We are pleased to announce that ChemDoodle 3D v4 is available.

ChemDoodle 3D v4 is a major update to ChemDoodle 3D with a significant amount of work invested in the molecular modeling engine. Other notable features include a new widget for creating atomic orbital graphics, new protein models, Connolly surfaces and surface color functions, and the generation of armchair/zigzag/chiral carbon nanotube geometries. Check out all the new features below. This update also includes all of the API improvements to our application engine present in ChemDoodle v9, such as customizable shortcuts and native file choosers on macOS. Please keep telling your students, friends and colleagues about ChemDoodle and ChemDoodle 3D. Thank you!

Various molecule models in ChemDoodle 3D running on macOS

Various molecule models in ChemDoodle 3D running on macOS

New features in ChemDoodle 3D v4:

  1. Building and Modeling –
    1. A very accurate implementation of the MMFF94 and MMFF94s force fields can now be used by the Minimizer widget when building molecules. When comparing calculations by ChemDoodle 3D to the author’s MMFF94 dataset, only 6 of 761 structures do not match to the ten-thousandths place, with the largest difference being 0.0061 kcal/mol. When compared to the author’s MMFF94s dataset, all 265 structures match to the ten-thousandths place. This makes ChemDoodle 3D one of the most accurate implementations of the MMFF94 and MMFF94s force fields in the industry. An option is provided to include or exclude published MMFF94 Bond Reduction Factors.
    2. You can now set which optimizer function is used, between steepest descent, conjugate gradients and BFGS.
    3. You can now set which line search function is used, between coarse, fine and Newton.
    4. You can now control whether a cutoff distance is used to throttle non-bonded interactions (vdW and electrostatic) and control that cutoff distance value.
    5. There is a new option to use a Morse oscillator for the bond stretch function for the Universal Force Field.
    6. The Minimizer widget now presents an option to display force field specific atom typing labels for the referenced structure. For the MMFF94 force fields, both the generic Numeric and specific Symbolic atom types are properly attributed in ChemDoodle 3D.
    7. When optimizing structures, the Minimizer widget will now display an error when a unknown atom type is present.
    8. The select and manipulate states have been merged to make building molecules significantly faster and easier. Simply use a selection tool to make selections for editing, or hover individual atoms and bonds to move and manipulate them.
    9. An advanced system has been added to place new bond connections to atoms in the most optimal location in 3D around the atom. Use this to efficiently create molecules and quickly build coordination complexes.
    10. Implicit hydrogen counts can now be set for atoms. Implicit hydrogen overrides will be displayed in a label on the atom.
    11. The escape key will cancel previewed actions.
    12. The delete/backspace key now erases selections.
  2. Macromolecular Structures –
    1. New model types for proteins, including an advanced cylinder and plank model as well as a cartoon model. The cylinder and plank model allows for many customizations, including an exclusive method for rendering the void spaces of helices.
    2. Generate armchair, zigzag and chiral nanotubes based on an improved Tubegen algorithm. Build periodic systems of nanotubes and calculate various properties of the structure. Related graphene sheets can also be generated.
    3. You can now color PDB files by chain. Multicolored meshes are now possible for models. Color by rainbow.
    4. Chain residues are now numbered in the Selector widget.
  3. Surfaces – Solvent excluded surfaces (Connolly) can now be generated. Surfaces can now be colored by function, including: Gasteiger charges, QEq, QTPIE, AMR98 and AlogP98.
  4. Periodic – Unit cells now act like individual shapes, and can be edited accordingly with multiple unit cells in the same scene. Supercell dimensions are now better controlled with bounds instead of multiplicities.
  5. Graphics and Interface –
    1. A new Orbitals widget is provided for creating advanced atomic orbital graphics based on quantum numbers.
    2. Shapes can now be copied and pasted along with structures.
    3. Automatic shapes are now removed when their constituents are deleted.
    4. Context sensitive cursors are now implemented across the tools, with accessibility options.
    5. Controlling the light direction now properly adheres to the rotation algorithm set in General preferences.
    6. Atom labels will now properly disappear if the atom rendering is hidden.
    7. Fixed the location of dropped molecules from the Molgrabber widget.
    8. Updated elemental data, including Allred-Rochow electronegativities for better calculations.
  6. Chemical Files – Significant improvements to the MMTF interpreters, fixing all reported and known issues. Improvements to the CIF interpreters to read a wider range of files. Also fixed a centering issue with CIF input.