Release Notes

February 16th, 2011: Molegro Molecular Viewer v2.2.0

This release brings KNIME workflow support to Molegro Molecular Viewer. This makes it possible to integrate MMV with existing workflows, such as accessing databases and preparing ligands using third-party software. After having upgraded MMV, please visit molegro.com/knime to install the KNIME plugins.

Changes:

  • Support for KNIME workflows.
  • It is now possible to append MVDML workspaces to an existing workspace.
  • Molecule import now moves partial charges from hydrogens to the heavy atom they are attached to: since hydrogen bonds in MMV are handled by special terms in the scoring function, which does not take the hydrogen charge into account, moving the charge from hydrogens to heavy atoms ensures no charges are lost. Notice that MMV's internal charge scheme does not assign charges to hydrogens, so this change is only relevant to molecules prepared by third party software.
  • Better preparation of nitrogens in aromatic rings: for molecules without explicit hydrogens, MMV would sometimes wrongly protonate the nitrogens in aromatic rings.
  • Fixed the difference between the Hide Distant Residues thresholds in the workspace GUI and in the Pose Organiser. (Pose Organiser only took heavy atoms into account).
  • Linux build are now compiled on build machines (both 32 and 64 bit) using a newer version of the GCC compiler. The new build requires libstdc++.so.6.0.0 or later. Please contact us, if you run into problems with missing dependencies.

October 25th, 2010: Molegro Molecular Viewer v2.1.0

New Features and Changes:

  • Support for reading Molegro Virtual Docker version 4.2 MVDML files.
  • PDB and Mol2-Parser:
    • The name of combined fragments should be more clean and intuitive now (e.g. 'PHP-ALA-ANI [B]'). Water molecules now also include chain ID in their names.
    • Improved thresholds for detecting covalent bonds.
    • Proper residue ordering for residues with insertion codes.
    • Fixed problem with PDB-export when indices were larger than 99.
    • Also added a PDBSource field showing the originating chains of a compound (shown in the Properties Window).
    • If a PDB file contains 'PDB Compliancy' information, the PDB Parser now reads the element type in last column, instead of deducing the atom-type from the PDB Atom Name.
    • Mol2 parsing: the base filename now used as molecule name, if the Mol2 molecule name is empty or equals '****'.
  • PDB/SDF Import Notes:
    • For PDB files the PDB header is now stored as part of the workspace. For SDF files the first 4 lines and any annotations are stored.
    • A workspace may contain an arbitrary number of import notes, and each molecule may have a reference to one of these notes.
    • Imported notes can be shown using the context menu on any molecule in the Workspace Explorer or by selecting a molecule in the Workspace Explorer and pressing the 'Show ... Notes' button.
    • Notes can be also viewed and deleted using the Workspace Properties dialog.
    • Notes are stored together with the workspace in the MVDML file format.
    • Notes that are no longer referenced by any molecules are automatically removed.
  • Added support for Custom Coloring of selections:
    • Improved selection support: In the 3D GUI Context menu it is possible to select/deselect atoms, molecules, molecules (carbon only), rings (for ligands/cofactors/poses), and amino acids (for proteins).
    • The atoms in a selection can be set to a custom color using the 3D GUI Context menu.
    • Entire molecules can be set to a custom color using the Workspace Explorer Context menu.
    • The custom coloring is persistent - it will persist after changing rendering/coloring styles, and takes precedence over any coloring style.
    • Custom Coloring information is stored together with the atoms in MVDML files.
  • Visualization Settings:
    • It is now possible to customize the appearance of hydrogen bonds and electrostatic interactions in the Visualization Settings dialog.
    • It is possible to change the default visualization settings from the Visualization Settings dialog (available in the 'Views' tab).
    • The default settings can be restored to factory settings (the initial default settings).
    • Visualization and camera settings are now stored in the MVDML file.
  • Help-system: the user manual (in PDF format) is now accessible from the Help menu or the Toolbar.
  • Labels: It is now possible to choose only to label 'selected' objects. Labels now appear in groups in the Workspace Explorer. Also added PDB Atom Name and PDB Index as atom labels.
  • The sequence viewer now shows broken chains.
  • Option to show hydrogen bonds between amino acids in a residue chain: invoke using 'Tools | Show Protein Hydrogen Bonds'.
  • The secondary structure detection (used for ribbons) has been updated.
  • Added option to hide selected residues.

January 13th, 2010: Molegro Molecular Viewer v2.0.0

New Features and Changes:

  • Support for reading Molegro Virtual Docker version 4.0 MVDML files.
  • A new built-in raytracer makes it possible to create publication quality graphics and generate high-resolution output.
  • Graphics improvements: molecular surface rendering and 'tube' backbone rendering has been improved. Wireframe view now shows double, tripple, and delocalized bonds.
  • Tripos atom types. MMV now reads and writes the Tripos atom types in Mol2 files. The Tripos atom types are also used in the PLANTS scoring function.
  • Molecule import: The Mol2 importer now supports metal ions with UNK residue name and the handling of 'Dummy' atom records has been improved. The Mol2 exporter now properly handles molecules with more than 10000 atoms. The importers and exporters now work better with 'unknown' atom types. The PDB parser now reads the atom serial number (it can be inspected in the Properties window). DataSources now support reading of ligands from MVDML files. There is also a new option to import ligands as cofactors (in Import Molecules dialog).

November 11th, 2008: Molegro Molecular Viewer v1.2.0

New Features and Changes:

  • Support for reading Molegro Virtual Docker version 3.0 MVDML files.
  • Sidechains may now be colored according to their hydrophobicity (using the Hydropathy Index introduced by Kyle and Doolittle). The new coloring style can be invoked by choosing the 'Color Proteins by Hydrophobicity' scheme. The molecular surfaces now also use this index when coloring according to hydrophobicity.
  • The logging output directory can now be changed from Preferences.
  • Updated 'Hide Residues' dialog. It is now possible to check whether enabled residues within the specified radius should be shown (useful if different residue types for the whole protein should be enabled or disabled).

Bug Fixes:

  • Removed a bug which under certain conditions could crash MMV when invoking the Sequence Viewer.
  • Modified PDB export so that a numeric index is appended to atom element names. This seems to be a requirement for some third-party PDB importers.
  • Removed a memory leak in the Data Sources import system.

April 14th, 2008: Molegro Molecular Viewer v1.1.0

New Features and Changes:

  • Support for Unicode: A new preference option has been added: Parsing | Default File Encoding. This setting is used when importing and exporting SDF, Mol2, or PDB files. MVDML and other XML-based files are always encoded in UTF-8 format.
  • Pose Organizer speed improvements: it is now much faster to apply MDM-models (created by Molegro Data Modeller or the Data Analyzer in MVD) and to inspect the MVDResults in the Data Analyzer.
  • Pose Organizer: default sorting criteria is now changed from 'Ligand + MolDockScore' to 'Ligand + Rerank Score'.
  • Added check (on first startup) for whether 'check for updates on startup' should be enabled.
  • Added support for file associations on Mac OS X for Mol2/SDF/PDB files (mol2, sdf, sd, mdl, mol, pdb, ent) and MVD workspace files (MVDML).

Bug Fixes:

  • Preferences: the protein size threshold check counted all atoms (including hydrogens). Now only heavy atoms are counted.
  • The Pose Organizer would crash if the pose referred to in the MVDResults file was missing or corrupted and the context menu was accessed.
  • The Pose Organizer would sometimes crash in dynamic mode, when changing the visualization scheme or graphical options.

Jan 14th, 2008: Molegro Molecular Viewer v1.0.0

First public release.