Justin Westerfield

Progress report on my Relion bayesian polishing job on a local computer:

```
+ Performing loop over micrographs ...
166.67/166.67 hrs .....................~~(,_,">

+ Combining frames for micrographs ...
4.05/122.07 hrs .~~(,_,">
```

I think it's going well.

#CryoEM

Zotero finally has an Android app 🙌

Seems like some of this could be alleviated with a temporary visa given to those awaiting a visa renewal decision. Currently, non-EU citizens cannot leave Sweden while awaiting a decision, because there's no guarantee they would be able to return.

International PhD students advise against doctoral studies in Sweden - Universitetsläraren Sweden is no longer an attractive country for international early-career researchers, says the SULF Doctoral Candidate Association in a new report.

SULF's Doctoral Candidate Assocation warns internationals against starting a PhD Sweden and it seems like most of the complaint is with Migrationsverket, the Swedish Migration Agency. The negative effects of these excessive wait times are starting to pile up.

universitetslararen.se/2025/05/08/i...

The number of postdocs employed in Sweden keeps going up.

www.uka.se/om-oss/nyhet...

The program is out for the 2025 Membrane Protein Folding GRS! Applications are open until the end of May. Join us this June in Castelldefels, Spain!
🧪🧬🥼🔬
www.grc.org/membrane-pro...

Calling all membrane/membrane protein folks! Join us this summer in Barcelona for the Membrane Protein Folding Gordon Conference and Seminar. GRS chaired by @justmwest.bsky.social and myself! We are soliticiting abstracts from trainees for talks! Deadline - April 6.

www.grc.org/membrane-pro...

Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes - Nature Communications The organization of membrane proteins is critical to cellular function. Here the authors explore how computational protein design, MD simulation, and cell-free systems can be combined to elucidate how...

Proteins preferentially insert into membranes that have a similar hydrophobic thickness to the protein, even without cells or chaperones! Implies sufficiency of physical properties of membranes and proteins for proper sorting to organelles.

Cool paper! 🧪

doi.org/10.1038/s414...

Feels a bit strange to call out preprints specifically, as if preprints constitute some sort of threat.

At least there's hope that things will change by Feb 1st.

Oh my. This would have enormous ripple effects throughout research. Like tsunami effects.

I'll go with... 601? 🤔

It's especially pernicious that getting anything done requires ignoring all the Bad Things in the news, yet that plays directly into the hand of the Bad Things

Or on Mac:
Alt+- for en dash (–)
Alt+shift+- for em dash (—)

On windows it's apparently the same with one caveat—you have to use the '-' on the numeric keypad (haven't tried though)

Very nice work outlining a new method to determine dimerization energies of TMDs in unbiased MD simulations 🧪

My colleague and I are co-chairing the GRS on Membrane Protein Folding this Summer near Barcelona, Spain ⛱️

If you are a grad student or postdoc and work on membrane protein folding, apply!

www.grc.org/membrane-pro...

As academic Bluesky grows, researchers find strengths—and shortcomings Platform fosters collegial interactions among scientists, but potentially limits interactions beyond the academic community

link to original article: www.science.org/content/arti...

(iv) The head of each agency shall include in every contract or grant award:
...
(B) A term requiring such counterparty or recipient to certify that it does not operate any programs promoting DEI that violate any applicable Federal anti-discrimination laws.

Insane.

I like my lab coats to feel like I'm wearing an armored vehicle but also a snuggie

Is this because of the DEI components of the grants they review? Re: the exec. order for agencies to shut down all DEI activity?

Just learned that one of the most productive scientists I know uses a cardboard box as a reference manager.

I'll be over here existentially questioning the value of my neatly curated zotero library.

chaotic neutral

Does this account for the cost of clearing and smoothing the road? I wonder mountain bikes on natural terrain would fare against fish eFISHency.

Beautiful night in Stockholm 🌃

Amazing, thank you!!

If anyone knows of starter packs for biochemistry / biophysics, I would love to check them out!

Goodreads has a popular list of books everyone should read. It's 33k books. Reading a book a day, this would take 90 years. Goodreads, this is not a serious list.

Update: found this helpful documentation here

In case anyone finds this in the future, you have to turn the iterator into a list to use it more than once :)

python code showing two for loops, where only the second one should print.

Anyone familiar with BioPython? When I read a file with SeqIO, I see strange behavior.

If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine.

What am I missing?

Screenshot of email where they refer to a preprint titled ""

Something tells me they did not, in fact, read my preprint.

Has anyone figured out how to name the individual chains for a job in the #Alphafold3 server? The output of a job with mutliple chains just has them labeled as A, B, C, etc.