Macs in Chemistry

Insanely great science


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

/bin/bash -c "$(curl -fsSL"

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 Apple 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.

echo $PATH   

Then searched for Pymol

brew search pymol
==> Formulae

Then tried to install

brew install pymol

And got this error

Installing pymol from brewsci/bio
==> Installing dependencies for brewsci/bio/pymol: cmake, ninja, icu4c, boost, msgpack-cxx, brewsci/bio/mmtf-cpp, catch2, brotli, giflib, imath, jpeg, libpng, openexr, libtiff, webp, jpeg-xl, libvmaf, aom, dav1d, freetype, fontconfig, frei0r, ca-certificates, gmp, bdw-gc, libffi, m4, libtool, libunistring, pkg-config, readline, guile, gettext, libidn2, libtasn1, nettle, p11-kit, openssl@1.1, libevent, libnghttp2, unbound, gnutls, lame, fribidi, pcre, gdbm, mpdecimal, sqlite, xz, python@3.9, glib, libpthread-stubs, xorgproto, libxau, libxdmcp, libxcb, libx11, libxext, libxrender, lzo, pixman, cairo, gobject-introspection, graphite2, harfbuzz, libass, libbluray, cjson, cmocka, mbedtls, librist, libsoxr, libvidstab, libogg, libvorbis, libvpx, opencore-amr, little-cms2, openjpeg, opus, rav1e, flac, libsndfile, libsamplerate, rubberband, sdl2, snappy, speex, srt, leptonica, tesseract, theora, x264, x265, xvid, libsodium, zeromq, zimg, ffmpeg, libxfixes, libxi, libxrandr, libxxf86vm, expat, libxdamage, mesa, freeglut, glew, glm, libxml2, isl, mpfr, libmpc, zstd, gcc, szip, hdf5, netcdf, openblas, numpy, qt@5, pyqt@5 and sip

Installing brewsci/bio/pymol dependency: brewsci/bio/mmtf-cpp
Error: An exception occurred within a child process:
RuntimeError: /opt/homebrew/opt/cmake not present or broken
Please reinstall cmake. Sorry :(

So uninstalled cmake and reinstalled.

brew uninstall cmake

brew install cmake  

brew install pymol

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

Create surfaces and export as poverty

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

Export to POV-Ray

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

List of tools tested

Last update 14 December 2021