Blake Riley

Proudly Melburnian, fuelled by coffee, dabbling in music & 3D printing.
Now in NYC, Postdoc @asrc_gc: allostery in human PTPs w/ #xrays & #xtals.

Views my own.

[Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social @RolandDunbrack]

Demis -- I think AlphaFold3 is really exciting. As Reviewer #3, I got great results from the server. I tried hard to get @Nature to urge you to release the code but was unsuccessful. I did not get it for re-review so I don't know if you responded. So why no code? @GoogleDeepMind

[Blake Riley @blake_riley]

@DanielKeedy Yep. A foreshock ahead of the big one, when the sun falls out of the sky on Monday?

[Blake Riley @blake_riley]

Great to see former colleagues @DanielKeedy, Liliana & @DrAliEbrahim connect-the-(diffraction)-dots I left behind in my postdoc! Congrats to LG on her first 1st auth too!

[Daniel Keedy @DanielKeedy]

New #keedylab #preprint! How does a protein structure differ at physiological temp vs. high pressure (vs. traditional cryo temp)? Liliana Guerrero (Margent) & @DrAliEbrahim looked into it: https://t.co/zUcKZiBECj Great collab w/ Qingqiu Huang & Aaron Finke at @MacCHESSCornell !

[Blake Riley @blake_riley]

@ingeneousmachin No worries - I got really excited about this too, but looks like for now I'll be hammering work's GPUs. Also thanks for sharing a tracking GitHub issue I can subscribe to!

[Blake Riley @blake_riley]

@ingeneousmachin Sure, this change makes the code run, but I think it's on CPU.
I think the actual decision on device is in rfdiffusion.inference.model_runners.Sampler.initialize()?

[Blake Riley @blake_riley]

@ingeneousmachin @YanEVgene Cheers for the instructions Jake!

Perhaps a little simpler on this step: I'm just replacing the imports only with `from contextlib import nullcontext as nvtx_range`.
Then calls to nvtx_range act as no-ops, without needing to un-indent them.

[Blake Riley @blake_riley]

@fraser_lab @stephanie_mul @yifan_ucsf @DocuSign Huge congrats Steph!

[Blake Riley @blake_riley]

I think it's time to admit defeat and declare tab-bankruptcy.

[Blake Riley @blake_riley]

@andrewwhite01 Android here: not really.
The Latin characters are all the same width, but whitespace, punctuation is not --- so alignment is not consistent. Those 'other characters' might be halfwidth though?

[Blake Riley @blake_riley]

@fraser_lab I'm assuming your map transforming is done using matrix_copy?
If that's not enough, does "set matrix_mode, 1" help? (Might not, haven't tested it myself).
I'm interested, since I have the same sentiment towards chimera syntax.

[Blake Riley @blake_riley]

@FrankABOlivier Huge congrats mate!

[Daniel Keedy @DanielKeedy]

The Keedy lab at the @asrc_gc is seeking a computational #postdoc! Lots of exciting project directions linking protein structure, dynamics, allostery, bioinformatics, design, ... We're well funded, & are in a green pocket of NYC. Apply here: https://t.co/Gc0kRLoG3K RTs welcome!

[Blake Riley @blake_riley]

@GntlmnScientist @lulu_catapano Yeah, that's a frustration for me too. Built-in keybindings and NCS ghosting are dropped (for the moment?), as per the release notes.
I'm hoping they come back real soon.

[Blake Riley @blake_riley]

@LucasFarnung @AnaCasanal It's not yet ready for Mac.

People involved in the brewsci/homebrew-bio (@brew_sci) community are working on it.
When the work is done, it'll be as easy as `brew install coot` 🍻🎉.

[Blake Riley @blake_riley]

@NJ_McKenzie Nice! Have you put a 3D printer near your desk yet? :P

[Matt Parker @standupmaths]

If you’ve not had 11:12am in your local time yet today: get ready for the palindrific 2021-11-22-11:12:02

The rest of us can wait for 11 December.

[Blake Riley @blake_riley]

Big fan of the Gemmi toolkit for #xtallography (@ccp4_mx / GΦL), and its cif & mtz command-line tools.
Now also available via : 💻 `brew tap brewsci/bio; brew install gemmi`
👏 @MacHomebrew & @brew_sci

[Dr Sheena McGowan @DrSheenaMcGowan]

Are you interested in discovering news ways to combat antimicrobial resistance? We have an exciting opportunity for an early career molecular microbiologist to join our multidisciplinary team. See details here and please feel free to share!
https://t.co/0wAJzi4fdH

[Blake Riley @blake_riley]

@kaczmarski_joe Yeah, this is me.
Side chains & cartoon, outlines are great.
Surface reps, not so much - I find it more useful to tweak the depth cue and ambient occlusion settings.

[Blake Riley @blake_riley]

I don't think I've ever seen a more perfect coffee mug! Thanks Eta!