James Lingford
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jameslingford.bsky.social
James Lingford
@jameslingford.bsky.social
170 followers 240 following 62 posts
PhD student in structural biology with @greening.bsky.social and @knottrna.bsky.social at Monash Uni. (he/him)

Interested in hydrogenases, evolution, protein design.

💻 https://www.jameslingford.com/
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jameslingford.bsky.social
Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
October 27, 2025 at 2:14 AM
jameslingford.bsky.social
Recent advances in the inference of deep viral
evolutionary history journals.asm.org/doi/10.1128/...

A review on structural phylogenetics utility and limitations
September 2, 2025 at 10:35 PM
jameslingford.bsky.social
Got this setup working where I can now run .ipynb notebooks right from inside the terminal with a combination of neovim, quarto, kitty, and this neovim plugin called molten: github.com/benlubas/mol...
Never have to abandon my precious vim setup again
July 11, 2025 at 7:29 AM
jameslingford.bsky.social
Some matplotlib work in progress
June 27, 2025 at 7:13 AM
jameslingford.bsky.social
Closer... I think at this point the solution lies in manually making a list of the hex codes, but that's for another day.
June 24, 2025 at 7:58 AM
jameslingford.bsky.social
Revisiting this topic now that I've forced myself to use PyMOL. Using this script to install the viridis family of colour palettes: github.com/smsaladi/pym... and running '"spectrum count, palette=magma, MODEL_NAME". The palette is not there still. They must modify the magma palette somehow
June 23, 2025 at 10:56 PM
jameslingford.bsky.social
Learning some Blender molecular nodes from @sarahjpiper.bsky.social @ccemmp-outreach.bsky.social
June 13, 2025 at 4:03 AM
jameslingford.bsky.social
Little shell scripting solution to the problem of finding a group A in column1 of a table that is entirely made up of group B in column2, and sorting for the biggest homogeneous grouping.
cat sortme.txt AAA foo AAA foo AAA foo AAA bar AAA bar BBB baz BBB baz CCC buzz sort sortme.txt | uniq -c | awk '{print $2,$1,$3}' | tee tmp | cut -f1 -d " " | uniq -c | join -o 1.1,1.2,2.2,2.3 -1 2 -2 1 - tmp | sort -k1,1n -k3,3nr
June 11, 2025 at 1:49 AM
jameslingford.bsky.social
I'm sick of typing "conda activate ENV" or "conda deactivate" to switch virtual environments. Now I've added a conda/mamba env switcher function that uses fzf to my ~/.zshrc.
Example of the fzf pop-up window for switching virtual environments function con () { mamba deactivate mamba activate "$(mamba info --envs | fzf --color 'border:#94e2d5,label:#cdd6f4' --reverse --tmux center,40%,40% | awk '{print $1}')" }
June 3, 2025 at 7:12 AM
jameslingford.bsky.social
Awk command to unwrap wrapped lines in fasta files. It's just neat!
awk '/^>/ {if (NR==1){print} else {printf "\n%s\n", $0}; next;} {printf "%s", $0}' input_file.faa
May 18, 2025 at 11:47 AM
jameslingford.bsky.social
Bioenergetics and the evolution of cellular traits [review]:
doi.org/10.1146/annu...
The energetic cost of cellular traits. Costs were calculated for individual proteins, for macromolecular complexes, or, in the case of Escherichia coli, for a single cell (shown for comparison). Calmodulin: 148 amino acids; ATP synthase: 4,955 amino acids (E. coli); dynein-2 motor: 12,084 amino acids (human, PDB ID: 6SC2); ribosome: 7,459 amino acids and 4,566 ribonucleotides (E. coli); vesicle: diameter 50 nm [membrane cost including proteins D 1.45 109 ATP mm 2 (86)]; nuclear pore complexes: 50–110 MDa (yeast and vertebrates) (2, 7); eukaryotic flagellum: 11 mm in length; and E. coli: estimated using the fourth cell budget method. Abbreviation: PDB ID, Protein Data Bank identifier.
May 10, 2025 at 5:05 AM
jameslingford.bsky.social
Reading old papers is cool because you never see this sort of casual tone anymore. www.sciencedirect.com/science/arti...
Not surprisingly, Fearnley and Walker [30] could confirm the sequence relationships with the ORF7 gene of the E. coli formate-hydrogen-lyase sys- tem. Once I realized the possible implications of these links, it was only logical to compare the sequence of the PSST gene [29] with those of the small subunits of nickel hydrogenases. The result is summarized in Fig. 1. For me, working on Complex I since the early 1970's and ex- ploring nickel hydrogenases since the late 1970's, this was a most amazing and also an amusing result. It indicates that one of the subunits of mitochondrial Complex I owes its structural information to the strictly conservative part present in the small subunit of all nickel hydrogenases
April 28, 2025 at 6:11 AM
jameslingford.bsky.social
ChimeraX tip: to get a lined border around an internal surface requires superposing two separate copies of your model. One for showing the surrounding cartoon structure, and the other showing just the surface (and select that one to give it a border)
www.jameslingford.com/blog/chimera...
Showing the surface of an internal cavity
April 19, 2025 at 6:56 AM
jameslingford.bsky.social
A modified viridis palette looks pretty nice too.
rainbow palette viridis; col modify blackness - 40; col modify whiteness - 40; col modify saturation - 50; col modify lightness + 30; lighting flat
April 17, 2025 at 11:00 AM
jameslingford.bsky.social
Made my terminal colours pretty, so now I'm a true hacker 😎
Catppuccin mocha palette applied to the following tools: - tmux - kitty - fzf - lsd - starship
April 17, 2025 at 10:52 AM
jameslingford.bsky.social
Alright, this might be as good as it gets:

rainbow palette magma; col modify blackness - 70; col modify whiteness - 80; col modify saturation - 70; col modify lightness + 22;

Increasing the lightness recreates the washed out transparent look without touching the transparency setting
RFdiffusion colour scheme in ChimeraX rainbow palette magma; col modify blackness - 70; col modify whiteness - 80; col modify saturation - 70; col modify lightness + 22; style ball; car style helix thickness 0.1; car style strand thickness 0.1; car style coil thickness 0.2; graphics sil width 1.5; lighting flat;
April 16, 2025 at 8:12 AM
jameslingford.bsky.social
Close to recreating it in ChimeraX:

1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20

Room for improvement, needs more desaturation
Trying to recreate the Baker lab RFdiffusion colour palette
April 16, 2025 at 6:31 AM
jameslingford.bsky.social
Something I've been wondering is what sort of settings the Baker lab is using to get these gorgeous PyMOL figures with? (I'm assuming it's PyMOL?)
A figure from the Baker labs RFdiffusion2 paper.
April 16, 2025 at 5:25 AM
jameslingford.bsky.social
Crash course in MD-sim today 💻
April 11, 2025 at 5:09 AM
jameslingford.bsky.social
Screwed up my Linux machine by trying to be clever. So here we go again with a fresh install
EndeavourOS Linux with i3wm desktop. Terminal = kitty and tmux. Shell = zsh.
April 7, 2025 at 1:06 AM
jameslingford.bsky.social
Hydrogenase-driven ATP synthesis from air
www.biorxiv.org/content/10.1...

New work from us where we put the Huc hydrogenase to work to see if it can generate a proton motive force. It can!
cc: @ashleighkropp.bsky.social @rhyswg.bsky.social @greening.bsky.social
Cartoon display of the bioenergetic scenario for Huc using either bd-I oxidase or bcc-aa oxidase as pmf-generating unit, driving ATP synthesis by the F1F o-ATP synthase.
March 19, 2025 at 3:21 AM
jameslingford.bsky.social
Goodbye @lorneproteins.bsky.social 2025, and thanks for the great conference. I'll miss getting to see hundreds of cockatoos whenever I step outside
Two sulfur crested cockatoos
February 12, 2025 at 9:59 PM
jameslingford.bsky.social
Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work
www.biorxiv.org/content/10.1...
January 13, 2025 at 9:09 AM