more like background than actual model-associated objects. You can turn axes off and on without clearing their diameter or color using showAxes = TRUE or showAxes = false.
Jmol 11.1.12 introduces a new way to select atoms based on distance from a plane. The plane can be defined most easily by a set of atoms using draw, then used to display a subset of the atoms. The sign of the distance value for "within" determines which side of the plane is being referred to. This is best determined by experimentation.
Jmol 10.9.77 adds the capability to load a wider range of unit cell blocks. The range should include 555 (the base unit cell). The third parameter, 0 or 1, indicates whether(1) or not(0) to "normalize" the symmetry operations by moving the geometric center of the generated set of atoms back into unit cell 555.
Jmol 10.9.71 allows you to select the currently clickable atoms. In conjunction with slabbing, this means that you can now select for just those atoms that are within the depth/slab range. A later slab off; restrict selected now allows you to manipulate the model with that particular slab maintained. Be sure to do a refresh just before selecting.
Jmol 10.9.72 introduces 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".
Jmol 10.9.71/79 allows you to select the exact lattice translation for a given symmetry operation. The reference point is the untransformed, untranslated file atoms - Jones-Faithful x,y,z - which are always designated n555.
Note that you can use other comparisons -- !=, <, >, <=, and >=. If you use any of these comparisons with a simple symmetry operation, the usual comparison will be returned. If you use this new nijk syntax, then the atom must match the given symmetry operation; the comparison is ONLY for the ijk part.
Jmol 10.9.55 extends spacegroup and unitcell capabilities to standard XYZ, mmCIF, and MOL files. Coordinates are not fractional in these files, so the presumption is that we have the final Cartesian coordinates, but we want to "reverse engineer" the system and see how that molecule packs in its crystal. For this we have to have some additional information of spacegroup and unitcell.
Jmol 10.9.54 adds the capability to explore space groups and molecular packing of proteins in PDB files. This opens the door also for the same using any Cartesian-coordinate file, provided unit cell and space group information are provided. At least for now it is possible with PDB files.
To select all special positions (positions that can be generated by more than one symmetry operation from the original set of atoms), use select specialPosition.
Jmol 10.9.51 adds the capability to read space group names (Hermann-Mauguin or Hall) and from these to generate the set of operators. In the case of Hall symbols, this assignment is definitive; in the case of Hermann-Mauguin symbols, cell parameters are also used in order to identify the unique axis, but there still may be ambiguities in this case. The current implementation is for testing only -- some changes should be expected. To indicate 2", use a pair of single quotes: 2''. In addition, you can supply a desired space group name with a file to specify that you want to override the space group indicated in the CIF file.
without qualifiers, "show spacegroup" interprets the name of the spacegroup given in the file. Note that this may not be consistent with the operators used to calculate the atom positions if those are explicitly given in the CIF or RES file. Jmol will only use the space group name to generate operators if they are not otherwise given in the file.
In 10.9.52 you can load a file and script what spacegroup to use, overriding the spacegroup indicated in the file itself. No check is done to ensure that the chosen space group is compatible with the cell dimensions. The "space group" can just be a list of x,y,z operators.
Jmol.js supports Asynchronous JavaScript, allowing web developers to create pages that draw from any molecular data resource on the web. To use this service, nothing more than Jmol.js is require. No server-side application is needed. Currently the both of the two known AJAX-JS servers are supported -- one at St. Olaf College serving up RCSB biomolecular structures as well as just about any uncompressed structural model files anywhere on the web, and the American Mineralogical Society's AJAX mineral structure server at the University of Arizona.
6. new "select/restrict cell={i j k}" and "unitcell {i j k}" and better polyhedral rendering
Jmol 10.x.18 allows for the selection of specific unit cells. Coordinates such as {1.5 1.5 1.5} are allowed. In conjunction with this, "unitcell {i j k}" shifts the unit cell and the unit cell axes ("set axesUnitcell") to a new origin. See poly.htm
4. points, lines, and planes; specifying coordinates
Jmol 10.x can now draw point, line, and triangular or rectangular planes based on single atom positions, group average positions, or specific molecular coordinates. see draw.htm
Jmol 10.x.03 introduces a way of specifying fractional coordinates: {1/2, 1/2, 1/2}. A "1" in the denominator is optional: {0.5/, 0.5/, 0.5/}, and in such cases only one slash is necessary: {0.5/, 0.5, 0.5} or {0.5, 0.5, 0.5/}. These may be used in defining the center, in creating draw objects, in defining rotation, spin, and moveto orientation axes, and positions of dipole moments. See fraction.htm
2. symmetry, unit cells, and multiple lattice reading
Jmol 10.x now allows extensive reading of SHELX and CIF symmetry and lattice information. Multiple unit cells can be displayed. see sym.htm and the Jmol Crystal Explorer
Jmol 10.x along with its associated new Jmol.js library now allows for the retrieval of a wide range of data related to the model. see vibrate.htm, and try the bracketed links, below:
