I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

I am still finding interesting things to do with protein #embeddings — now coloring #AlphaFold models by the 3-component UMAP reduction of the per-residue embedding. Look at those bright Phe residues in the disordered region — somehow #protT5 encodes them as "different" than the others.

In my experience so far these protein language models are uncannily able to highlight the same regions of the protein that I'm interested in already.

(#ChimeraX, using a sequence coloring format file)

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!