Macs in Chemistry

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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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