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...
July 24, 2025 at 2:44 AM
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...
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....
February 24, 2026 at 7:55 PM
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 cheat sheet brought to you by Alejandro Pereira. www.rbvi.ucsf.edu/chimerax/dat...
February 20, 2026 at 12:21 AM
ChimeraX cheat sheet brought to you by Alejandro Pereira. www.rbvi.ucsf.edu/chimerax/dat...
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...
September 25, 2026 at 12:43 AM
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...
ChimeraX 1.9 has been released! Session view can now be automatically saved and restored. New 'Find Cavities' tool identifying pockets in models. www.rbvi.ucsf.edu/chimerax/dow...
Download UCSF ChimeraX
www.rbvi.ucsf.edu
December 14, 2024 at 9:08 AM
ChimeraX 1.9 has been released! Session view can now be automatically saved and restored. New 'Find Cavities' tool identifying pockets in models. www.rbvi.ucsf.edu/chimerax/dow...
Density animation generated using ChimeraX, using "cootmode" display settings from chimerax-trimmings.
Movie recorded thusly:
cofr showpivot false; movie record; rock y 30; wait 600; movie encode ~/Desktop/rock_movie_more.mp4 framerate 40; stop
Movie recorded thusly:
cofr showpivot false; movie record; rock y 30; wait 600; movie encode ~/Desktop/rock_movie_more.mp4 framerate 40; stop
June 13, 2025 at 6:34 PM
Density animation generated using ChimeraX, using "cootmode" display settings from chimerax-trimmings.
Movie recorded thusly:
cofr showpivot false; movie record; rock y 30; wait 600; movie encode ~/Desktop/rock_movie_more.mp4 framerate 40; stop
Movie recorded thusly:
cofr showpivot false; movie record; rock y 30; wait 600; movie encode ~/Desktop/rock_movie_more.mp4 framerate 40; stop
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...
May 1, 2025 at 12:35 AM
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...
Thank you so much for integrating Foldseek into the great ChimeraX.
March 7, 2025 at 8:47 AM
Thank you so much for integrating Foldseek into the great ChimeraX.
ChimeraX 1.9 has been released and is available now on our website
Download UCSF ChimeraX
www.cgl.ucsf.edu
December 13, 2024 at 5:49 PM
ChimeraX 1.9 has been released and is available now on our website
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...
January 16, 2026 at 9:50 PM
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...
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...
March 6, 2025 at 11:06 PM
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...
We are sharing a tool developed initially for internal use called VOSE (Volume Operations Simplified Edition) today. It is written specifically to work in ChimeraX (version 1.5+), with no additional libraries necessary to be installed.
github.com/jparmachelab...
github.com/jparmachelab...
GitHub - jparmachelab/ChimeraX-VOSE: ChimeraX Volume Operations Simplified Edition
ChimeraX Volume Operations Simplified Edition . Contribute to jparmachelab/ChimeraX-VOSE development by creating an account on GitHub.
github.com
June 14, 2026 at 10:10 PM
We are sharing a tool developed initially for internal use called VOSE (Volume Operations Simplified Edition) today. It is written specifically to work in ChimeraX (version 1.5+), with no additional libraries necessary to be installed.
github.com/jparmachelab...
github.com/jparmachelab...
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....
July 10, 2026 at 7:43 PM
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....
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...
March 6, 2026 at 9:08 PM
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...
Made a little plugin for cryoEM map subboxing in ChimeraX: github.com/mgflast/Chim...
July 31, 2026 at 9:06 AM
Made a little plugin for cryoEM map subboxing in ChimeraX: github.com/mgflast/Chim...
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...
Accuracy depends on how similar the ligands and binding pockets are to existing experimental structures.
www.rbvi.ucsf.edu/chimerax/dat...
August 20, 2025 at 9:01 PM
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...
Accuracy depends on how similar the ligands and binding pockets are to existing experimental structures.
www.rbvi.ucsf.edu/chimerax/dat...
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
July 8, 2026 at 5:00 AM
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
colored October sketches for cHimerAx and Furregan!
April 25, 2025 at 9:07 PM
colored October sketches for cHimerAx and Furregan!
Made a little prototype extension so these notes can be read/written navigated in ChimeraX too - the idea is to have a kind of "track changes" for building/analyzing/discussing structures that is intrinsically linked to the relevant sites
April 3, 2026 at 9:31 PM
Made a little prototype extension so these notes can be read/written navigated in ChimeraX too - the idea is to have a kind of "track changes" for building/analyzing/discussing structures that is intrinsically linked to the relevant sites
So it turns out that you can visualise 3D cells really well #chimeraX, better than #napari dare I say. Very intuitive. You can adjust different representations, surface, volume, etc, and to make a movie. I'm blown away because I learned ChimeraX for protein structure visualisation, not cells! 🤯
July 23, 2026 at 8:09 PM
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...
March 6, 2025 at 11:25 PM
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...
Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...
June 18, 2026 at 3:37 AM
Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...