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Category: Hints and Tutorials

Tutorials, Hints, Tips and Tricks

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Applescript Hints and Tutorials Other Tips

Combining PDFs using an Automator Workflow

6 March 202318 May 2023 chris

Today I was sent a license agreement as a 6 page pdf file, I was asked to sign the document and send it back. All

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Hints and Tutorials Other Tips

Preview Tips

6 March 202311 May 2023 chris

PDF seems to have become the standard for online distribution of publications, this is despite many obvious limitations. In particular from the point of view

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Applescript Hints and Tutorials

Applescript Copy File to MobileMe and Create email message

6 March 202326 October 2023 chris

MobileMe is no longer available but this script could be modified to save in other online storage facilities. Whilst Apple now allow you to send

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Applescript Hints and Tutorials

Applescript and Unix

6 March 202326 October 2023 chris

Beneath the beautiful Mac OS X interface lies an industrial-strength UNIX system, many of the key UNIX-based scientific applications are now available under Mac OS

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Applescript Hints and Tutorials

Getting started with AppleScript

6 March 202326 October 2023 chris

This is the first of what will hopefully be a series of tutorials on Apple’s own scripting language Applescript. I should perhaps begin with a

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Hints and Tutorials Vortex Scripts

Vortex script using Openbabel for similarity searching

6 March 202315 May 2023 chris

An earlier script showed how to calculate molecular similarity between the first molecule in the file and all the other molecules using OpenBabel as shown

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Hints and Tutorials Vortex Scripts

Vortex script using MOE to calculate properties

6 March 202321 June 2023 chris

MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means

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Hints and Tutorials Vortex Scripts

Vortex script to analyze categories

5 March 202312 April 2023 chris

I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver

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Hints and Tutorials Other Tips Vortex Scripts

Options for Clustering large datasets of Molecules

5 March 202310 April 2025 chris

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that

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Data Analysis Tools Hints and Tutorials Vortex Scripts

Calculating molecular properties using the ChemAxon cxcalc

4 March 202325 April 2023 chris

ChemAxon’s Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a

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  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    Updated Mac mini and Mac Studio

    Apple have announced new Mac mini and Mac Studio machines. Mac mini has either M5 Pro chip or M6 chip M5 Pro 15‑core CPU with 5 super cores and 10 performance...

    https://macinchem.org/2026/08/26/updated-mac-mini-and-mac-studio/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    Installing the OpenADMET PXR anvil prediction

    I had a couple of issues installing the PXR model from OpenAMET on my Apple Silicon Mac (https://huggingface.co/openadmet/pxr-chemeleon-baseline) so I thought I'd...

    https://macinchem.org/2026/08/25/installing-the-openadmet-pxr-anvil-prediction/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    mlxmolkit updated

    mlxmolkit is a GPU-accelerated molecular toolkit on Apple Silicon, it is a port of nvMolKit that uses Cuda. There are now three pipelines Molecular Clustering — Morgan FP → Tanimoto...

    https://macinchem.org/2026/08/25/mlxmolkit-updated/
  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    Some conferences and meetings that might be of interest.

    9th Artificial Intelligence in Chemistry Symposium (https://www.rscbmcs.org/events/aichem9/) Wednesday 2nd – Friday 4th September 2026,...

    https://macinchem.org/2026/08/23/some-conferences-and-meetings-that-might-be-of-interest/
  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    Is anyone else picking blackberries, seems to be a very good year.
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