Comparing PyMOL on a M1 MacBook Pro Max with Intel MacBookPro (2016)

After a little hunting I found an open-source version of PyMOL for M1 Macs on Home-brew. Installation didn’t go as smoothly as I expected so I thought I’d outline the process I went through.

Installing Homebrew on M1 Mac

The install script is available here

This ran as expected but when I looked I could not see the usual installation. It turns out this script installs Homebrew to its preferred prefix (/usr/local for macOS Intel, /opt/homebrew for App..le Silicon). I presume this is so folks can have a separate installation for Rosetta. You can see the hidden folders in the Finder by pressing “Shift-Command-.” (Shift and Apple keys and full-stop).

So I checked that my PATH included the correct folder.

Then searched for Pymol

Then tried to install

And got this error

So uninstalled cmake and reinstalled.

All seemed to work fine

Then in Terminal type pymol

I tried a few simple tasks

Open a local copy of 3j3q.cif

Intel MacBook Pro took 16 seconds
M1 MacBook Pro took 6 seconds

M2 Mac Studio Ultra took 6 seconds

Create surfaces and export as POV-Ray

Imported a local copy of 7n30, added hydrogens and coloured ribbon by secondary structure.

Added surface

Intel MacBook Pro took 54 seconds
M1 MacBook Pro took 36 seconds

M2 Mac Studio Ultra took 29 seconds

Export to POV-Ray

Intel MacBook Pro took 23 seconds
M1 MacBook Pro took 13 seconds

M2 Mac Studio Ultra took 10 second

List of tools tested

Last update 14 December 2021