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Mercury Changelog

What's new in Mercury 3.10.0

Jan 17, 2018
  • MAJOR NEW FEATURES:
  • Anisotropic Displacement Parameters:
  • We have been working hard to replace the underlying technologies in the CSD system and this has allowed us for the first time to provide direct display within Mercury of the anisotropic displacement parameters (ADPs) for over 220,000 entries. We are releasing a file containing the list of structures which have anisotropic displacement parameters in this release. This file can be loaded into Mercury, and then the display style changed to "Ellipsoid". In ConQuest, you can see the list of structures with anisotropic displacement parameters by selecting: "View Databases" -> "Lists in CSD version 5.39" -> "ADPs available subset".
  • GENERAL CHANGES:
  • Where databases are shown in lists, e.g. in the Structure Navigator, the database location and number of entries are now shown in a tool tip, when the cursor hovers over the database name [Bug 17879]
  • When selecting atoms using 'Lasso' mode, only visible atoms will now be selected. Previously, when an entire structure was loaded but invisible,
  • invisible atoms would get selected
  • Fixed bug that on (at least some) Macs, the mouse/touchpad periodically stopped working. [Bug 18107]
  • Fixed bug that using Finder to open two different files on Mercury, or using ConQuest's "Analyse Hitlist" features, was broken on Mac OS 10.13. [Bug 18349]
  • PICKING MODE:
  • Measure Torsions:
  • The styles of the measurements can now be changed with a context menu between wireframe and stick. The width of the lines can also be changed. See also "Display menu" and "Toolbars Manage Styles..." [Bug 16475]
  • Fixed ability to remove individual distance/angle/torsion measurement by right-clicking on them. [Bug 18052]
  • MORE INFO DIALOG:
  • The spacegroup number is shown after the spacegroup name and is linked to International Tables Online (this requires a licence from the IUCr/Wiley) [Bug 13337]
  • An overbar in the spacegroup symbol (e.g. in P-1) is now displayed as an overline rather than as a dash [Bug 1635]
  • The packing coefficient has been added to the available items. [Bug 18284]
  • TOOLBARS:
  • New Toolbar: Select By SMARTS. Enter a SMARTS string, such as C=O, and press Return, to select all matching atoms. See http://daylight.com/dayhtml_tutorials/languages/smarts/index.html for more information. [Bug 18227]
  • Manage Styles... Edit... Style Settings:
  • The rows for distances, angles and torsions showing a style dropdown that did not do anything and where only colour could be changed have been removed and replaced with a new button "Measurement Settings..." producing a dialogue containing all the editing functionality for the measurements in one place. The dialogue allows defining the display style, colour and width for measured distances, angles and torsions. [Bug 16475]
  • FILE MENU:
  • Open:
  • When reading CIF and SHELX Res files, Mercury now calculates bonds for actinoid structures, as radii have been added for Cm, Bk, Cf, Es, Fm, Md, No and Lr [Bug 17749]
  • Save As:
  • Changed writing of Mol2 files for structures in a space group setting that cannot be represented in Mol2 files. The structure is now written without cell information, rather than having an incorrect cell. [Bug 18180]
  • EDIT MENU:
  • Edit Structure:
  • Added button to remove all formal charges from a molecule (sets all formal charges to zero). Added button to remove all selected atoms. Note that you can hold down the Alt key to lasso-select multiple atoms, or change the Picking Mode to "Lasso Atoms". [Bug 17966]
  • Change Spacegroup Setting:
  • Added enlarged F-centred settings of I-centred tetragonal space groups. Corrected some C-centred settings of primitive tetragonal space groups.
  • Change Spacegroup to Subgroup...
  • A new dialog has been added that allows a spacegroup to be transformed to a subgroup. This may be repeated until the spacegroup is reduced to P1. [Bug 11041]
  • DISPLAY MENU:
  • Styles -> Measurement Settings:
  • A new item and new dialogue for controlling the appearance of all displayed distance, angle and torsion measurements. [Bug 16475]
  • Colours -> Element Colours... The periodic table now includes elements up to atomic number 118 and the colours for each of these elements can be customised [Bug 17473]. The periodic table example files have also been updated to include the new elements.
  • Symmetry Elements...
  • Fix bug that symmetry elements were displayed for both reference and comparison structure when viewing the results of a packing similarity search, irrespective of the state of the 'Reference', 'Comparison', 'Both' radio button in the 'Show Structure' group box. [Bug 17810] Fix bug that multiple copies of symmetry elements were displayed after undo and/or redo of certain editing operations [RT 108826]
  • Fix bug that repeatedly opening the Symmetry Elements dialog added glide planes multiple times. [Bug 18014]
  • View along:
  • Ability to view along Unit Cell and Miller directions.
  • Show Hydrogens:
  • A bug that caused the 'Show Hydrogens' checkbox to become inconsistent with the display state of hydrogen atoms has been fixed. [Bug 17799]
  • Show All:
  • A bug that caused the wrong atoms, bonds and/or graphics primitives to be shown after undoing a 'Show All' operation has been fixed.
  • CALCULATE MENU:
  • Powder Pattern:
  • Ability to customise the colour of the simulated powder pattern. Select Customise -> Display -> Line colour. [Bug 16316, RT 71214]
  • Molecule Overlay...
  • Fix bug that molecule overlay incorrectly reported mismatching atoms (e.g. for molecules with carboxylate groups) [Bug 17998]
  • CSD-MATERIALS MENU:
  • Motifs:
  • When creating new motifs, the list of available substructures is now in alphabetical order, rather than random order. [Bug 17911]
  • Crystal Packing Similarity:
  • Fixed bug that the reference molecule was missing from view for some comparisons. [Bug 17574]
  • Fixed bug that Symmetry Elements were displayed for both reference and comparison structure, irrespective of the state of the 'Reference', 'Comparison', 'Both' radio button in the 'Show Structure' group box. [Bug 17810]
  • Hydrogen Bond Propensities:
  • Further usability improvements in Polymorph Assessment -> Hydrogen Bond Propensities...
  • Fixed bug that the wrong functional group could be displayed in the Sketcher when editing. [Bug 18090]
  • Fixed bug that running a Hydrogen Bond Propensity calculation for a molecule with several potential intramolecular hbonds such as YIGPIO03 could give an intramolecular table in the formatted output tab of the Calculate Propensities pane of the wizard which did not not display correctly. [Bug 18343]
  • Fixed bug that Hydrogen Bond Propsensity wizard did not honour removal of databases after they have been used in a calculation. [Bug 18348]
  • Fixed an empty Frequency column in the final results table. [Bug 17083]
  • H-bond Co-ordination Quick-view: Fixed issue that some hydrogen bonds were missing from the view [Bug 18099]
  • CSD Python API menu:
  • The MercuryInterface helper class will prevent accidental use of Mercury scripts within the Hermes application. [JIRA GOLD-515] Additional feedback is provided within the script execution progress dialog. [JIRA GOLD-515] Fixed bug that Mercury did not automatically set the Python installation to the default Miniconda package on OSX. [Bug 17976]

New in Mercury 3.9.0 (Feb 21, 2017)

  • THE CSD DATABASE:
  • The 2017 release contains over 840,000 entries (CSD version 5.38) – an increase of more than 55,000 entries
  • Targeted enhancements have alsbeen made ta record-breaking 73,985 existing CSD entries, including:
  • Enrichment of pharmaceutical structures, including addition of DrugBank IDs Addition of validated metal oxidation states tover 21,000 entries
  • Inclusion of article DOIs for many older entries
  • Manual addition of structures from non-electronic data
  • Enhancement of many entries from 35 years of historical structures
  • CSD-SYSTEM:
  • The new CSD Python API has been improved for usability include:
  • Seamless installation of the CSD Python API within the CSD 2017 release An upgraded CSD Python API menu in Mercury with even more scripts
  • Enhancements tMercury and ConQuest including the ability to:
  • Make use of touch-screens with Mercury for pinch, pan and zoom
  • Sketch a molecule within Mercury and convert ta 3D model
  • Perform additional crystallographic transformations in Mercury (such as inversion,
  • switching space group settings or changing origin choice)
  • Utilise twnew metal-organic framework (MOF) subsets within ConQuest
  • CSD-MATERIALS:
  • Enhancements have been made tthe graphical user interface for studying crystal packing similarity and dissimilarity
  • Significant advances have alsbeen made in the layout and usability of the Hydrogen Bond Propensity application
  • The quality of conformers containing flexible rings produced using our CSD-driven Conformer Generator has been improved
  • CSD-DISCOVERY:
  • Improvements have been made in our leading docking software GOLD including the ability to:
  • Make the most of your unlimited processes with streamlined licensing on clusters
  • Automate and integrate preferred workflows with our first implementation of GOLD
  • in the CSD Python API
  • Receive faster more robust development of GOLD in the future as a result of
  • extensive updates tthe underlying code
  • CSD-Discovery now includes a complete ligand-based workflow allowing you to:
  • Produce experimentally realistic ensembles of conformers using our CSD-driven Conformer Generator
  • Generate your pharmacophore from known binders using the improved Ligand Overlay application
  • Screen your virtual library using the Field-Based Ligand Screener in the CSD Python API Python

New in Mercury 3.8.0 (Nov 17, 2016)

  • Major new features:
  • New CSD-Community menu providing access to CSD Deposit and Access Structures services online as well as the CSD Teaching Database, enCIFer and CellCheckCSD. New CSD-System menu providing access to searching in WebCSD and ConQuest as well as integration of geometry analysis using Mogul and interaction analysis using IsoStar.
  • CSD-Discovery menu extended to provide direct access to protein-ligand docking using GOLD, analysis of protein-ligand interactions and flexible overlay for multiple ligands. CSD-Materials menu extended to provide direct access to solution of crystal structures from powder diffraction data using DASH.
  • Changes - General:
  • POV-Ray output now correctly honours the size, orientation, location, colour and font of labels from Mercury [16443]

New in Mercury 3.7.0 (Nov 17, 2016)

  • Major new features:
  • New CSD-Discovery menu providing access to both full interaction mapping and conformer generation functionality.
  • New CSD-Materials menu in place of the previous Solid Form menu. This contains all the previous Solid Form options plus a range of new functionality including multi-component screening functionality, a new hydrate analyser tool and conformer generation. Improvements to the hydrogen bond propensity functionality including expansion of the functional group library as well as the statistical coordination models.
  • Easy identification and classification of chiral centres (R or S) within Mercury when bond type information is available. [13328, 17095]
  • Changes - General:
  • Ability for Mercury to read/write INS files [9017]
  • POV-Ray output now honours the hiding of aromatic ring torus [16429]
  • Updated documentation to describe matrix output when a crystal packing similarity calculation is performed [14230]
  • Improved treatment of ether oxygens in UNI calculations [12852]

New in Mercury 3.6.0 (Jul 6, 2015)

  • A new Scripts menu is available in Mercury which allows you to run built-in or user- created Python scripts utilising the CSD Python API directly from Mercury. This allows the user to construct and share tailored scripts using the whole spectrum of CSD functionality to answer your targeted research questions.
  • The Hydrogen Bond Propensity functionality has been extended to provide the option to browse to a directory containing a user-defined functional group library.
  • A new option has been added to Mercury to allow the user to animate the contents of the current display through rotation or oscillation about a chosen viewing axis.
  • A collection of features has been added to Mercury to aid scientific communication through simple, intuitive generation of high-impact structural representations:
  • The ability to generate high-resolution graphics directly from Mercury using POV-Ray has been added with a very intuitive interface.
  • A further extension is also included to allow easy generation of high- resolution movies from Mercury using POV-Ray.
  • An interface has also been added to directly produce 3D printable model files from Mercury of any molecule, packing pattern or extended framework.

New in Mercury 3.5.0 (Jun 15, 2015)

  • MAJOR NEW FEATURES IN MERCURY:
  • A new Full Interaction Mapping tool is available as part of the CSD Solid Form module. This tool for visualising CSD interaction data in 3D is built on top of existing CSD interaction knowledge base technology (IsoStar). Full Interaction Mapping allows you to assess your molecule's interaction preferences at the click of a button and in the context of its observed crystal structure.
  • A box-clipping display option has now been added which allows the user to restrict the contents of the rendered image based on the size of a 3D box, fixed relative to the centre of the structure. This is particularly useful combination with visualisation of complex structural objects like void surfaces or Full Interaction Maps.
  • A VARIETY OF IMPROVEMENTS TO MERCURY:
  • Hydrogen Bond Propensity Tool enhancements:
  • The 2D chemical diagram in the Hydrogen Bond Propensity tool has been further enhanced to include element colours and better layout.
  • A diagram has been added to illustrate distance & angles tolerances in the contact definition page.
  • The Hydrogen Bond Propensity chart has been improved to handle large number of points better and display of the selected target structure(s).
  • A variety of user-requested improvements:
  • The layout of dialogues within the main Mercury interface has been modified to better cope with low resolution displays
  • A range of Data Analysis usability enhancements have been made including optimisation of the function and layout of the calculator tool and improvements in the link with the 3D visualizer.
  • MOGUL’S RING ANALYSIS EXTENDED TO HANDLE FUSED RING SYSTEMS:
  • Mogul's assessment of ring conformations has now been extended to include fused as well as non-fused rings. More than 96% of the entries in the Cambridge Structural Database (CSD) contain some kind of ring system and 55% of these entries contain at least one fused ring system – this means that the rings analysis in Mogul can now be applied to a much greater proportion of both the structures within the CSD and also those structures being experimentally determined right now.
  • CSD System software now supplied as a digital download:
  • As part of our continuous improvement process and assessment of customer needs, the CCDC routinely seeks input from the users of our products. Many users have indicated a strong preference for CCDC to issue new software revisions and updates via download rather than via physical media. This change greatly improves convenience and offers the added benefit of reducing our overall environmental carbon footprint. Beginning with 2015 revisions, each CCDC product will be available as a digital download from the CCDC web servers. In addition, for users requiring physical media, CCDC will for a small fee offer the new revisions on USB media stick, rather than DVDs.

New in Mercury 3.0 (Jan 3, 2012)

  • Ability to display only asymmetric unit, by right-clicking on the 3D view, and selecting Packing->"Asymmetric unit"
  • Ability to customise the colours of all elements

New in Mercury 2.4.6 (Jan 3, 2012)

  • Display menu:
  • Data Analysis Module...
  • (A CSD System licence is required to access this functionality.)
  • Improvements have been made to the selection of fields for CSD data import.
  • Fixed a bug that caused the value of Z' to be displayed incorrectly when importing additional CSD data items into a spreadsheet.
  • Fixed a bug that prevented old selections of structures not being deleted within the structure navigator.
  • Fixed a bug where axis labels were not swapped over when selecting Axes > Swap axes.
  • Fixed a bug where if a data column is highlighted and then hidden it incorrectly remained 'active'.
  • File menu:
  • File writing: Added ability to export structures in MDL .mol file format. [13086]
  • Other changes:
  • Some improvement have been made to the stability and responsiveness of the program when importing saved data analyses and when reading ConQuest hits.
  • Updated the About dialogue which incorrectly reported Mercury 2.4.5 to be "development" version.

New in Mercury 2.4.5 (Oct 3, 2011)

  • Data Analysis Module (Licensed Mercury Only):
  • The data analysis tools enable you to:
  • Analyse the results of ConQuest substructure searches when you have defined some parameters (e.g. bond lengths, angles) as part of the search query. The values of these parameters in the hits can be tabulated and explored.
  • Investigate other data sets, which may be read in from .csv (comma-separated value) or .tsv (tab-separated value) files.
  • Plot data, e.g. as histograms and scatter plots.
  • Explore data interactively. All spreadsheets, plots, and tables you produce are linked to one another and to the visualiser, and all data views are updated dynamically, based on your selections.
  • Carry out statistical analyses, including calculation of descriptive statistics (mean, standard deviation, etc.), correlation matrices and hypothesis (significance) tests.
  • Access advanced features focussed towards structural analysis such as Principal Components Analysis (PCA), cone angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.
  • Powder Pattern improvements:
  • Further reduced the minimum allowed wavelength in powder pattern simulations from 0.2 Angstroms to 0.1.
  • Bug Fixes and Improvements:
  • Fixed a bug that Mercury was unable to save .MRYX files if certain objects, including Planes and Centroids, were present, or if the Polymer Expander dialogue was open.
  • Fixed a bug that, after reading a .MRY file, Mercury would sometimes crash when making certain changes, such as as turning of the display of hydrogen atoms.
  • Made some improvements to the auto-update mechanism
  • Various other miscellaneous improvements and fixes

New in Mercury 2.2 (Jan 9, 2009)

  • Major new features:
  • New "Graph Sets" facility, for displaying H-bonding patterns, according to their Bernstein and Etter notation.
  • Support for hardware stereo added.
  • New "Labels" toolbar provides easy control over atom labelling, giving the ability to label atoms with many new properties.
  • Mercury now provides an interface to the MOPAC semiempirical quantum chemistry program, for use with MOPAC 2007 and newer.
  • Other changes
  • The Searches tab can now be separated from the Structure Navigator, so that both can be seen at the time.

New in Mercury 1.4.2 (May 16, 2008)

  • Note that Cambridge Structural Database System subsribers should use Mercury CSD 1.5, which is installed from the CSD System 2007 CDs.
  • File menu
  • File reading:
  • Mol2: The "NO_CHARGES" keyword is now handled correctly, fixing a problem that sometimes atoms were created with absurd charges, in turn causing "Auto Edit Structure" to add incorrect numbers of hydrogens.
  • PDB: "Temperature factors" and ANISOU records are now read, allowing atomic displacement ellipsoids from PDB files to be displayed in Mercury. Mercury has been adjusted to handle a number of common errors in PDB files, such as CONECT records containing negative atom numbers, and atoms bonded to themselves.
  • SHELX .res: Fixed a problem that atoms on special positions were sometimes given incorrect occupancies. This would then cause errors in their simulated powder patterns.
  • File writing:
  • Mol2: A bug has been fixed which caused Mercury to write out an empty CRYSIN record if no unit cell data was available.
  • PDB: A bug has been fixed which caused Mercury to mis-align some atom labels in output PDB files. "Temperature factors" and ANISOU records are now written, when atomic displacement ellipsoids is available to Mercury.
  • Display menu
  • Related bug fixes
  • A bug has been fixed that appeared when atoms were selected and then hidden. Subsequently, changes to atom style, colouring, and labelling were (wrongly) only applied to the atoms that had been hidden. Now, such subsequent changes are correctly applied to all atoms.
  • Calculate menu
  • Planes... Fixed a crash that occurred when editing the transparency of a deleted plane or centroid.
  • Miscellaneous Bug Fixes
  • Fixed a problem that hiding all atoms in an aromatic ring could sometimes hide various other aromatic rings.
  • Fixed a problem that the display style of aromatic rings was sometimes wrong when there were many rings displayed, involving atoms in a variety of display styles.