Macs in Chemistry

Insanely Great Science

Disabled access to technology


Hats off to Apple for putting disabled access to technology front and centre in the Apple event last night. I’m sure most of the reports will focus on the MacBook Pro but I’d like to give a mention to the accessibility help available.

The AppleStore has a page dedicated to accessibility, and the system preferences pane also has a section on Accessibility.



Script for 3D printing from Jmol


A Jmol Script for Programmatic Conversion of Crystal Structures into 3D Printable Files can be downloaded here created by Vincent F. Scalfani, Antony Williams and Valery Tkachenko.


SeeSAR 5.4 released


There has been a new update to SeeSAR, this latest update brings.

2D molecule browsing - time to look at things from a different angle

While the molecule table offers great functionality for prioritizing compounds based on the data, it does not provide an overview of the molecules themselves. This release, however, sees the introduction of 2D molecule browsing. The table now offers two views - the one you already know and a 2D browser - flick between them using the switch below the table. Both views are always kept in sync so if you add a filter or sort etc. the 2D browser will show you the same result in the same order as the table. Also try expanding the table area to see how more molecules fit into the view.

Fantastic new 3D graphics features

This release also brings with it some great new 3D graphics improvements. As much as we all like visualising the binding site surface, it lay often times in the way… The binding site surface can now be switched to transparent allowing you to see through it and therefore making the analysis of the binding site and molecules within much more comfortable. Also, the feeling of depth in the 3D view has been improved to help orientation - a so-called "fog effect" fades out the protein and molecules that are further away to bring the foreground more into focus.

Persistent amino acid labels and better view of reference

So far, labels on binding site components unfortunately disappeared when browsing through different molecules in the table. Now amino acid, co-factor and water labels remain present if you change to a different molecule in the 3D view and even if you enter the molecule editor. The view of the reference compound has also been improved. For better visibility, the thickness of the bonds has been increased and instead of coloring the whole molecule in a uniform blue color, only the carbon atoms are colored blue so that hetero atoms can be distinguished more easily.

There is a review of an early version of SeeSAR here.


Free hands-on workshops on Structure-Based Drug Design


Chemical Computing Group are running a free hands-on workshops on Structure-Based Drug Design

CAMBRIDGE – December 1, 2016 St John's Innovation Centre Cowley Road, Cambridge, Cambridgeshire, CB4 0WS, UK

09:00-12:30 Structure-Based Drug Design and Ligand Modification Molecular Surfaces and Maps / Ligand Interactions / Conformational Searching / Ligand Optimization / Ligand Selectivity / Protein Alignements and Superposition

12:30-13:30 Lunch break*

13:30-17:00 Advanced Structure-Based Drug Design Pharmacophore Modeling / Docking / Fragment-based Design / Scaffold Replacement / R-Group Screening / Project Search / Protein-Ligand Interaction


Note: Computers will be provided. No prior software experience required.
*Lunch and refreshments will be provided.


Mobile Science Apps


The Mobile Science site is a resource for finding scientific applications for iOS devices. The is an option for people to vote for apps and while this is needs to be taken with a pinch of salt I thought it might be interesting to highlight the current top 10.

  1. ChemDoodle Mobile
  2. Medicinal Chemistry Toolkit
  3. WolframAlpha
  4. Elemental
  5. Papers 3 for iOS
  6. Findings - LabNotebook
  7. Stanford iOS course
  8. Asteris
  9. Approved drugs App
  10. Open Drug Discovery Teams