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ChimeraX

@chimerax.ucsf.edu
942 followers 4 following 30 posts

UCSF ChimeraX - software for visualizing biomolecules

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ChimeraX @chimerax.ucsf.edu · 25/09/2026
Make natural language requests to ChimeraX with the new Pellaeon plugin developed by Yam Amir that works with many free and paid large language models. Get Pellaeon using ChimeraX menu Tools / More Tools.... cxtoolshed.rbvi.ucsf.edu/apps/chimera...
PAR1 molecular structure shown in ChimeraX using Pellaeon chat bot.
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ChimeraX @chimerax.ucsf.edu · 14/07/2026
A new ChimeraX tool Geopickr from Ben Barad's lab oversamples dense protein arrays on spheres, tubes, filaments, and arbitrary surfaces for geometry-assisted subtomogram averaging. Available from ChimeraX menu Tools / More Tools....
Image of cell membrane with Geopickr picked particles.
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Reposted by ChimeraX
James Lingford @jameslingford.bsky.social · 17/06/2026
Something that I am very excited about: the latest version of @chimerax.ucsf.edu (v1.12) now has a cavity analysis function
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ChimeraX @chimerax.ucsf.edu · 10/07/2026
A new ChimeraX tool MorphometricsX from Ben Barad's lab colors cell membranes in electron tomography according to thickness, curvature and other properties. Available from ChimeraX menu Tools / More Tools....
ChimeraX user interface for MorphometricsX
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ChimeraX @chimerax.ucsf.edu · 20/03/2026
An endowed professorship in biocomputing, visualization, and informatics at UC San Francisco is open, duties include leading ChimeraX future developments. aprecruit.ucsf.edu/JPF05877
aprecruit.ucsf.edu
Faculty Position – In-Residence
University of California, San Francisco is hiring. Apply now!
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ChimeraX @chimerax.ucsf.edu · 11/03/2026
ChimeraX works with Acer, Sony and Samsung 3D eye-tracking displays that do not use glasses. Thanks to Andre Michaelis for adding Samsung support and a 3D mouse pointer (menu Tools / More Tools... / XR3D). www.rbvi.ucsf.edu/chimerax/dat...
Samsung 3D display showing a molecule, 3D mouse pointer, and atom identification label.
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ChimeraX @chimerax.ucsf.edu · 06/03/2026
The new circoscontacts ChimeraX command shows circular residue contact plots. Created by Peter Carlton at Kyoto University and available from ChimeraX menu Tools / More Tools... cxtoolshed.rbvi.ucsf.edu/apps/chimera...
ChimeraX Contact Circos plot.
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ChimeraX @chimerax.ucsf.edu · 24/02/2026
The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....
ChimeraX screenshot showing CubeNTube plugin.
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ChimeraX @chimerax.ucsf.edu · 20/02/2026
ChimeraX cheat sheet brought to you by Alejandro Pereira. www.rbvi.ucsf.edu/chimerax/dat...
Cheat sheet for ChimeraX.
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ChimeraX @chimerax.ucsf.edu · 16/01/2026
The ChimeraX DAQplugin computes DAQ scores showing the agreement between atomic models and cryoEM maps. Available from ChimeraX menu Tools / More Tools. cxtoolshed.rbvi.ucsf.edu/apps/chimera...
PDB 7jsn colored by DAQ scores of fit in cryoEM map.
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ChimeraX @chimerax.ucsf.edu · 30/12/2025
CiliaBuilder creates 3D structural models of cilia and centrioles within ChimeraX constructing microtubule-based architectures, including doublets, triplets, and various ciliary configurations from theoretical models. youtu.be/OEJJZ-qedoY
ChimeraX screenshot showing CiliaBuilder user interface.
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ChimeraX @chimerax.ucsf.edu · 20/08/2025
Here's how to predict binding of tens or hundreds of small molecules to protein assemblies using Boltz 2 in ChimeraX. Accuracy depends on how similar the ligands and binding pockets are to existing experimental structures. www.rbvi.ucsf.edu/chimerax/dat...
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ChimeraX @chimerax.ucsf.edu · 24/07/2025
ChimeraX 1.10.1 is available now, incorporating critical bugfixes since last month's release. www.cgl.ucsf.edu/chimerax/dow...
cgl.ucsf.edu
Download UCSF ChimeraX
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ChimeraX @chimerax.ucsf.edu · 24/07/2025
ChimeraX daily builds can predict binding affinity of small molecules using Boltz 2 on your Mac, Windows or Linux computer. www.rbvi.ucsf.edu/chimerax/dat...
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ChimeraX @chimerax.ucsf.edu · 27/06/2025
UCSF ChimeraX version 1.10 has been released! www.rbvi.ucsf.edu/chimerax/dow...
rbvi.ucsf.edu
Download UCSF ChimeraX
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ChimeraX @chimerax.ucsf.edu · 10/06/2025
LocScale-SURFER is a ChimeraX extension that shows cryoEM density maps after removing detergent micelles based on output from command-line program Locscale-2.0. Install it using ChimeraX menu Tools / More Tools.... More details at cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Membrane protein shown with part of micelle density removed to reveal transmembrane protein regions.
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ChimeraX @chimerax.ucsf.edu · 31/05/2025
ChimeraX can predict protein, nucleic acid and ligand atomic models on your Mac, Windows or Linux computer using Boltz. This table shows how long it takes in minutes using different computers. www.rbvi.ucsf.edu/chimerax/dat...
Table of Boltz prediction run times for different computers and different size molecular assemblies.
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ChimeraX @chimerax.ucsf.edu · 15/05/2025
Due to a mismatched version of SciPy targeting fewer macOS versions than we support, users with ARM macs running macOS below 14 should use the 1.10 release candidate or 1.11 daily builds. Since we are close to a release, a 1.9.1 is not planned at this time.
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ChimeraX @chimerax.ucsf.edu · 07/05/2025
The first release candidate for ChimeraX 1.10 is available now. www.cgl.ucsf.edu/chimerax/dow...
cgl.ucsf.edu
Download UCSF ChimeraX
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ChimeraX @chimerax.ucsf.edu · 01/05/2025
ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics. www.rbvi.ucsf.edu/chimerax/dat...
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ChimeraX @chimerax.ucsf.edu · 20/03/2025
ChimeraX AlphaFold prediction is working again. It was broken the past couple days because Google Colab updated from Python library numpy from version 1 to 2. Thanks to ColabFold developer Milot Mirdita for making Colabfold work with numpy 2.
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ChimeraX @chimerax.ucsf.edu · 19/03/2025
We've just been notified that our previous article in Protein Science (2023) is among the 10 most cited papers for that year! You can find 'UCSF ChimeraX: Tools for structure building and analysis' at doi.org/10.1002/pro....
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ChimeraX @chimerax.ucsf.edu · 17/03/2025
ChimeraX can be used to find pockets and cavities in protein structures using the Find Cavities tool or kvfinder command. This feature is available in daily builds from 10 March 2025 or later.
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ChimeraX @chimerax.ucsf.edu · 06/03/2025
ChimeraX can cluster different backbone conformations of distantly related proteins found with Foldseek, here clustering similar structures to CRAF kinase. www.rbvi.ucsf.edu/chimerax/dat...
Two clusters of proteins with similar structure to CRAF kinase PDB 8jnb found with Foldseek and clustered with UMAP.
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ChimeraX @chimerax.ucsf.edu · 06/03/2025
ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...
Nipah virus G protein with 16813 ligands (mostly waters) mapped from similar structures.
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ChimeraX @chimerax.ucsf.edu · 06/03/2025
ChimeraX can display deep mutational scan data where all possible single mutations of a protein are assayed using high-throughput experiments. www.rbvi.ucsf.edu/chimerax/dat...
Critical residues of ABCg2  seen in deep mutational scans.
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ChimeraX @chimerax.ucsf.edu · 06/03/2025
Sony Spatial Reality 3D display shows molecular structures and electron microscopy data at HD resolutions with no glasses. www.rbvi.ucsf.edu/chimerax/dat...
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ChimeraX @chimerax.ucsf.edu · 06/03/2025
Anisotropic B-factors can now be shown as ellipsoids in ChimeraX daily builds, shown here for the heme in myoglobin. www.rbvi.ucsf.edu/chimerax/fea...
B-factor ellipsoids for heme in myoglobin.
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ChimeraX @chimerax.ucsf.edu · 13/12/2024
ChimeraX 1.9 has been released and is available now on our website
cgl.ucsf.edu
Download UCSF ChimeraX
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