Crystal Community

Jmol/JSmol Community

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Crystal Community

This subcommunity of for Jmol users that use Jmol for display and analysis of crystal structures.

Tips from Users

This section is where you can add tips on how to use Jmol within the context of crystallography.

• By default unit cells are not shown. You can turn this on either with the menu or popup menu, or using the script command 'set unitcell on'. --- Egon Willighagen

What we would like to have in Jmol

The project is lacking manpower and could do with more developers, so development is not going top speed. Nevertheless, it's good to decide on what we would like to see added. So please add you requests here, and discuss what others have suggested.

• Translation of atoms/molecules to have fractional coordinates in [0,1>
• Interpretation of symmetry operations
• Use of transparency for not fully occupied positions
• Ability to export polyhedra, planes, (iso)surfaces, electron denisty maps, etc. to povray file for high-resolution images.

(* Reading xsf file input (as used by e.g. xcrysden))

What we already have in Jmol

A notable set of new capabilities has been added in Jmol v.11. See Bob Hanson's documentation and demonstration page on indicated section numbers:

• Ability to display electron density maps: see Electron Density Maps and Electron Density: Cloud vs. Isomesh Map.
• specification of fractional coordinates (17)
• selection of specific unit cells (30)
• capability to read space group names (Hermann-Mauguin or Hall) and from these to generate the set of operators; 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. (53)
• you can instruct Jmol to ignore CIF file-derived operators and force name-derived operator generation (53)
• you can load a file and script what spacegroup to use, overriding the spacegroup indicated in the file itself (53)
• display the operators in xyz notation (54)
• display the index of the symmetry operator that generated an atom (54)
• select positions that can be generated by more than one symmetry operation from the original set of atoms (54)
• selecting atoms based on which symmetry operator generated them (54)
• space groups for PDB, mmCIF, XYZ, and MOL files (57, 58)
• select the exact lattice translation for a given symmetry operation (91)
• planar slices using Miller indices (92)
• load a wider range of unit cell blocks (97)
• Reading of symmetry information in CIF files

Crystallography Journals using Jmol

The IUCr journals web site is using Jmol to visualize published crystal structures: on a journal table of contents page, click on any "3d view" button.

Contributors

NicolasVervelle, Pimpim, AngelHerraez, EricMartz