Macs in Chemistry

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ChimeraX on Apple M1 CPUs

News just in from ChimeraX team https://www.rbvi.ucsf.edu/chimerax/data/czi-nov2021/apple_m1.html.

We are making a version of our ChimeraX molecular graphics program that runs natively on Apple's new M1 CPUs for faster interactive calculations. We'll report some speed-up timings and describe difficulties porting from Intel to the Apple M1 CPU. A native Apple M1 version of ChimeraX is not yet available, but we expect to release it within 6 months.

Difficulties porting ChimeraX to Apple M1 CPUs

  • ChimeraX Python and C++ code needs no changes.
  • ChimeraX uses 90 packages developed by others.
  • 60 are pure Python from the PyPi repository.
  • 30 are binary packages that need Apple M1 versions.
  • 6 binary packages do not have Apple M1 distributions: ambertools, h5py, imagecodecs, netcdf4, pytables, scipy.
  • Qt 6 window toolkit is distributed for Apple M1 but not Qt 5.
  • ChimeraX uses Qt 5, the stable Qt version from 2012 - 2021.
  • Qt 6 with html support was released September 2021.
  • Apple M1 applications must be either all native M1 binaries or all Intel binaries, no mixing.
  • Need to distribute either a large univeral package that includes both Intel and M1 binaries, or two separate ChimeraX versions.

Potential advantages of native Apple M1 ChimeraX

  • Better OpenGL driver stability with Apple M1 GPU.
  • No graphics driver crashes among 43 ChimeraX bug reports in 2021 with Apple M1.
  • About 100 ChimeraX graphics driver crashes reported on Intel Macs in past 2 years.
  • Better C++ crash stack traces with native M1 app than with Intel emulation.
  • Intel ChimeraX crashes on M1 often give no C++ stack trace.
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UCSF ChimeraX version 1.4 has been released

 

ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from https://www.rbvi.ucsf.edu/chimerax/

Updates since version 1.3 (Dec 2021) include:

  • search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures
  • display AlphaFold predicted aligned error (PAE) plots
  • can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR)
  • AlphaFold prediction of multimers (of limited size) on Google Colab
  • independent centers of rotation available as mouse mode
  • join models with Build Structure tool or command
  • define axes for display and/or use in measurements
  • increase/decrease VDW radii relative to their current values
  • switch PDB residue numbering scheme (author/canonical/uniprot)
  • align sequences with Clustal Omega or MUSCLE
  • calculate % identity in sequence alignments
  • window toolkit updated to Qt 6.2.3 from 5.15.2

There is a ChimeraX workshop here https://youtu.be/M2K72Kgk718.

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Accessing Alphafold2 from ChimeraX

 

A new video showing how to access Alphafold2 from ChimeraX.

We run AlphaFold to predict the structure of the protein avidin (from chicken). We start the computation using ChimeraX which runs it on Google Colab servers.

Added to the RSC CICAG Open Source tools for Chemistry play list https://www.youtube.com/playlist?list=PLBQwbn0mPhvWfOx6ce_vUjr54ftLBmSH0.

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