Macs in Chemistry

Insanely Great Science


QuickLookProtein is a macOS Quick Look extension to preview protein/3D structure files (PDB, SDF, CIF).

It works in all places where macOS uses Quick Look, e.g. in Finder and Spotlight. In Finder, just select the protein structure file and press Space to open Quick Look.

The rendering of the 3D structure is performed using 3Dmol.js.

The extension is packaged into a main app, whose purpose is to set a few settings used for the display of the 3D models. QuickLookProtein requires macOS Big Sur (version 11.0+).


ISOLDE updated


ISOLDE 1.2.0 is available, and ready to install for @UCSFChimeraX 1.2! As usual, just get the ChimeraX 1.2 release from then install ISOLDE via "Tools/More Tools. Code is on GitHub

ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments.

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use.

You can view snapshot here


Mol*: fast, interactive 3D visualisation of biomolecules in your browser


The PDB in Europe have just introduced a new viewer for biomolecules, Mol*, is a new 3D molecular viewer developed in collaboration between RCSB PDB, PDBe, and CEITEC, from RCSB PDB and PDBe pages.

On the PDBe pages, Mol* has now replaced the LiteMol viewer in all instances, including on the PDBe search and entry pages e.g. Access Mol* from any 3D View tab for Structure Summary pages at Both the LiteMol and NGL viewers at PDBe and RCSB PDB, respectively, will no longer be actively developed.

Here is the structure of Aldehyde Oxidase PDB ID 4uhw.



Illustrate a small Fortran program for creating non-photorealistic illustrations of molecules


First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and the Fortran on a Mac page is one of the most frequently read. I've just been sent details of another Fortran program and I've added it to the page.

Illustrate is a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. It is used to create the RCSB Molecule of the month.



3decision for looking at protein structures


At the latest Bio-ITWorld 3decision was recognised with an award

3decision – next generation structural knowledge management solution

Although wildly used, rational structure-based drug design (SBDD) techniques are far from being applied to their fullest potential. The major hurdles lie in the inconsistent data persistence and the complexity of analyzing structural data. Moreover, the structural data is often analyzed by domain experts only and their knowledge and experience are not well shared and exposed to other communities. Abbvie has addressed these pitfalls by co-developing a web-based structural knowledge management solution called 3decision. It allows Abbvie to transform a massive amount of data coming from in-house and public 3D structures and sequences, into applicable knowledge for drug discovery projects. The collaborative aspects within SBDD projects are in focus and the user interface allows all types of users to easily generate, test and connect their ideas with each other. The development of 3decision allowed Abbvie to dramatically increases the ROI of SBDD work and protein structure production.

seq_brows_bioit 3decision is a web-based collaborative platform for storing, analyzing and sharing protein-ligand structures, sequences, and associated data, it works fine on a Mac and Google Chrome is recommended browser