A reader recently pointed out BlendMol part of a suite of software tools developed by the Jacob Durrant Lab.

BlendMol is a Blender plugin that can easily import VMD 'Visualization State' and PyMOL 'Session' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with popular analysis programs (i.e., VMD/PyMOL). Users can import into Blender the very molecular representations they set up in VMD/PyMOL.

This looks like a very interesting open-source project available on GitHub, however looking at the software page https://durrantlab.pitt.edu/durrant-lab-software/ I see there are a number of other interesting packages.

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables ‘plug-and-play’ trajectory visualization.

Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.

Looks like a great resource.

 

When a wrote "A few thoughts on scientific software" I was somewhat surprised by the interest and amount of feedback I got. I've since added two more pages based on the feedback,

A listing of open-source cheminformatics toolkits and Open Source Python Data Science Libraries.

If you have any other suggestions feel free to let me know.

 

Whilst this website is aimed at providing a resource for Mac using chemists regular readers will know that much of the content is platform agnostic and includes much code/software that will be of interest to all scientists.

I recently got a rather sad email

It seems that Third Street Software quietly disappeared, breaking the syncing for Sente (reference management).

I've also heard about a couple of other smaller software developers who are finding life very tough and it started me thinking about the status of scientific software, after exchanging emails with a number of people in the industry (many thanks for their input) I thought I'd collect a few thoughts on my blog.

You can read it here https://www.macinchem.org/reviews/scientificsoftware/software.php.