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Category: Hints and Tutorials

Tutorials, Hints, Tips and Tricks

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Download multiple PDB files using a Jupyter notebook

1 April 202322 January 2024 chris

The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists

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Hints and Tutorials Other Tips

LaTeX and MathML support in Pages and iBooks Author

13 March 202310 April 2023 chris

The latest version of Pages (version 6.1) and iBooks Author (version 2.0) include support for LaTeX and MathML, this is an interesting addition that will

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Data Analysis Tools Hints and Tutorials Reviews Science Apps Software Reviews

A Review of Instant JChem

13 March 202310 April 2023 chris

ChemAxon are a software company that produce a variety of cheminformatics applications and software development modules. A key driver for development has been maintaining portability among

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Applescript Hints and Tutorials

Search un1Chem from ChemDraw

12 March 202326 October 2023 chris

Un1Chem is a new web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical

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Applescript Hints and Tutorials

Convert ChemDraw to Tiff

12 March 202310 April 2023 chris

ChemDraw from CambridgeSoft has excellent Applescript support. I’m sure many chemists use ChemDraw to create the structures and figures for publications, and whilst ChemDraw can

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Hints and Tutorials Vortex Scripts

Generating IUPAC names for molecules

11 March 202326 October 2023 chris

I was recently asked if I could generate IUPAC names for a series of molecules for a patent filing. There are many chemical drawing packages

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Hints and Tutorials Vortex Scripts

Using JDBC Driver to access Athena from Vortex

11 March 202312 May 2023 chris

This tutorial was created by Jackson Pullman (jackson.pullman@yale.edu) Getting Started Amazon Athena is an interactive query service that makes it easy to analyze data in Amazon

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Hints and Tutorials Vortex Scripts

A collection of Vortex scripts to aid cluster analysis

11 March 202310 April 2023 chris

Exploration and sorting large datasets of molecules often involves the use of clustering techniques to group together molecules with similar properties. It can be used

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Hints and Tutorials Vortex Scripts

A Vortex script to calculate the Blood-Brain Barrier (BBB) SCORE

11 March 20234 January 2024 chris

A recent publication described “The Blood–Brain Barrier (BBB) Score” DOI a scoring function to determine the likelihood of a molecule being brain penetrant. The blood–brain barrier (BBB)

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Hints and Tutorials Vortex Scripts

Vortex script to determine the Amino Acids in a collection of peptides

11 March 202312 November 2024 chris

I’ve recently become interested the comparison of the amino amino-acid composition of peptides, to allow comparison of cyclic versus linear peptides, or brain penetrant verses

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    @macinchem.bsky.social 1 day

    Vortex script using BioTransformer

    Prediction of the metabolism of small molecules is very challenging and so having a variety of different tools is always useful. I've previously written Vortex scripts to use SMARTCyp...

    Vortex script using BioTransformer

    Prediction of the metabolism of small molecules is very challenging and so having a variety of different tools is always useful. I've previously written Vortex scripts to use SMARTCyp and...

    macinchem.org

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    @macinchem.bsky.social 3 days

    BBEdit updated

    BBEdit everyone's favourite text editor has been updated to 15.5.5 This update contains only fixes for reported symptoms. Please see the release notes for previous versions for details on what is...

    https://macinchem.org/2026/02/20/bbedit-updated/
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    @macinchem.bsky.social 4 days

    AI Club for Biomedicine

    Well it was standing room only at the last nights Cambridge Cheminformatics Network meeting Co-folding special. Many thanks to all the speakers I'm sorry we did not have time...

    https://macinchem.org/2026/02/19/ai-club-for-biomedicine-2/
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    @macinchem.bsky.social 6 days

    Apple Event March 4th 2026

    Apple today announced a "special Apple Experience" in New York, London, and Shanghai, taking place on March 4, 2026 at 9:00am ET. Interesting that it is taking place simultaneously...

    Apple Event March 4th 2026

    Apple today announced a "special Apple Experience" in New York, London, and Shanghai, taking place on March 4, 2026 at 9:00am ET. Interesting that it is taking place simultaneously in...

    macinchem.org

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    @macinchem.bsky.social 1 week

    Grant funded high-throughput screening

    Apply for funding to run a high throughput screen (HTS) using AstraZeneca’s compound library and screening robots. There are two funding opportunities per year that are open to...

    https://macinchem.org/2026/02/16/grant-funded-high-throughput-screening/

Recent Posts

  • Vortex script using BioTransformer
  • BBEdit updated
  • AI Club for Biomedicine
  • Apple Event March 4th 2026
  • Grant funded high-throughput screening
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