PrimeXP - interactive model editor

The PrimeXP graphical interface (left) showing a structure with 50% displacement ellipsoids for non-H atoms and the terminal emulator (right). The axis direction gnomon in the upper left has a 3-state toggle (off/on/on+labels). The yellow column of buttons on the right side of the graphics window are an homage to George's XP program. The code is modular, so would be straightforward to re-tool these as rows of drop-down menus, as per more modern GUIs.

A typical ellipsoid plot in 'TELP' mode from PrimeXP. The program currently has 28 different 'ATYP' atom types for ellipsoids and spheres, with or without various kinds of shading/octant views, and it now includes anisotropic displacement parameters in the style of Hans-Beat Bürgi's PEANUT plots. Unlike XP, TELP in PrimeXP is fully 3D-interactive, as are the 'peanuts' (vide infra ).

The same molecular orientation, but with 3D-shaded ellipsoids and spheres on a blue gradient background. Colours may be specified using 6-digit hexcodes (~16 million colours), 3-digit hexcodes (~4 thousand colours), or 148 named 'web' colours. The label colours may be set individually (via colour name or hexcode), but default to black or white, automatically switching based on the overall luminosity of the scene.

Model editing using PICK is similar to its counterpart in the original XP. In PrimeXP, however, PICK is fully 3D interactive, and the PICK sequence can be interrupted by mouse clicks on any visible Q-peak or atom.

Although it was not written with proteins in mind, PrimeXP is capable of rendering protein structures, such as the above 1.1 Å resolution structure of BPTI.

The RING/X command automatically places a dummy 'X' atom at the centroid of each ring (default 3-8 membered rings), as in the above C₇₀ buckyball/buckybowl complex. In contrast to CENT/X in XP, that's 46 dummy atoms placed by a single 'RING/X' command, without having to explicitly specify any ring atom names (CENT/X is also available, of course).

Disorder visualization in PrimeXP is flexible and can be shown in a number of ways. One such view is given above, in which major occupancy groups are drawn with 3D shading and minor disorder moieties are shown as boundary ellipses. Note also the colour blending in the bonds. A click button cycles through split-coloured bonds, blended bonds, and grey/black (depending on the scene).

There are also many ways to construct packing plots in PrimeXP. The above shows a perspective view down the c-axis of a di-periodic perovskite-like structure (same structure as the disorder plot (vide supra ), but with minor disorder removed). Orthogonal projections are also available at the click of an on-screen button.

Real-time translation-libration-screw (TLS) visualisation. The translation (T) and libration (rotary oscillation, L) tensors can be represented by 3x3 symmetric positive-definite matrices, and so may be visualized as ellipsoids, similar to atomic displacement ellipsoids. The screw (S) tensor on the other hand, represents the coupling of translation and rotation. This requires an asymmetric 3x3 matrix, which can't be drawn as an ellipsoid. In PrimeXP, the S-tensor is visualized as an elongated round-ended bicone. The long axis of the bicone corresponds to the direction of screw propagation, and is wider in the middle where atomic movement is greatest.

Old-style 2D electron-density contour plots similar those made by the EDEN command inXP are possible if a *.fcf file in 'LIST 6' format is available to PrimeXP 's version of EDEN. In the above, the blue contours represent experimental electron density for the carbon and fluorine atoms. The model did not have hydrogen atoms included, so they show up as prominent positive contours in the difference map (green) at the expected positions. The small red contours indicate where the difference map happened to be negative. This view may be zoomed in and out by mouse action.

Probably more useful nowadays than 2D electron-density contours are 3D representations. Above is such a plot of the same molecule, again showing observed density in blue and difference density in green. In 3D, the electron density may be zoomed in/out and rotated in real time. The EDEN command also creates a conditional four-state click button on the graphical display that cycle through different visualisation styles (cage contours, diffuse clouds, clouds and cages superimposed (as above), and off).

Anisotropic displacement parameter plots in the style of Bürgi's PEANUT program are now possible in primeXP. Both RMSD (root-mean-square-displacement) and MSD (mean-square-displacement), as either mesh-contours, 3D solid rendered (as above), or both (mesh superimposed on 3D solid) are possible. These are fully 3D interactive and can be freely mixed with other atom visualization styles, globally, by group selection, or on a per-atom basis. Difference 'peanuts' might follow.

Graphical representations of coordination geometries by polyhedral convex hulls around selected central atoms are now implemented. The program identifies bonded ligands, calculates the 3D faces connecting them, and reports the coordination number (CN), number of faces, and calculated volume for each generated polyhedron. The resulting polyhedra are rendered with semi-transparent faces and wireframe edges along with the atoms and bonds present in the structure. As with all other 3D view modes, these are fully rotatable and zoomable via mouse action.