September 16th, 2014: Marvin 6.3.4.

No changes.

August 5th, 2014: Marvin 6.3.3.


  • Import/Export

    • OLE objects created by Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.

    • OLE opened in 3D rotation mode (F7) mode.

July 7th, 2014: Marvin 6.3.2


  • Applet

    • Communication problem involving JavaScript was fixed.

June 4th, 2014: Marvin 6.3.1

New features and improvements

  • Image I/O

      • New image IO parameter "aminoAcidBondColoringEnabled" has been introduced for peptide bond coloring.

    • Import/Export

      • SKC

        • If they are set to visible in ISIS, "Atom numbers" are imported as atom mapping from SKC.


    • Clipboard handling

        • If a structure had been pasted onto an empty canvas and MarvinSketch was closed without modifying the structure, the structure was not saved.

        • Files with "smiles" extension did not load by dragging them and dropping into MarvinSketch.

        • Clicking on the Transfer button (of MarvinSketch) after editing a structure in MarvinView caused NPE.

      • Editing

          • If a template was merged to an atom of an abbreviated group which did not have any attachment point, the abbreviated group was not ungrouped.

          • Bond shortcuts did not work until the user pressed the "Bond" button on the "Tools" toolbar.

        • Image I/O

            • Bond set coloring image export parameter was not effective, and in some cases it was able to modify the atom set coloring.

            • When saving a structure in pdf format, the image was cut too narrow.

            • Circled charge was not copied into PDF clipboard format on Mac. Currently it is represented without the circle.

          • Molecule Representation

            • Valence Check

              • False valence error appeared on aromatic rings containing Nitrogen-like atoms in their aromatic form.

            • S-groups

              • The direction of S-group labels was changed at wrong angle.

          • Painting

              • The " * " character was not supported in (among others) Arial, Times New Roman, and Lucida font family.

              • The leftname/rightname rendering of abbreviated groups have been incorrect in several cases such as "OMe".

            • Name to Structure (n2s)

              • Some substituents separated by a space from an acid parent were wrongly interpreted as esters.

              • The naming webservice was not working in the applet.

            April 18th, 2014: Marvin 6.3.0

            Marvin JS 6.3.0 history of changes

            New features and improvements

            • Painting

              • Bond properties are displayed on the canvas.

            • Clipboard handling

              • When the clipboard format is not recognized as a chemical object, the format chooser dialog is not displayed and Marvin does not import anything. Forum

            • MarvinSketch Menu

              • The "Switch Transformation" menu item is removed from the "Edit > Transform" menu.

              • The "Graph Invariants" menu option is removed from the "View > Advanced" menu.

            • MarvinSketch Dialogs

              • Look&Feel option has been eliminated from the "Preferences" dialog.

            • Import/Export

              • CXSMILES, CXSMARTS

                • R-logic is supported by the CXSMILES and CXSMARTS formats.

                • Atom properties of homology groups are supported by the CXSMILES/CXSMARTS formats.

              • CDX, CDXML

                • 3-letter abbreviated amino acid labels can be imported from CDX. Forum

              • Name to Structure (n2s)

                • Japanese Name to Structure is supported. It requires a separate license.

                • The custom dictionary can be encoded in UTF-16 (both UTF-16BE and UTF-16LE variants) even if the system default encoding is different. The file needs to start with a byte order mark (BOM) character.

              • Document to Structure (d2s)

                • OSRA 2.0 is supported.

                • A format option has been introduced allowing the user to select an optical structure recognition tool: CLiDE, OSRA or Imago when more than one is installed on the computer. For instance, d2s:osra will request OSRA to be used.

              • Structure to Name (s2n)

                • Locants with a number and an atom type are written, for instance, as N6 instead of 6-N following the latest IUPAC recommendations.

            • Molecule Representation

              • Method chemaxon.struc.MolBond.equals() compares the bonds by reference and not by the end points.

              • Clean 2D

                • Clean 2D of structures containing explicit hydrogen atoms is improved. Forum

            • Applet

              • When the Marvin Applet does not work because the Java version is outdated, a proper warning message is displayed.

            • Licensing

              • Reading of licenses has changed: now licenses in the ChemAxon home directory are read even if the CHEMAXON_LICENSE_URL environment variable or the chemaxon.license.url java system property is set.

            • Structure Checker

              • "Double Bond Stereo Error Checker" has been introduced, which searches for invalid either double bonds. Its corresponding fixer converts the invalid either double bonds to plain double bonds. Documentation

              • "Stereo Inversion Retention Mark Checker" has been introduced, which identifies stereo inversion/retention marks on single molecules and in reactions. Its associated fixer removes the stereo inversion/retention marks from the structures. Documentation

              • "Valence Error Checker" detects all valence errors in Markush structures, even if the valence error is inside R-group definitions. Its fixer corrects all fixable valence errors in Markush structures.

            • Calculations

              • Solubility

                • Aqueous Solubility Predictor has been added to Calculator Plugins. Documentation

              • Stereo Analysis

              • Conformations


            • Editing

              • Trying to merge an S-group on a multicenter atom threw a NullPointerException.

              • Hovering over a rounded rectangle with the mouse cursor caused a NullPointerException.

              • Replacing a selected single atom with a hydrogen using the toolbar button resulted in a "HH" atom.

              • Bonds could not be drawn from hydrogen atoms to other atoms.

              • The "Absolute" chiral flag disappeared from the canvas when the reaction arrow was deleted.

              • The brackets of an S-group disappeared when the group became part of a reaction.

              • Replacing an amino acid in a sequence merged the new amino acid in the wrong direction.

              • When single atoms in a chain were replaced by amino acids, attachment orders were incorrect.

              • Rotation of molecules in 3D did not work properly.

              • If a query property was set for an atom and - in a later step- a bond was drawn from this atom, the value of the atomic query property changed to zero regardless from its original setting.

            • Load/Save handling in UI

              • Changing the background color when a 3D structure was converted to 2D, then saving in PNG format saved the structure with the earlier, 3D background color.

            • Clipboard handling

              • Structure display options were not preserved when structures were copy-pasted as Marvin OLE objects.

              • Pasting a file in a one-line molecule format (e.g., SMILES) on the canvas merged the lines of the file content. Currently, only the first line of the file is pasted.

            • MarvinView GUI

              • The "Save Selection..." menu option could not be used for selecting structures for saving from a multimolecule file.

            • Import/Export

              • MRV, CML

                • CML and MRV import threw java.lang.ArrayIndexOutOfBoundsException when reading parallel bonds atoms. Now chemaxon.formats.MolFormatException is thrown instead.

              • SMILES, SMARTS

                • SMARTS string starting with parentheses was recognized as SMILES.

              • CXSMILES, CXSMARTS

                • Chiral flag (or molecular absolute stereo) was not exported to CXSMILES if enhanced stereo existed in the molecule.

              • InChi, InChiKey

                • Coordinate bond was exported as single bond to InChi. From now, we do not export these bonds according to the IUPAC recommendation.

              • Name to Structure (n2s)

                • The multiplying prefix "eicosa", a non-IUPAC variant of "icosa" was not supported.

                • The Chinese names of some alkanoic acids, such as ????, were not supported.

                • Some common names containing "chloride" were imported without a chlorine atom.

                • Some chiral heterocenters were reversed in anhydrides.

                • Some names with cis and trans stereodescriptors for rings were imported without stereochemistry.

                • Entries in the custom dictionary that consist of an empty structure failed to be imported.

                • The stereochemistry of some sugars, for example, 1-(2-Deoxy-2,2-difluoro-β-L-erythro-pentofuranos-1-yl)uracil, was wrong.

                • Stereochemistry was missing on some chiral centers of steroid derivatives.

              • Document to Structure (d2s)

                • The encoding of HTML files was not always detected from the META tag.

                • When the extraction of OLE embedded structures from Office documents was disabled using the d2s:-ole format option, the optical structure recognition of images was disabled as well.

                • The character position field of structures was sometimes higher by a few characters when extracted from HTML documents with CRLF (\r\n) line endings.

                • The CLiDE optical structure recognition tool was not automatically detected on 64 bit versions of Windows.

                • When using OSRA, some structures with implicit hydrogens were wrongly filtered out.

                • After processing only a part of an HTML document, the processing of the next HTML document could give some incorrect results.

              • Structure to Name (s2n)

                • IUPAC numbering was not displayed for some classes of structures, for instance, secondary amines.

                • The common names generated for some structures with a chloride counter-ion did not include the ending "chloride".

                • In a few cases, generated traditional names were imperfect, for instance, "nitrobenzeen" instead of "nitrobenzene".

            • Molecule Representation

              • Clean 2D

                • Clean failed on atoms having two chain ligands with the same length.

              • Implicit/Explicit Hydrogen Conversion

                • Hydrogen atoms were added with invalid coordinates to carbon atoms having triple bond in 3D. Forum

            • Image I/O

              • R/S stereo labels on chiral atoms were partly covered by bonds during EMF export. Forum

            • Structure Checker

              • "Bond Angle Error Checker" reported incorrectly for molecules containing S-groups.

              • The first letter of a typed word did not appear in the search box of the "Configure Checkers" panel.

            • Calculations

              • Remove Predictor from Marvin GUI, Chem Term, cxcalc and cxtrain.

              • Conformers

                • Lowest energy conformer calculation has been fixed.

                • Marvin - Conformers Plugin options has been improved along with corresponding documentation.

            Deprecated and removed methods

            Known issue

            • Structure Checker

              • Online documentation help link does not work on Linux OS.