Macs in Chemistry

Insanely Great Science

Scientific Applications under Ventura Updated

 

Overview

After a period of open beta testing MacOS 13 Ventura is here.

ventura

If you want an overview of Ventura I'd recommend the excellent arstechnica review.

Ventura supports both Intel and Apple Silicon Macs, but as you might expect some of the older Intel machines are no longer supported. The list of supported Macs:

  • 2017 iMac/iMac Pro and later
  • 2018 MacBook Air and later
  • 2017 MacBook Pro and later
  • 2019 Mac Pro and later
  • 2018 Mac mini and later
  • 2017 MacBook and later
  • 2022 Mac Studio and later

You can find out your Mac model by tapping on the Apple icon in the menu bar and going to About This Mac. Apple will still release security updates and new Safari updates for macOS 11 (Big Sur) and 12 (Monterey)

Scientific Applications

I've contacted all developers I know and their responses to date are shown below, first impressions are this is a relatively benign update.

4-Peaks

Absoft

alvaScience all our products support macOS 13 Ventura.

Amsterdam Modeling Suite

Anaconda Supports MacOS- 64-bit x86 & M1

APE OSX 10.11+ (M1 Universal)

Avogadro

BBEdit The following versions of our products are recommended for use with macOS 13 “Ventura”: BBEdit 14.6.1, Yojimbo 4.6.2

Brainsight

ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem.

ChemDraw All working as expected

ChemDoodle ChemDoodle 2D and ChemDoodle 3D are both fully supported on macOS 13 Ventura with no known issues

ChimeraX Open the downloaded DMG file and drag ChimeraX to your Applications folder. Includes native versions for M2, M1 and Intel Macs. Works on macOS 10.15 and newer.

Chirys View

Conquest and Mercury from CCDC

Cresset

CrystalMaker Requires a Mac running macOS 10.12.2 "Sierra" to macOS 13.x "Ventura" (recommended)

CYLView 20

DataWarrior Seems to be working fine.

Delta

DEVONagent fine on Intel, not tested on Apple Silicon.

DEVONthink fine on Intel, not tested on Apple Silicon.

Elemental Fine under Ventura and on Apple Silicon

EndNote

EnzymeX

EverNote

Fujitsu ScanSnap .

GAMESS

Gaussaian installation using Home-brew seems to be working fine.

gFortran Standalone installer of GCC 12.2, including gfortran, for macOS Ventura (macOS 13) Apple silicon and Intel

Highlights

Homebrew For most seems to work fine, remember to reinstall Xcode command line tools.

[iBabel)[https://www.macinchem.org/ibabel/version5/ibabel5.php] no issues reported

IDL

Igor Pro According to reports from Igor users, Igor Pro 9 runs well under Rosetta2.

iNMR

JalView

KaleidaGraph

KNIME no issues with initial tests

Manuscripts no issues reported

Matlab MATLAB is compatible with macOS 13 (Ventura) Running MATLAB and Simulink on Apple silicon Macs is supported in MATLAB R2020b Update 3 and newer. On Apple silicon Macs, MATLAB runs using the Rosetta 2 environment.

Mathematica both Intel and Apple Silicon supported macOS 11 (Big Sur) to 13 (Ventura)

Mendeley

Microsoft Office Desktop apps fine, some issues with Exchange Server.

Mnova

MOE Initial tests showed no issues with this version.

Molsoft Yes ICM-Pro runs on Mac OS Ventura

MOPAC

NAG Fortran compiler

OpenBabel no issues reported

ODYSSEY ntel or M1 chip Macintosh (only), 2GHz chip or faster OS 10.12 (Sierra) through OS 13.X (Ventura) 128 GB disk space or higher (SSD Recommended) 4 GB RAM or higher

Orca

Papers

PGOPHER Regrettably, further updates to PGOPHER will no longer be available

pro Fit pro Fit 7.1 requires Mac OS 12 (Monterey) or later.

PYMOL Home-brew formular supports Ventura https://formulae.brew.sh/formula/pymol.

Python Python 2.7 is no longer included - use Python 3 instead. Python works fine on Apple Silicon and is "mad fast!".

QMForge 2.4

R Package R-4.2.2-arm64.pkg is a ‘native’ build for ‘Apple Silicon’ (aka ‘M1’) Macs and runs on macOS 11 or later (Big Sur, Monterey, Ventura, …).

RDKit All seems fine (Note: -Python 2.7 is no longer supported - use Python 3 instead)

Samson "We're happy to announce that SAMSON works perfectly on #macOS 13 #Ventura."

Schrodinger

SeeSAR SeeSAR & infiniSee work just fine.

Simply Fortran Fortran development environment for macOS 12 or higher on Intel, experimental build for Apple Silicon. Mac OS 13.

Sketch Version 94.1 supports Ventura

Spartan Intel or Mx chip 4 GB RAM or higher OS 10.12 (Sierra) through OS 13.X (Ventura) 128 GB disk space or higher (SSD Recommended)

SPSS existing users report no issues, some reports of installation issues.

Stardrop

Swiss-PdbViewer Swiss-PdbViewer is a 32 bits application and will * NOT * run.

TensorFlow and TensorFlow Addons

UCSF ChimeraX Details on building M1 version https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html

VMD

Vortex Vortex works perfectly on both Intel and Apple Silicon Macs under Ventura

WINE

Wizard

wxMacMolPlt

Xcode need to update to latest version. Remember to reinstall command line tools

XQuartz OpenGL and OpenCL are still here, even on Apple Silicon Macs

I’ll add more updates later, feel free to contact me and thanks for the comments to date.

Last update 4 December 2022

Comments

Structure-based searching SQLite

I've been experimenting with SQLite a software library that provides a relational database management system, it is self-contained, serverless, and requires little or no admin.

SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most used database engine in the world. SQLite is built into all mobile phones and most computers and comes bundled inside countless other applications that people use every day.

In th first tutorial I described looking at using it for very fast exact lookup of chemical structures. This tutorial https://www.macinchem.org/reviews/exactsearch/exactsearch.php takes you through setting up the database, storing chemical structures as SMILES strings and then accessing it using a Jupyter Notebook.

The second tutorial https://www.macinchem.org/reviews/exactsearch/usingexactsearch.php shows how to create a python script to access from the command line, and using AppleScript to access it from ChemDraw. This allows you to get the structure for a specific identifier or check for the identifier for a drawn structure.

The third tutorial https://www.macinchem.org/reviews/exactsearch/substructuresearch.php shows how to use the fabulous Chemicalite to support high performance chemical structure-based searching of a SQLite database of over 2 million structures.

mols2gridall

Comments

Using SQLite for exact search

I've been experimenting with SQLite a software library that provides a relational database management system, it is self-contained, serverless, and requires little or no admin.

SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most used database engine in the world. SQLite is built into all mobile phones and most computers and comes bundled inside countless other applications that people use every day.

In particular I've been looking at using it for very fast exact lookup of chemical structures. This tutorial https://www.macinchem.org/reviews/exactsearch/exactsearch.php takes you through setting up the database, storing chemical structures as SMILES strings and then accessing it using a Jupyter Notebook.

The second tutorial https://www.macinchem.org/reviews/exactsearch/usingexactsearch.php shows how to create a python script to access from the command line, and using AppleScript to access it from ChemDraw. This allows you to get the structure for a specific identifier or check for the identifier for a drawn structure.

CD result

Comments

Updated Multicentre Cheminformatics Meeting

As many know we have been holding regular cheminformatics network meetings in Cambridge for many years. These have been a great means to find out about new science, network and then socialise in a nearby pub. As we try to spread the word I'm really delighted to announce a multi-centre cheminformatics meeting.

30 November 2022, 3.30-5pm UK / 4.30-6pm CET:

Cross-Site Cambridge/Oxford/Berlin Digital Drug Discovery Meeting!

Cambridge: Cambridge Crystallographic Data Centre, Union Road https://goo.gl/maps/4BjUv46WhaNdV6po6
Oxford: Phase II Biochemistry Seminar Room, New Biochemistry Building off South Parks Road https://goo.gl/maps/qSogPUHLYzQMHRUC7
Berlin: Institut für Pharmazie, Königin-Luisestrasse https://goo.gl/maps/w4N4LT2tYcBgC3NP6

Please turn up 10 minutes before the start time to register where needed

  • Programme

Why is it so Hard to Search Ultra-Large Chemical Libraries?
Roger Sayle, NextMove Software, Cambridge
https://www.nextmovesoftware.com/people.html

Fragmenstein: Stitching Compounds Together Like a Reanimated Corpse
Matteo Ferla, Oxford Protein Informatics Group, Department of Statistics
https://www.matteoferla.com/

Data-Driven Methods for Active Compound Design and Risk Assessment
Andrea Volkamer, Charité Berlin and Saarland University
https://volkamerlab.org/

  • After-event locations (~5.15pm GMT/~6.15pm CET onwards)

Cambridge: The Alma, Russell Court
Oxford: The Royal Oak, Woodstock Road
Berlin: Luise Dahlem, Königin-Luise-Straße

Please join us in person (just turn up at the event location 10 minutes before the start time in case local registration is needed) or for joining remotely please register here: https://zoom.us/meeting/register/tJApf-uhrD0vH9S1U-9p6il24hB5RHtEh1ii.

Comments

RDKit updated

The latest version of RDKit has been released. https://github.com/rdkit/rdkit/releases/tag/Release202209_1.

RDKit_logo

  • The new RegistrationHash module provides one of the last pieces required to build a registration system with the RDKit.
  • This release includes an initial version of a C++ implementation of the xyz2mol algorithm for assigning bonds and bond orders based on atomic positions. This work was done as part of the 2022 Google Summer of Code.
  • A collection of new functionality has been added to minimallib and is now accessible from JavaScript and other programming languages.
Comments