Macs in Chemistry

Insanely Great Science

ChemDoodle 3D v6.6 Update Available

Just got this message

We are pleased to introduce version 6.6 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $15, and we have a free trial available at: https://www.chemdoodle.com/3d

Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more.

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Comparing the M2 MacBook Air

I've updated the pages comparing the new Apple Silicon machines with those with the older Intel chips https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php. In addition to the MacBook Pro M1 Max I've now added the M2 MacBook Air.

M2MacBookAir

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5th Artificial Intelligence in Chemistry Symposium

The lineup for the 5th Artificial Intelligence in Chemistry Symposium (Thursday-Friday, 1st-2nd September 2022) is now complete for both oral and poster presentations. It really is a fantastic selection of topics and speakers and it is clear this event is now a highlight of the scientific calendar.

The details are here https://www.rscbmcs.org/events/aichem22/

Registration is now open, register here https://www.eventsforce.net/hg3/221/home. In person registration deadline: Monday 29th August 17:00 (BST)

AI_in_Chemistry_1st_Announcement-FINAL-pdf-722x1024

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WebMolKit: switched to Apache 2.0

Just saw this.

WebMolKit is a cheminformatics library that I’ve been working on for a long time: it runs on all kinds of JavaScript engines (browsers, desktop via Electron, command line via NodeJS). Its flagship feature is a powerful chemical sketcher, but it also has many supporting functions for handling molecules. As of now, the licensing terms have been switched to Apache 2.0, which basically means you are allowed to use it for non-open projects, as long as proper credit is given

I've updated the Open Source Cheminformatics Toolkits page

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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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