ChemDoodle 3D Version History

6.6.0

August 09, 2022

Executive Summary

ChemDoodle 3D v6.6 is a feature update to ChemDoodle 3D. Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more.

Additions

  1. ChemDoodle 3D now allows full scene modeling simulations. Most small molecule force fields are optimized for describing individual discrete molecular structures. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. To do this, you can change the optimization scope to optimize the entire scene. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates.
  2. A new function to align molecular structures in 3D. Accessed via the Molecule>Align... menu item, choose the mapping algorithm, whether to overlap the structures, or allow inversions.
  3. Bond deduction has been significantly improved, allowing options for enforcing maximum valencies and changing the bond distance tolerance when using the Molecule>Deduce Covalent Bonds... menu item or opening a file with no bond information. New bond order perception algorithms are now available, including "All Single", Antechamber and Auto-UFF.
  4. A new optimizer for the molecular modeling engine is implemented, FIRE (Fast Inertial Relaxation Engine). The FIRE optimizer differs from the other optimization methods described here in that it does not employ a line search. Instead, it moves in successive small time steps, tracking the momentum of each particle as it slides to a lower energy state. Unlike a naive steepest descent approach where the momentum would be changed only by adding in the current force vector, in this method, the momentum is first steered partially toward the new downward direction before adding in the force. This gives it a slight added push downwards and compensates for the inherent inaccuracies in any discrete process. The result is a smoother descent toward a minimum than you would get using conjugate gradients or BFGS.
  5. Multicolor mesh support is included for 3MF model output, but be aware many programs may not be able to read or support such data.

Fixes

  1. Fixed bug where turning on the optimizer could not be undone to restore original coordinates.
  2. Corrected 3MF model file output.
  3. Fixed bug when writing SLN strings where a bond order before a ring closure wasn't properly cleared.
  4. Improvements with XYZ file edge cases and reading of error files.
  5. Stopped behavior where the bond deducer was executed for bonds beyond the ones defined in MMTF files.

6.5.0

November 19, 2021

Executive Summary

ChemDoodle 3D v6.5 is a feature update to ChemDoodle 3D. You can now export your created molecules and chemistry scenes into model files for 3D printing and other CAD applications. Many formats are supported, along with thorough mesh data output and options for each type. We have also added support for three more RCSB formats: BinaryCIF, PDBx/mmCIF and PDBML. The last major new feature is CIP stereochemistry support for cumulenes.

Additions

  1. Export your ChemDoodle 3D creations into many popular 3D model file types for import into other CAD applications and for 3D printing:
    1. 3D Manufacturing Format {.3mf}
    2. Additive Manufacturing File Format {.amf}
    3. COLLADA Digital Asset Exchange {.dae}
    4. Extensible 3D Graphics {.x3d}
    5. Polygon File Format {.ply}
    6. STereoLithography {.stl}
    7. Virtual Reality Modeling Language {.wrl}
    8. Wavefront Object File {.obj}
    ChemDoodle 3D supports as much of each format as possible, including meshes, normals, materials, transparency, colors and multicolors. Note some formats are less capable. For instance, the STL format cannot store colors, so use a more capable format like the VRML formats to suit your application. ChemDoodle 3D implements many format specific options, such as both binary and ASCII support for STL and PLY files and caching and compression for VRML files.
  2. Added support for cumulene CIP stereochemistry, M and P. You may also display these as Ra and Sa (axial chirality).
  3. Added support for three new RCSB formats: RCSB BinaryCIF (.bcif), RCSB Macromolecular Crystallographic Information File (.cif, .mcif, .mmcif) and RCSB Protein Data Bank Markup Language (.xml, .pdbml). Both input/output of small molecule information and full model input are supported.
  4. You may now manually edit atom charge values (including non-integer values) using the Molecule>Edit Atom Charges menu.
  5. Changed the default nucleic acid ladder platform color to blue.

Fixes

  1. Fixed issue where the applied scene texture is not removed upon restoring style sheet defaults.
  2. Changing stereochemistry view from E/Z to cis/trans and vice versa now takes effect immediately.

6.4.0

September 25, 2021

Executive Summary

ChemDoodle 3D v6.4 is a feature update to ChemDoodle 3D. The major new feature is the ability to add charges, radicals and electron pairs to atoms. This allows us to create a unique VSEPR force field which is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures. Other notable features include more file output options and the export of atom typing data from our modeling engine.

Additions

  1. Electron pairs and single electrons (radicals) can now be added to atoms as physical objects. ChemDoodle 3D will automatically place them in appropriate positions around an atom, or you may manually place them. Use the Molecule>Reset Electron Positions menu item to restore the default automatic placement behavior. Radicals will be input and output from all relevant file types.
  2. Charges may be assigned to atoms. Charges will be input and output from all relevant file types.
  3. A new VSEPR force field has been implemented in the molecular modeling engine. The Valence Shell Electron Pair Repulsion (VSEPR) force field is a very specific Points-On-a-Sphere (POS) force field. The entire purpose of this force field is to produce ideal shapes for VSEPR theory. The VSEPR force field is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures. Because the purpose of the VSEPR force field is to generate shapes, energy calculations are irrelevant to the user, as they have no physical significance. When using the VSEPR force field, the Minimizer widget will instead display the current molecular geometry and VSEPR shape of the atomic center you are editing. There is also an Enhanced Repulsion option included that when enabled, electrons will exhibit enhanced repulsion vs bonds. The repulsion constants are defined to produce close to accurate results for water and ammonia in the gas phase. There is no guarantee any other molecules will produce accurate experimentally measured results. This option is great for demonstrating why centers with electron pairs do not have ideal VSEPR shape angles. Please see chapter 5 of the ChemDoodle 3D User Guide for more information.
  4. A new Molecule>Save Atom Types... menu item function will output all atom typing information for applicable molecular modeling force fields in ChemDoodle JSON format to be used in other applications.
  5. There is now an option to center or not center coordinates on output. The default behavior is to center. This option is found in the Preferences in the Files tab.
  6. Added in relevant chemical file options from ChemDoodle 2D.

Fixes

  1. Corrected issue where atoms with large vdW radii would be cutoff when generating surfaces.
  2. Fixed problem where looped aromatic systems caused issues with MMFF atom typing.
  3. Handled the input of improperly formatted CONECT records in PDF files.
  4. Corrected Selector widget checkbox behavior when shapes were present in the scene.

6.3.0

June 07, 2021

Executive Summary

ChemDoodle 3D v6.3 is a feature update to ChemDoodle 3D. Notable additions include 3D textures for creating engaging graphics and the Moré-Thuente line search in the force field optimization engine, which is more modern than the Newton line search.

Additions

  1. 3D textures can now be used to create more engaging graphics. Textures apply a surface styling to the objects rendered in the scene. This is done by defining some pattern in three dimensions, similar to how you would see three dimensional patterns if you were to cut into a block of wood. The objects are then crafted out of this pattern to produce the graphics, allowing you to produce a number of interesting styles.
  2. A Moré-Thuente line search along the force field optimization search direction can be chosen. This algorithm brackets the optimal step along the search direction and then approximates it using a combination of quadratic and cubic interpolation techniques.
  3. Added a Bond style to disable unsaturated bond rotations from facing the viewer.
  4. Updated CWC support to v9.2.0.

Fixes

  1. PDB and MMTF access through the RCSB is now HTTPS.
  2. ChemDoodle 3D can now better extract ATOM and HETATM records of incorrect length in PDB files.
  3. Improved interpretation of bond geometry loops in CIF files, especially those from the CCDC.
  4. Corrected optimization issues where the molecule would not appear when loading from or linking with ChemDoodle 2D.
  5. Fixed issue where lone molecules with a single atom failed to output shapes correctly to ChemDoodle JSON.

6.2.2

January 23, 2021

Executive Summary

Version 6.2.2 corrects a compatibility issue with certain AMD graphics cards on Windows platforms leading to an empty scene rendering. Simply update to correct the issue.

6.2.1

November 11, 2020

Executive Summary

Version 6.2.1 corrects an issue in the v6.2 update that prevents the deferred shader from working properly.

6.2.0

November 06, 2020

Executive Summary

ChemDoodle 3D v6.2 is a feature update introducing stereoscopy functions. Anaglyphs are fully implemented and compatible with all shaders. Anaglyphs allow users to see the rendered scene in ChemDoodle 3D in three-dimensional augmented reality from your computer screen. Anaglyph glasses are required, and red-cyan, green-magenta, and amber-blue anaglyph glasses are supported, which can be purchased cheaply from online retailers. The Dubois method has been implemented for the most comfortable anaglyph viewing and you can control both the focal length and eye separation parameters to customize the anaglyph to your preference. Now you can fully visualize the 3D molecules you are building in 3D! Please see chapter 13 of the ChemDoodle 3D user guide for more information.

6.1.0

August 28, 2020

Executive Summary

ChemDoodle 3D v6.1 is a significant update to ChemDoodle 3D with a focus on the molecular modeling engine. Notable additions include parallel processing support, an implementation of the General Amber Force Field, improved Minimizer widget performance, and a new tool for easily twisting bonds to change torsion angles. This update is recommended for all users.

Additions

  1. Support for parallel processing of our force field calculations leading to significant runtime reductions. This parallelization is for the faster optimization of a single system. For instance, if your large molecule was optimized in x seconds, you may now use ChemDoodle 3D with parallel processing to optimize the same molecule in a fraction of x seconds. Parallel processing is very powerful, but needs to be understood to be used correctly. Please read section 5.6.3 of the ChemDoodle 3D User Guide for a full explanation and analysis.
  2. An implementation of the General Amber Force Field (GAFF) is now available in ChemDoodle 3D. This implementation is accurate, except we use Gasteiger-Marsili charges instead of the recommended RESP or AM1-BCC charge models. We hope to include AM1-BCC charges in the future. The theory of the GAFF force field is not perfect, as the authors demonstrate several issues with atom typing, and the parameter set (we use the antechamber v1.8 parameters in ChemDoodle 3D) is not complete, so molecules that are fully typed may still not be compatible as an inversion or torsion may not be handled. The GAFF force field is mainly used with the Amber force field for proteins and nucleic acids, and Amber comes with its own tools for GAFF functions, so the GAFF implementation in ChemDoodle 3D is mostly an academic exercise for us. Please see section 5.3.2 of the ChemDoodle 3D User Guide for more information.
  3. A new easy-to-use tool for twisting bonds and controlling torsion angles. Mix this with the Minimizer widget to observe rotational energy profiles and calculate barriers to rotation. Section 9.6.4 of the ChemDoodle 3D User Guide.
  4. New content function for linearly compacting all objects in the scene. Linearly compacting all content in the scene will place all content in a line with minimal spacing between each item. Section 9.4.1 of the ChemDoodle 3D User Guide.
  5. New content function for gridding all objects in the scene. Content will be partitioned into a grid with row and column counts you define, from left to right, then top to bottom. If there is more content than the total spaces available in the defined grid, the remainder will stack in the z direction, away from the camera. Each "cell" in the grid will have the amount of space equal to the largest item in the grid. A small buffer space pads each "cell". Section 9.4.2 of the ChemDoodle 3D User Guide.
  6. Edit atom coordinates by form to exactly define values. You can do this for all atoms in the scene, a selection of atoms, or individual atoms. Section 9.6.5 of the ChemDoodle 3D User Guide.
  7. The dielectric constant for electrostatic calculations in force fields can now be defined in the Preferences window under the Functions tab.

Fixes

  1. The Minimizer widget and auto-optimize system has been refined to be quicker, more efficient and more responsive. Corrected the issue where changing force fields didn't update atom typing until the following repaint, if enabled. Changing force field parameters will now see immediate updates to the graphics. Previously, scenes with large molecules would interact slowly when the Minimizer widget was visible, and the auto-optimizer was off. This has been significantly improved.
  2. The molecular modeling chapter (chapter 5) of the ChemDoodle 3D User Guide has been rewritten to be more informative and thorough.
  3. Multi-structure content from MolGrabber and other sources will now be linearly compacted when placed into the scene and 3D coordinates are generated. This stops the structures from being too far away from each other.
  4. Corrected issue with printing images from ChemDoodle 3D on high-DPI screens.
  5. Fixed print preview issue where a doubling of the image appeared. This error only affected the preview.
  6. Corrected issue where the workspace could corrupt if an external monitor where ChemDoodle 3D was being displayed was disconnected.

6.0.0

July 12, 2020

Executive Summary

ChemDoodle 3D v6 is a massive update to ChemDoodle 3D. Included are dozens of new advanced graphics options, including outlines, screen space ambient occlusion, depth of field, additional after effects and more. This allows you to create all kinds of art from your scientific models. ChemDoodle 3D v6 also now automatically supports high-DPI interface scaling on Windows and Linux (macOS Retina scaling was already functional). This update is recommended for all users.

Additions

  1. Full automatic support for high-DPI interface scaling on Windows and Linux (macOS Retina scaling was already functional).
  2. A new deferred shader implemenation allowing for many new advanced graphics effects. Techniques include screen space ambient occlusion (SSAO) for ultra-realistic shading, two different outlining algorithms including artistic stroking, depth of field and anti-aliasing. Dozens of options for the deferred shader. Please see chapter 12 of the ChemDoodle 3D User Guide for an in-depth discussion on using these techniques to create graphics.
  3. New after effects. Now including Blur (Gaussian), Blur (Kuwahara), Blur (Median), Dilate, Edge Detection, Pixelize, Posterize, Sharpen. Dozens of options are available for the after effects. Please see chapter 12 of the ChemDoodle 3D User Guide for an in-depth discussion on using these effects to create graphics.
  4. A new feature to center the camera around the current selection. The center camera button will now center around selections if a selection exists, otherwise the entire scene will be centered.
  5. A new feature to center the camera around a single atom.
  6. We have restored the ability to customize image output, including scale and transparency. There should not be any further issues on standard graphics cards with outputting custom images, but if you do, you can always turn on Compatibility mode in the Preferences window under the Files tab in the Images section.
  7. Warning messages will now appear if your current setup does not support OpenGL 2 or 2.1.
  8. Surfaces can be saved and loaded in ChemDoodle JSON. Surfaces can now be exported to ChemDoodle Web Components output.

Fixes

  1. Fixed copy and paste issues of images from ChemDoodle 3D into other applications. Images with transparent backgrounds can now be copied to the system clipboard.
  2. Fixed issue where stopping animations would not update the picker cache, causing issues with selection.
  3. Fixed issue where a warning message displayed regardless of whether a warning was present when using the Optimize menu items.
  4. Resolved issue on macOS where saving files and images after already having saved a file or image, would cause the format chooser to be uncancellable.

5.2.0

March 05, 2020

Executive Summary

This update includes the latest ChemDoodle Web Components 9 library and fixes several issues, improving the stability of ChemDoodle 3D v5. This update is recommended for all users.

Additions

  1. The built-in ChemDoodle Web Components library has been updated to v9.1.0, along with the necessary changes to the component builder.

Fixes

  1. Fixed legacy PDB import issues.
  2. Reduced the Twitter tweet allowed length to 270 from 280. Twitter uses text weight, not character count and this is a safer value.
  3. The DMG icon for macOS is now properly displayed.
  4. Fixed other minor issues reported.

5.1.0

January 13, 2020

Executive Summary

This is a feature update to ChemDoodle 3D v5. Major changes include new 3D stereochemistry support and better feedback when force field atom mapping issues occur.

Additions

  1. 3D structures can now be handled by our advanced CIP stereochemistry engine. Chiral centers will be assigned R and S configurations, while both cis/trans and E/Z configurations can be deduced on double bonds. Configurations will update in real time as you edit molecules in 3D space. This is the exact same accurate CIP engine from ChemDoodle 2D, so you can be confident in the results.
  2. Force fields now report both warnings and errors when resolving the structure. Warnings will still allow optimizations, but calculations will be dubious.
  3. Minimizer widget will now show specific warnings and error descriptions for molecules that fail to resolve.
  4. UFF will now show incompatible structure errors for 0 order bonds (bond contributions use ln(0) = -infinity).

Fixes

  1. Fixed bug where double clicking on a file to open on Windows did not work properly.
  2. Corrected some issues with the copy/paste and read/write of measurements.
  3. Included missing executable details for Windows.
  4. Included more application registry keys on installation for Windows, including DisplayVersion, which is required for many management systems.

5.0.2

December 03, 2019

Executive Summary

This is a bug-fix update to improve the stability of ChemDoodle 3D v5, and is recommended for all users.

Fixes

  1. Fixed issue that caused license corruption issues to occur after prolonged use of the software.
  2. Added MMFF94 and MMFF94s options to the Molecule>Optimize menu.
  3. ChemDoodle 3D now remembers which color chooser was last used, and will default to that picker the next time a color needs to be chosen.
  4. Resolved errors in ChemDoodle Web Components output.

5.0.1

November 16, 2019

Executive Summary

This is a minor bug-fix update to improve the stability of ChemDoodle 3D v5 and fixes an issue related to loading fonts on some machines as well as resolving issues with the update announcement window. This update is recommended for all users of ChemDoodle 3D v5.

5.0.0

November 13, 2019

Executive Summary

ChemDoodle 3D v5 includes all the infrastructure improvements provided in ChemDoodle v10. New inter-application features are now available to quickly visualize structures drawn from ChemDoodle 2D. ChemDoodle 3D v5 is required for these inter-application features to work.

4.0.1

July 21, 2019

Executive Summary

This is a bug-fix update to improve the stability of ChemDoodle 3D v4. This update is free and recommended for all users of ChemDoodle 3D v4.

Changes

  1. Fixed issue where MMFF94 force fields were not working properly with the Minimizer widget.
  2. Fixed issue where image copy/paste of the scene used low resolution output on Retina displays.
  3. Added option to disable the automatic selection of content when switching to a selection tool. This new option is found in the General preferences, in the Drawing Controls section.

4.0.0

April 14, 2019

Executive Summary

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.

Features

  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.

3.0.0

April 30, 2017

Executive Summary

ChemDoodle 3D v3 is finally here! Build and play with your molecules in real time in 3D. Generate the best graphics for your scientific figures. This is the 3D chemistry software you have been waiting for! Check out all the new features below.

Features

  1. Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
  2. Fully customizable and dynamic real-time shadow rendering.
  3. Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
  4. New bond types, more aromatic ring representations, more cheminformatics functions.
  5. Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
  6. Fully customizable surfaces can now be built for selections of atoms.
  7. Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
  8. Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
  9. Style sheets (and scene settings files) can now be created, saved and loaded.
  10. Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
  11. Full support for the new RCSB Macromolecular Transmission Format.
  12. A more advanced copy and paste system.
  13. After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
  14. Outlines are now rendered for highlighted and selected objects.
  15. Model settings in the Visuals panel in Preferences are now organized by model type.
  16. A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
  17. Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
  18. Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.

2.0.1

May 04, 2016

Executive Summary

This is a bugfix update mainly addressing HTTPS protocol issues with NIH Cactus and related issues.

2.0.0

January 19, 2016

Executive Summary

ChemDoodle 3D v2 is a massive update from the first version included in ChemDoodle 7 and can be used independently from ChemDoodle desktop. The graphics and data were the focus of this update. Protein and nucleic acid models can be loaded from PDB files and periodic systems can be loaded from CIF files in addition to small molecules. All of the graphics are customizable, including the models. More graphics capabilities include fogging and compasses. An entire advanced selection system has been implemented to select content by mouse, function or list. Enjoy and please spread the word!

New Features

  1. A Java installation is no longer required.
  2. Full Retina display support on Mac OS X.
  3. Support for high DPI Windows hardware.
  4. The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format... menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
  5. Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
  6. Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
  7. An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
  8. Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
  9. A compass can be added on the bottom left of the scene or through the camera's origin.
  10. 3D scenes can now be printed.
  11. Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
  12. Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
  13. Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
  14. Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
  15. Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
  16. Dozens more improvements and additions.