CrystalMaker is a program for building, displaying and manipulating all kinds of crystal and molecular structures. Spectacular, photo-realistic models are just one drag-and-drop away. Support Communities / Mac OS & System Software / OS X Mavericks. Announcement: Upgrade to macOS Mojave With features like Dark Mode, Stacks, and four new built-in apps, macOS Mojave helps you get more out of every click.
. Improved Vector Metrics. Atom vectors drawn in the 'Through Atom' style now have a more balanced appearence. The tail of the vector is drawn slightly longer to make the overall vector appear centred on the atom. Note that both 'From' and 'Through' vector styles have the same length from the atom centre to the tip of the vector cone; this is the 'length' specified in the vector panel.
The vector tail is a cosmetic addition. Miscellaneous Changes. This version includes minor bug fixes for screen tools, movement of the Lattice Plane tool, rotation of selected atoms, and visualizing coordination details for massive structures via the Distances Explorer.
The Bond Angle tool now only writes output to the log when the measurement has been locked, i.e., the user has clicked for a fourth time to “finalize” the measurement. Previously, output was displayed whenever the mouse moved, which tended to fill the log. Fixed a rare problem when dragging the Lattice Plane, which could cause the program to become unresponsive. Rotating selected atoms in a crystal now works correctly in thermal ellipsoid mode.
The Distances Explorer again works correctly with massive structures ( 200,000 atoms). Refreshed Site Browser. The Site Browser has been redesigned to offer a clearer, fresher look. List row height has been increased and the background colours have been made lighter. Automatic View Numbering. A new Rename Views Numerically command has been added to the Overview Window's Actions menu. This command will rename all View thumbnails, apply numbers in sequence.
This is useful if you are working with a large animation and would prefer simple, numbered views - rather than having the original filename(s) included in view titles. Miscellaneous Changes. This version includes documentation updates and minor bug fixes for polyhedral display and the Show Molecular Cell command. Fixed a problem with polyhedral face generation (introduced in the previous update), whereby individual faces could show fragmented views, owing to an incorrect sorting of their vertices.
Fixed a subtle issue with the Show Molecular Cell command where, for 'lopsided' structures, the command could fail. The Make Polyhedron command no longer prints diagnostic output to the Console window.
Updated online help and user's guide. Colour Atoms by Coordination. A new Colour by Coordination contextual menu item has been added to the Site Browser (and its actions menu in the floating palette). This will apply a rainbow colour scheme to all atoms, ranging from blue (zero coordination) to red (maximum coordination). In this way, you can easily track variations in coordination number across a complex disordered system (although this may also be instructive in ordered systems too). Miscellaneous Changes. This version includes documentation updates and minor bug fixes for polyhedral display and the Place Molecule command.
Fixed an exceedingly-rare issue with the display of polyhedra where large faces included co-linear atoms. Fixed a memory condition with the Place Molecule command for a crystal structure. Updated online help and user's guide. Projected Bond Distances. The Bond Distance tool now prints the projected distance (in the plane of the screen) in the Log.
This complements the displayed distance (in three-dimensions of the plot) which is also printed in the Log. This feature should be useful to electron microscopists, who have to work with structure projections in two dimensions. Load Site Label 'Properties'. The CrystalMaker Text format (CMTX) now allows you to load floating-point 'properties' for each crystal site or atom. Instead of entering a site label as a character string (e.g., 'T1'), you can enter a floating-point number (e.g., '0.1234').
This then allows you to display this value as an atom label. Note: You should use a floating-point number, not an integer - otherwise the file might be interpreted as a STRUPLO-format file and your 'properties' will be ignored. Miscellaneous Changes. This version includes a minor enhancement to the Relax Molecule command and a fix for reading certain CIF files. Improved the Relax Molecule command, with more sophisticated four-body potentials. An extremely-rare issue with reading CIF files which contain nested single quotes on the last line of the file, has been resolved. Improvements to CIF Import.
In this release we have streamlined the syntax checking for symmetry, relegating the warnings for non-standard spacegroup symbols to the Log - provided that the same input file contains a valid list of general equivalent positions (required, as part of the CIF file format, but occasionally ignored by third parties). CrystalMaker also now correctly handles the import of B iso values, which are converted to the more-generally-used U iso format, during thte import process. Miscellaneous Changes. This version includes a minor enhancement to the Bend command and the addition of a command to the toolbar Range menu.
The Selection Bend command now uses the horizontal plot centre as its reference point, rather than the three-dimensional centre-of-gravity. Whilst both methods are equally valid, the new scheme ensures that the bent lattice is centred with respect to the starting conditions. The Show Asymmetric Unit command has been added to the window toolbar's Range popup menu. 3D Printing Support. CrystalMaker can now generate STL files - which are widely supported by 3D printers - thereby making 3D printing so much simpler, without the need to convert a COLLADA 3D file in a third-party program.
CrystalMaker uses the STL binary format, resulting in very compact files. To generate such a file, choose the new File Export STL 3D File menu command. Miscellaneous Changes. This version includes improved density output, a workaround for reporting operating system versions, fixes for the Make Polyhedron command and for CCL file import. Improved 'atom density' output. The calculation now lists both the density of sites and the density of atoms (taking into account site occupancies).
Workaround for determining the operating system version for OS X 'Yosemite' and later. Fixed an occasional crash related to the use of the Make Polyhedra command. Spacegroup symbols which end in a digit (e.g., 'I m a 2') are now correctly loaded from CCL files. Apple Bug Fix. We are pleased to report that, having reported a bug with 'multi touch' on OS X 10.10.2 and later, the latest 'Yosemite' update, version 10.10.4, now allows 'multi touch' to work again with CrystalMaker.
COLLADA 3D iBooks/Yosemite Workaround. We have devised a workaround for an issue with the latest version of 'iBooks Author' running on OS X 10.10 'Yosemite'. An error in iBooks Author meant that some COLLADA 3D files (which previewed correctly in the Finder and Preview.app) were not rendered in iBooks Author.
Although we discussed the problem with Apple, it became clear that the timescale for fixing the issue at their end was longer than we would have liked, and we therefore decided to take our own action. We have changed the way in which the initial model view is presented, using a clearer representation which seems to work with the current iBooks Author running on both OS X 10.10 'Yosemite', as well as earlier versions fo the operating system.
Improved COLLADA 3D Export. In addition to the iBooks Author-specific changes, we have streamlined the COLLADA 3D export, removing the lighting options sheet (CrystalMaker's rendered lighting is automatically applied, in place of the crude default COLLADA 'head on' lighting). Exported models are now automatically centred: this will help users who wish to print models by loading them into the free 'Blender' program for conversion to proprietary printer formats. Miscellaneous Changes. This version includes miscellaneous bug fixes and system workarounds. Fixed an issue with atoms appearing too small when switching from a stereo-pair plot back to 'mono' mode.
Atom vectors are now retained when the plot range is expanded. Atom vectors are again read correctly from a binary file. Fixed a rare issue in which the program could crash when reading from a saved crystal binary file. Fixed a rare crash relating to display sleep - a workaround for a system memory issue. Smoother Multi-Touch. Trackpad-controlled Rotation and Magnification gestures are now much smoother and take into account the time required to replot the structure.
Measure Bonds. A new Measure Bonds command provides a listing of all the visible bonds in the current structure, including atom information, bond lengths and the total number of bonds. The total number of bonds is also listed (in the Log) when choosing the Measure Chemical Formula command. Robust Relax Molecule.
A number of improvements have been made to the Relax Molecule command to cope with possible system memory issues, and to provide a workaround for a system bug with display sleep. The relaxation will now automatically stop if it detects a low-memory condition. This prevents a subsequent crash, and preserves the current state of the relaxation. We have discovered an apparent system bug associated with display sleep. Memory requirements dramatically increase, as it appears that video and other memory is not being correctly purged by the system. To mitigate the effects of this bug, CrystalMaker now looks out for display sleep/wake events and takes appropriate action, suppressing screen updates as necessary.
Miscellaneous Changes. This version includes performance improvements and miscellaneous bug fixes. The Set Range command is now considerably faster.
The Crystal Editor now prevents invalid rhombohedral angles (≥ 120°) being applied. Crystal and molecule binary files saved by recent Windows versions and including single-character element symbols can now be correctly read. Fixed a rare 'Error generating atom spheres' error that could occur when attempting to transform the unit cell by projecting onto a lattice plane. The Make Polyhedron command now correctly adds any new sites to the zeroth unit cell. Fixed a memory issue with the Relax Molecule command. Redesigned Symmetry Options.
The Symmetry Options dialog (accessed from the Crystal Editor) is now resizable vertically, making it possible to see a complete list of General Equivalent Positions (GEPs) for all spacegroups. The list now features slimline '+' and '-' buttons as well as a status bar. Clicking anywhere in the list activates the Customize option. Multiple selection is now possible (via dragging or command- or shift-clicking) which allows for the removal of multiple GEPs in one step. Miscellaneous Changes. This version includes improved documentation and miscellaneous bug fixes.
Minor updates to Online Help, User's Guide and the Tutorial. The File Import commands for LAMMPS and GROMACS now work correctly. Fixed a rare failure in the new Show Nearest Neighbours command. The One Cell button in the Plot Range window now functions correctly. Tabbing between columns the GEPs list of the Symmetry Options window now works correctly. 'Grow' Atoms and Bonds to Repair Broken Bonding/Molecules.
Atoms with incomplete bonding can now have their coordination repaired, making nearest-neighbour atoms and their bonds visible. Similarly, 'broken' molecules can be repaired. In both cases, missing atoms and bonds are caused by plot range truncation. Two new menu command, Selection Show Nearest Neighbours, and Selection Show Entire Molecule, will intelligently expand the plot range in the appropriate directions, to 'grow' the selection, whilst keeping the rest of the structure the same. Show Asymmetric Unit. CrystalMaker now makes it even easier to isolate single molecules in a molecular crystal.
A new menu command ( Transform Optimize Range Show Asymmetric Unit, keyboard shortcut: command-shift-U) will display the original asymmetric unit (as loaded from a raw text file). For most molecular crystals, this will correspond to one or more intact molecules. This new command complements the existing Show Molecular Cell command, which displays the complete contents of one unit cell, optimized to ensure that all molecules are intact.
Please note that the Show Asymmetric Unit command will take an existing structure and show the asymmetric unit. If the fractional coordinates of the asymmetric unit have been changed (e.g., earlier versions of CrystalMaker automatically wrapped the asymmetric unit sites into the same unit cell), then the results may be unpredictable, and some molecules may appear broken.
Add Hydrogens. CrystalMaker can now automatically add hydrogen atoms to any molecule.
The program assumes that the structure needs to be fully saturated and performs a relaxation on the new hydrogens to yield an optimum geometry (the positions of pre-existing atoms are not relaxed, thereby making this command suitable for adding hydrogen atoms to molecular structures refined using X-ray data). The hydrogen positions should refine quickly - but if you wish to stop the relaxation, you can do this in the normal way, by clicking the Stop Relaxing button in the window toolbar, or by choosing the same command from the Transform menu. Note: if you require double or triple bonds (e.g., taking a C—O unit and adding hydrogens to make H 2C=O instead of H 3C—OH), you may need to delete some of the newly-added hydrogen atoms. Relax Selection. It is now possible to relax part of a structure, (e.g., a side-chain of a molecule, or atoms on a surface), instead of the entire structure.
One simply needs to select the atoms to be relaxed, and click the Relax button in the window toolbar (or choose: Transform Relax Selection). New 'Make Polyhedron' Bonding Option. The Make Polyhedron command has been improved with a new, default, bonding option that generates appropriate global bond specifications, based on the selected distance range. As a result, polyhedra will be preserved as your plot range changes, and most users will find this more intuitive than the older default option, which was to generate only symmetry-related bonds for the current plot range. The Make Polyhedron window has been redesigned to include the new default bonding option (together with the older options). Descriptions have been added to clarify the various choices.
One-Click Atom & Bond Addition. It is now possible to define a complete molecule - with all atoms and chemical bonds - using just the Add Atom tool. Simply hold down the shift key as you click; a bond will be added between the new atom, and the previously-added one.
To change the 'anchor point' for a new bond, click on an existing atom with the Add Atom tool. The clicked atom becomes highlighted, indicating that any new bond will be extended to this atom. For example, using the Add Atom tool, you could create a methane molecule, CH 4 (5 atoms and 4 bonds) in the following steps:.
Choose C from the Atom Picker. Click in the Graphics pane to add the C atom. Note that this is shown highlighted, ready for bonding.
Choose H from the Atom Picker. Hold down the shift key and click in the Graphics pane. A new H atom appears, bonded to the original highlighted C atom. The new H atom is highlighted.
Click to add your second H atom. This will be shown highlighted. Hold down the shift key and click on the C atom. A bond is added between the second H atom and the C atom, and the C atom is once again highlighted. Hold down the shift key and click to add a third H atom and a bond to the C atom, in the same step. Click to add a fourth H atom. Again, this latest atom will be shown highlighted.
Hold down the shift key and click on the C atom to bond this to the fourth (and highlighted) H atom. Note that, for more extended molecules, you may wish to shift- click between C atoms to define a backbone, then use the new Add Hydrogens command. Two New File Formats Supported. CrystalMaker can now import crystal structure files generated by two popular energy modelling programs: LAMMPS program (Sandia National Labs) and GROMACS. These formats can be auto-detected, so users can drag-and-drop data files into the program for instant display.
As with other file formats, CrystalMaker supports multi-structure files, displaying individual structures as thumbnails in the Views pane of the Overview window. Rotate Selection in a Crystal. As part of our new crystal-engineering tools, it is now possible to rotate a selected group of atoms - in 'crystal' mode (previously this was limited to 'molecule' mode). To rotate a selection, you must click the Rotate Selection button in the bottom right-hand corner of the Tools palette.). Select Symmetry-Related Atoms. You can now quickly select all atoms that are related by symmetry in your crystal.
Simply select one atom, and choose the new: Selection Select Symmetry-Related Atoms menu command. All symmetry-equivalent atoms (i.e., those with the same site in the asymmetric unit) are shown selected. Smart Range Extension.
CrystalMaker 9 now caches atom attributes before changing the plot range, so that custom atom colouring, styles, labelling, etc., will be preserved after a range change. (Earlier versions of the software could reset custom atoms when the plot range was changed.). Miscellaneous Changes. This version includes an improved Plot Range window, new keyboard shoftcuts plus miscellaneous bug fixes:.
The Plot Range window now reports all ranges using positive fractional coordinates. This ensures that displayed values, as measured on screen (e.g., using the Atom Info tips) are reflected in the Range window. (Note that it is still possible to enter negative fractional coordinates, but these will be converted to positive values, as required by CrystalMaker's unit cell generation engine.). New keyboard shortcuts have been added, as follows: Show Asymmetric Unit: cmd - shift - U Define Cluster: cmd - option - K Edit Bonding: cmd - option - B Make Polyhedron: cmd - shift - M. The delay before showing an Atom Info Tip has been increased from 1 to 1.5 s. The Relax Molecule command now issues a warning when any atoms are hidden. Oxygen double bonds are now correctly identified by the Relax Molecule command.
Attempting to add hydrogens to a fully-saturated molecule no longer results in a phantom hydrogen atom being listed in the Site Browser. When adding new atoms to an existing molecule using the Add Atom tool, the atoms are correctly positioned in the vertical plane. Depth Fading now works correctly when building a new molecule with the Add Atom tool. Fixed a bug with the colouring of photo-rendered thermal ellipsoids. Editing thermal ellipsoid types using popup menus in the Crystal Editor now works correctly. Thermal ellipsoids are now correctly drawn as small spheres, when specified. New User's Guide.
The brand new, 10th edition of the CrystalMaker User's Guide is now complete, and is included with this version under the Help menu. This new edition covers all the new features in version 9, with a new layout and many more illustrations. This edition is optimized for viewing in two-page format. Miscellaneous Changes.
This version includes a new application icon, improved Place Molecule behaviour, plus miscellaneous bug fixes. Improved application icon.
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CrystalMaker 9 sports a higher-resolution application icon with some subtle highlights. The online help system has been reorganised to match the CrystalMaker User's Guide. A new section on 'Manipulation' has been included. The Place Molecule command now prompts the user to discard symmetry, before placing a molecule into a crystal structure. This version now correctly auto scales structures on loading from a text file.
The Crystal Editor now shows site occupancies that are greater than one. VASP files with non-orthogonal crystallographic axes, but with coordinates defined relative to orthogonal axes, are now correctly plotted.
A rare issue relating to rhombohedral lattices in the Transform Cell command has been resolved. Thermal ellipsoids defined with the 'blank' style are now correctly hidden, and not drawn as black (or white) circles, as before. Improved Copy Graphics Command. CrystalMaker now copies graphics to the clipboard in the TIFF format, instead of the old PICT format that has been used for the past 20 years. This is a workaround to fix a problem with many third-party programs (including Pages 5) which are unable/unwilling to work with the PICT format. CrystalMaker also displays a new Copy Graphics sheet, which makes it easier to scale the output size, in relation to the existing screen image. Please note that, because of the lack of support for PICT graphics, we no longer allow PICT vector images to be copied to the clipboard.
However, these can still be saved in a graphics file, via the File Export Vector Graphics command. Automatic Pen Scaling. When copying or exporting graphics, CrystalMaker now automatically scales pen widths (as used in bond lines, polyhedral edges and atom frames). This should help ensure that output better matches the screen display. As part of this change, the Scale Pen Widths checkboxes have been removed the Atoms and Bonds Inspectors. (For fine-scale control of line widths, users can resize the Graphics Window: making the window larger will reduce line widths in copied or exported graphics, whereas making the window smaller will increase line widths in copied or exported graphics.). Miscellaneous Changes.
This version includes Leap Motion status, improvements to the Add/Delete Bond tool, and a less verbose Relax Molecule command. If a Leap Motion Controller has been installed, the program displays a status message at startup.
The Add/Delete Bond tool now correctly highlights a sphere when it is clicked. The Add/Delete Bond tool no longer allows self bonding (e.g., by clicking repeatedly on the same atom). Less-verbose Relax Molecule command.
Less information is now printed in the Log during the course of the relaxation. Leap Motion Control. You can now rotate and scale your structure using simple hand gestures, and a controller. Improved Relax Molecule Tool. The molecular relaxation tool can now cope with unusual molecules such as the square-planar PtCl 4, and molecules with a see-saw geometry. Specifically, the algorithm now auto-detects the presence of S, Se or Te bonded to four halogens, and applies the correct bond angles and/or distances.
Miscellaneous Changes. This version includes improved online help and faster rotation.
New help links for each of the Overview window panes. The new command-arrow 90° rotation shortcuts now only apply if the graphics pane is active. This then allows use of these shortcuts when editing text in the Notes pane, or the Log pane of the Overview window. Rotating using a mouse wheel, or via a two-finger slide on the trackpad, is now much faster in 'Fast Rotation' mode. New Rotate Submenu. New commands, added to the Transform menu, allow easy rotation of the model through 90° left, right, up or down.
Keyboard shortcuts (cmd ←, cmd →, cmd ↑, cmd ↓) facilitate rotation. (Note that these new commands supplement the existing Rotator Controls on the Tools palette, which allow the user to specify a precise angle.). Faster multi-touch rotation and scaling. Using the trackpad to control rotation and scaling is now far more responsive in 'Fast Rotation Mode'. Miscellaneous Changes.
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This version includes a few, minor, bug fixes, plus an improved method for licensing verification, designed to assign our Department or Campus licence holders. Fixed a missing-icon issue with the 'Site Browser' window toolbar button. Fixed an issue with the Labels Inspector. Toggling the Scale labels with structure checkbox now immediately applies the change to the current structure. Improving licensing search for Department and Campus licences, makes it easier for IT personnel to install the software for multiple users on the same machine. (Personnel should contact us directly for instructions.).
Full Specifications What's new in version 10.3.3 This version supports SHELX 'part' numbers and CIF 'Disorder Groups'. These indicate alternate versions of the structure and are displayed as separate structures in the Structures List. General Publisher Publisher web site Release Date September 17, 2018 Date Added September 17, 2018 Version 10.3.3 Category Category Subcategory Operating Systems Operating Systems Mac Additional Requirements. macOS High Sierra. macOS Sierra. OS X El Capitan. OS X Yosemite Download Information File Size 286.54MB File Name crystalmakermac.dmg Popularity Total Downloads 2,668 Downloads Last Week 1 Pricing License Model Free to try Limitations Lets you display any text or binary file, but you cannot save changes or export graphics.