Cif files with inconsistent site labelling between multiple "loop" statements are now handled more gracefully. More refinements to the ring Selection algorithm mean that rings with side chains attached can now be reliably selected. When moving one or more atoms in a crystal, all coordinates are updated in real time, meaning that data export uses fully up-to-date data. Fixed a bug with the merge Atoms command which could cause atoms in neighbouring unit cells to be made visible. Lattice Planes menu commands are now corrected enabled. When searching for files by chemical formula in the library Browser, element proportions are now correctly used for crystal structures. The rotation Popover now works correctly with our optimized fast rotation mode. Version.2.1 faster Rotation and Scaling.
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They are: (Isolate selection; Isolate fragment; Isolate molecule). As a rebuttal quick reminder: "Fragment" refers to visibly-interconnected atoms, whereas "Molecule" refers to all interconnected atoms, regardless of their visibility. Earlier versions of the program used a single, default "voxel" size for all structures. Whilst this was designed to work well for typical inorganic structures, extended structures - such as Molecular-Organic Frameworks (MOFs) - have such massive unit cells that using the default value would require excessive amounts of (precious) system ram - over 50 gb for some structures. This version now computes a sensible voxel size, based on the current plot dimensions (and the same algorithm has been extended to the Electron Density map). Users can still override this value, using the sheet controls provided. Crystalmaker now includes all known crystal structures for the elements (at ambient conditions plus a number of additional phases formed at other temperatures and pressures. Many other structures have also been added - including a new "Pigments" thematic library. This version includes improvements to nearest-neighbour and ring selection, cif import - plus a number of bug fixes. Improved nearest-neighbour selection: the program now skips any hidden atoms (i.e., this behaves akin to the "Fragment" rather than the "Molecule" commands). Print to log buttons in the Angle- and d-spacing Calculators now display the window log if it isn't current visible.
Fixed a bug when entering a not valid symbol on the occupancy column in the Crystal Editor. Fixed previews (Structures list) scale. Numerous graphics glitches fixed including: Atom labels for Wireframe and Stick model; Bond labels for Wireframe model; Polyhedra dashed lines; Ellipsoid and bond outlines. Version.2.2 pacing Calculator. We long have a added a new calculator palette which displays the d-spacing for a specified lattice plane ( hkl indices) for the frontmost document window - and with the option to print the result in the window log. To access the calculator, choose: Calculate d-spacing Calculator. A new "Isolate" command has been added to the Graphics Pane contextual menu (and to the main Transform selection sub-menu). The Isolate fragment command combines two previously-separate steps: Expand Selection fragment and: Isolate selection. The three isolate commands have been moved to a submenu on the Graphics Pane contextual menu.
Toolbar customization is now saved and restored correctly. Window state (size and position) is correctly restored when opening a document; oversize/off-centred documents are reset to ensure all content is visible. Improvements to the graphics display for high-dpi displays. Cmtx files are now associated with Crystalmaker by default. Vasp gps import has been relaxed so that volumetric data can continue after reading an invalid number. The video tour web page no longer opens when launching the program. Fixed a bug in the export rotation movie: number of frames were being used as frames per second.
Fixed a potential bug with the lattice planes move to Intercepts command. Orientation matrices omat" cards) are now correctly read from Crystalmaker (cmtx) text files. Pressing the reset Matrix button in the cell Transformation sheet now clears any previously displayed error messages. Fixed a potential bug with the Add/Delete bonds tool: it had been possible to self-bond an atom, which could cause problems during subsequent operations! Improved cif import: importing thermal ellipsoids saved in the (very rare!) Bij format now works correctly. Improved removal of duplicate atoms for hexagonal or trigonal structure. Exporting ultra-high-resolution graphics (dimensions greater than about 16,000 pixels) now works correctly.
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Added new shortcuts to the Crystal and Molecule editors: double-clicking on an empty row now creates a new row (i.e., has the same effect as clicking the " button). Faster display of polyhedra with thick edges; a (rare) problem with edges becoming extended outside the structure has also been resolved. Improved ring selection algorithm. Porosity and surface datasets are now saved in a more efficient manner, resulting in considerable reduced file sizes (60-70 smaller). Faster rotation for massive crystal structures. The Add Molecular Centroids command now uses zero occupancy for its new, dummy sites - thereby leaving the structural formula unchanged. Atom labels now work correctly for "Stick "Wireframe" and "Thermal Ellipsoid" model types.
Site labels saved in the shelx files are now respected; thermal ellipsoids loaded from the file can now be displayed on screen. Fixed occasional glitches with multi-structure animations. Atoms without bonds, or off-centred structures could appear. These were related mehangai to a performance optimization in the previous version of the software and have now been resolved. Displaying "noisy" volumetric data should no longer cause a crash. The radii submenu of the Atoms Inspector Actions menu is now correctly populated at program startup. Volumetric data selection now only applies for visible datasets.
We have streamlined the way in which the "plot ellipsoid as sphere" option works. Previously in version x, one would click the Plot Ball-and-Stick Sphere button in the Ellipsoid style popover, and Crystalmaker would display the ellipsoid in the specified site's atom style. This worked well for some users, but changing the atom style required a round trip to the ball-and-Stick model type, which other users found confusing. In this latest version, all thermal ellipsoid styles are set from the same popover, and the "plot as sphere" option is now a checkbox. Leap Motion 3d controller Support.
This version of Crystalmaker X now supports the leap Motion 3D controller for hand-gesture controlled 3D rotation and scaling. This version includes better performance and miscellaneous bug fixes. New reapply bond Specifications command, added to the bond Inspector's Actions and contextual menus. This lets you regenerate bonding for all specifications in the current structure. Easier volumetric dataset creation: double-clicking on an empty row in the volumetric Data table now displays a popup menu letting you choose what type of dataset to create. Double-clicking on the minimum or maximum fields in the bonds Inspector now edits their values.
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In the latter case, a fuller sequence of structures is read from the file and added to the Structures List, ready for instance animation via crystalmaker's Play command. A new Rotate submenu has been added to the Transform menu. This includes commands to rotate left, right, Up and Down as well as Clockwise and Anti-Clockwise. Keyboard shortcuts are available, allowing for quick control over the orientation. The rotation steps are the same as in the rotate popover (default values are 90). Open Structure in New Window. You can now select a structure and create a copy in a new window, using the file new Window paper with Structure command, or via the Structure list's New Window with Selection contextual menu command.
The vibrations Explorer now includes ifrs significantly-enhanced functionality, accessed via a dedicated. Inspector pane (rather than occasional popover controls). Users can immediately adjust the animation parameters and opt to display the intensities of ir modes directly in the modes list (shortcut: click the modes list header to toggle between single- or double-column display - the latter with ir intensities shown). The ir spectrum can now be shown as a function of transmittance as well as absorbance, and the x- axis can be displayed in ascending or descending order (the latter option may be more familiar to chemists). You can now choose a peak-shape function, customize the peak width, add a shadow, change the line width or its colour. A new Calculate rings Through Atom command prints detailed information for rings, up to a default limit. Crystalmaker can now import structure files generated by the old x-windows "XCrysden" program. Crystalmaker can read molecule, crystal and animated (axsf) files.
actions menu. Whilst Surface maps are designed for periodic, crystal structures, you can opt to make your surface map aperiodic, by turning off the periodic checkbox in the surface map sheet. A new "Distance map" option makes it easier to visualize cavities and channels in complex crystal structures. For each unfilled point in space, the distance to the surface of the closest atom is saved. You can then customize the range of distances to be shown,. G., to visualize all areas that an ion of a particular size can access. Distance maps can be created either using the calculate volumetric Data submenu, or by using the Add Volumetric Data submenu on the volumetric Data actions menu. Powerful New Vibrations Explorer.
Because of the new (voxel-based) algorithm, some of the old surface options (e.g., colour-by-atom and mesh display) roles are no longer available. Sparse volumetric datasets now use bicubic interpolation to reduce noise and improve clarity. Varying degrees of "oversampling" are used, depending on the number of input data points. When adjusting iso-surfaces or iso-volume thresholds using the range popover, you now have the option of temporarily turning off the oversampling and using a "Fast Redraw" mode; this makes it eaiser to make finer-scale adjustments. Normal, high-quality drawing resumes at idle time. A new "Surface map" option is available, letting you visualize space-filling, van der waals, or Solvent-Excluded surfaces. Unlike the regular surface overlay, this is not a "real time" surface, but a "one off" calculation, allowing more control and greater flexibility. Whereas the surface overlay applies to all visible atoms - and is updated as atomic visibility changes - a "Surface map" is created once, and will persist even as the number of atoms changes. This allows you to control which atoms have a surface around them.
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Version.3, cavity finder. A new Calculate cavities command lets you detect large voids within an arbitrary structure - with the option of visualizing their positions and sizes directly write on the screen. A dialog lets you specify the minimum void size (hint: the default size of 2 Å works well for most structures the program then analyses the structure, locating empty regions large enough to position an atom of the required size - and proceeds to calculate. Results are printed in the window log. If you choose the visualization option, then new, dummy sites are created at the void locations. These are displayed as translucent spheres, whose radii match the sizes of the surrounding voids. Please note that this algorithm uses any existing radii in the structure; the program does not apply van der waals radii (although you could manually reset your radii to these values, if required). A new algorithm makes surface display considerably faster than before - particularly for massive structures.