Macs in Chemistry

Insanely Great Science

ChemDoodle 2D updated

 

The very popular chemical drawing application ChemDoodle has been updated to version 11.8

ChemDoodle 2D v11.8 includes significant improvements to many features, including excellent chain replacement nomenclature in IUPAC naming, support for allene/cumulene stereochemistry, improved bezier curve tools, current InChI support and more file options.

Full details of the update are here https://www.ichemlabs.com/news/read?post=cd2d118released.

You can get all the ChemDoodle applications (ChemDoodle 2D, 3D and mobile) for a single monthly ($15) or yearly subscriptions ($100), and as a one off lifetime purchase ($750).

More details on the store https://www.ichemlabs.com/store.

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Icons for Mac Hard drive

 

Someone asked me recently where I got the image for the Macintosh HD on my desktop.

macHD icon

Actually they are all available on your Mac.

macIcons

They can be found in

/System/Library/CoreServices/CoreTypes.bundle/Contents/Resources/

You will have to right-click (or control click) on CoreTypes.bundle and choose show bundle contents

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MacVector on Apple Silicon

 

Some one just sent me an email mentioning MacVector supports Apple silicon.

MacVector 18.2 requires Mac OS X 10.12 or later. It will NOT work on Windows, Mac OS 9 or on Mac OS X 10.11 or earlier. MacVector 18.2 is a "Universal Binary", meaning it will run natively on both Intel and Apple Silicon based Macintosh computers.

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MacBook M1 vs M1 Pro for Data Science and Machine Learning

 

When the first M1 MacBooks came out there were limited libraries available but over the last year most of the libraries needed for data science now support the new Apple silicon architecture.

Includes details for installing TensorFlow and the test dataset.

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Comparing energy usage between M1 Mac and Intel

 

Updated

Added a couple more comparisons.

The pages comparing cheminformatics/compchem apps on the MacBook Pro M1max are proving very popular. Several readers have asked me to compare energy usage which is an excellent suggestion.

Based on a suggestion I purchased Nevsetpo Power Meter UK Plug Power Monitor Watts Meter Plug and I've used it to test a selection of tasks. Once plugged into a socket it monitors total energy consumption of anything device plugged in. Both machines were fully charged and the "Optimised battery charging" was switched off.

I tried a few computationally intensive tasks and details of energy consumption are here..

M1chip

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RSC CICAG Open Source Tools for Chemistry Workshops

 

In 2020 RSC CICAG ran a 5 day virtual meeting on Open Source Chemical Sciences, this event had three streams Open Data. Open Publishing and Open Source tools for Chemistry. The Open Source tools for Chemistry workshops proved to be enormously popular and so CICAG held a series of monthly workshops through 2021. These workshops covered a variety of Open Source tools and resources ranging from visualisation tools, data analysis using cheminformatics toolkits, and online resources like the PDB.

These workshops were all recorded and are available on the CICAG YouTube channel, as we plan for this years workshops I thought it might be timely to remind everyone what is now available and also to thank all the presenters and developers who made the workshops possible. I've included links to all the workshops below

PDB workshop 2 using Mol*
PDB workshop 1 Registration system
Clustering using KNIME
Web apps for fragment-based drug discovery
Introduction to Cheminformatics and Machine Learning
Oxford Protein Informatics Group antibody modelling tools
Advanced DataWarrior
GNINA
Chemical Structure validation/standardisation
ChimeraX
DataWarrior
ChEMBL
UsingGoogleCoLab workshop
Fragalysis workshop
Knime workshop
PyMOL workshop

These workshops have now been viewed nearly 13,500 times and some of the comments are worth highlighting

I am not sure why this software is not famous. This is presumably the best chemoinformatics software I have seen, Great presentation!

Two hours of distilled pure science.

These workshops were sponsored by Liverpool Chirochem.

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Annual Site review

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 118,000 visitors spending an average of 1.5 minutes per session. Whilst the US and the UK were the two top countries but as the table below shows, there has been a steady following around the world. As might be expected the majority are Mac users (57%) but there are a substantial number of Windows (23%) and Linux users (4%). The mobile platforms iOS (9%) and Android (6%) make up most of the remainder.

macinchemVisitors2

The most popular page was again the Fortran on a Mac page, followed by the M1chip category page. The iBabel page is in third place. Interestingly, the next most popular page was Python coding within Xcode. Perhaps, suggesting that Apple should consider making it a bit more seamless to use Xcode with Python.

The Mobile Science site has seen increased visitor numbers.

The most popular apps viewed were.

Merck PTE
IBM Micromedex Drug Info
Python3IDE
PocketCAS: Mathematics Toolkit
Molecular Constructor
Radiology 2.0

Also popular were

Human Anatomy Atlas 2019
ChemTube3D.
The Periodic Table Project
Periodic Table

The Twitter feed @macinchem has steadily attracted new followers and currently has 1272 followers.

The most popular tweets were

Rutherford &Fry book
Malcolm Campbell award
Web apps for Fragment drug discovery
More Open Source workshops

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