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 https://brew.sh
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
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 /Users/chrisswain/miniconda3/bin:/Users/chrisswain/miniconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/moe2020/bin:/Applications/moe2020/bin
Then searched for Pymol
brew search pymol ==> Formulae brewsci/bio/pymol
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, email@example.com, libevent, libnghttp2, unbound, gnutls, lame, fribidi, pcre, gdbm, mpdecimal, sqlite, xz, firstname.lastname@example.org, 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.
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 https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php
Last update 14 December 2021