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A Review of ChemDoodle 3D version 3

iChemLabs recently announced the release of ChemDoodle 3D version 3, ChemDoodle 3D is a general purpose tool for building and visualising molecules in 3D.

ChemDoodle 3D is a scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.

Small Molecules

Like ChemDoodle desktop the 2D version, ChemDoodle 3D comes with a selection of widgets that provide access to specific functionality, for users of ChemDoodle Desktop a number of the widgets will be very familiar such as the "MolGrabber". Simply type in the name and a search of PubChem will provide a 2D representation, you can then either drag it to the main window or use the green arrow button. You will get a message asking whether to convert into 3D.


A reasonable 3D structure will be generated, ChemDoodle 3D uses the universal forcefield (UFF), the (UFF) was developed to provide a set of rules and procedures for producing appropriate parameters across the entire periodic table. ChemDoodle 3D uses a steepest descent minimization algorithm and a proprietary line search developed at iChemLabs to most efficiently reach a local minimum.

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations DOI

Some implementations of UFF use the QEq partial charge model, the original manuscript and authors of UFF determined the parameterization without an electrostatic model and so ChemDoodle does not include the electrostatic charges.

If the derived 3D structure looks like it was trapped in a local minima I found simply clicking on the jolt button served to bump the structure into a more reasonable minimum energy conformation, you can also select an atom and drag it.


There is also the option to use a Template-based Minimization (NIH Cactus) - This function uses the Cactus service from the NIH to build a 3D molecule based on templates. This function is very fast, but requires an internet connection and of course it might be unwise to submit proprietary structures.

You can build onto the structure using the atom and bond icons in the top left hand corner of the main display, if you have the minimiser widget active the structure will automatically minimise as you add atoms. However it appears that hydrogens are not always added and you add them using the "Add/Remove Hydrogens" function. I had a couple missteps with this, if you have a single atom missing from the structure and your choose "Add/Remove Hydrogens-All" then the default is to remove the remaining atoms, not add the missing atom. If you want to add to a single atom then you need to first select the atom and select "Add/Remove Hydrogens-Selected". This is really only an issue if you have the auto minimiser active, when removing all atoms will completely change the conformation of the molecule. It would also be useful to have a palette of templates of, conformations of rings, functional groups.

iChemLabs have produced a video introducing the builder tools.

ChemDoodle3D ver 3 now supports a greatly extended selection of display options for both atom/bond and surface displays. However when I first tried the display did not update as you change the options in the preferences and you can't rotate the molecule with the preferences window open. It turns out you have to select the surface before you open the preferences, alternative you can choose the selection tool and then right-click on the surface and choose "format surface".


Some of the format surface options are shown below, in addition to solid surfaces you can display mesh or dot surfaces at a variety of resolutions and surface textures. This allows the user very precise control of the output with shadows, gamma correction and many other advanced 3D graphics features.


As far as I could tell it is not possible to colour the surface by atom type/lipophilicity/charge etc.

The interfaces submenu shows some interesting integration with 3rd party applications

Interfaces > - This submenu provides access to third party interfaces, including ChemExper, LabArchives, and Twitter.



Importing files from the PDB is very easy, simply select "Import by PDB ID" from the Macromolecule menu, type in the PDB code and it will almost instantly appear in the main window in ribbon format.


The downloaded PDB file is stored under "Documents/ChemDoodle3DSettings/autosaves/2wei-autosave.ic3", but the user should save in their own directory for safe keeping. The display is very responsive even with very large proteins in the main viewing window. The ribbon can be coloured by residue but not by any property or by secondary structure (Helix/Loop/Sheet etc.) but I understand this is in development.

When remotely accessing files from the RCSB, the MMTF format is used by default as it is signicantly smaller and faster than the PDB format. The MMTF format also contains bonds and bond order information, which is very useful. You can switch instead to downloading the legacy PDB format in the Preferences window in the Functions tab by changing the Import Files as setting in the RCSB Online Connections section.

To make changes to the display the "Selector" widget allows the user to make very specific selections to the display, however you can't make similar selections in the main display by clicking on the ribbon, and you can't select side chains within a set distance of a selected ligand. I think it would also be useful to have a hide/display all hydrogens toggle.


You can put a surface on the protein and display waters as shown below, which gives an idea of the space around a ligand but there is no way to display the interactions between ligand and protein. If you want water to appear from RCSB data, make sure to select the waters first and then go into Preferences>Visuals>Models>Atoms and Bonds>Render Water Molecules


You can also mix different surface types and atom/bond displays to give highly customised displays.


ChemDoodle Web Components

iChemLabs also produce ChemDoodle Web Components

The ChemDoodle Web Components library is a pure Javascript chemical graphics and cheminformatics library derived from the ChemDoodle® application and produced by iChemLabs. ChemDoodle Web Components allow the wielder to present publication quality 2D and 3D graphics and animations for chemical structures, reactions and spectra. Beyond graphics, this tool provides a framework for user interaction to create dynamic applications through web browsers, desktop platforms and mobile devices such as the iPhone, iPad and Android devices. This library also has complete access to the entire ChemDoodle desktop API through AJAX, allowing for quick access to one of the most robust chemical graphics and informatics packages in existence directly through Javascript.

There is now the facility to export scenes to ChemDoodle Web Components. PDB scenes cannot yet be exported, but this is coming in the next version. The process allows for detailed control over all elements of the display. This is a great way to share ideas.


The generated object can then be copied to the clipboard and posted into a web page as shown below.


Sometimes when writing these reviews it is helpful think about the intended target audience, ChemDoodle3D ver 3 is not a molecular modelling/computational chemistry package, it could be used as the 3D molecular editor to create the input molecules, since the implementation of UFF is accurate and efficient. This might well be attractive for scientists who are already using ChemDoodle as a 2D chemistry drawing package, as it uses the same interface and drawing paradigms. ChemDoodle3D really excels at the creation of high quality publication ready graphics, the ability to specifically select every atom or bond enables the user to precisely create the desired image. It performs well using modest hardware that would be accessible to any student. Perhaps one of the real attractions however is the ability to use the ChemDoodle Web Components to easily share structures via the web.

Last Updated 2 August 2017