#pdb — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #pdb, aggregated by home.social.
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Did you know that you can add aliases to PDB with a ~/.pdbrc file?
I made one over the weekend with some very helpful aliases.
https://treyhunner.com/2026/04/customizing-pdb-with-pdbrc/
I can now use these to inspect an object (note that "dir" and "vars" are like the dir() & vars() functions but better):
attrs x
dir x
vars xAnd I can find the source for a function with this:
src func
And print non-dunder locals nicely like this:
loc
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Proteinreinigung gescheitert? Forschende testen ein KI-Agenten-System, das automatisch ähnliche Proteine, Literatur, die #PDB und Methoden durchforstet, um Protokolle gezielt zu verbessern. Noch nicht laborgeprüft, aber vielversprechend - Der Artikel von Andrea Pitzschke: https://www.laborjournal.de/editorials/3457.php
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Can you answer this question about quitting #pdb without the extra confirmation? https://software.codidact.com/posts/295305
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@JoelKlebanoff @w7voa she won't use human capital. She'll use ai. Copy and paste the #pdb into #chatgopt and you make govt more efficient!
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#Trump doesn't need the President's #PDB
Trump has #StephenMiller to tell him everything Trump needs to know
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#Trump, meanwhile, reportedly doesn’t read the #PDB [doesn’t read period], & if the Politico report is accurate, he’s receiving in-person briefings only once every 10 days.
Broadly speaking, a couple of angles are worth keeping in mind in response to reporting like this. The first is probably obvious: Trump is dealing w/serious #NationalSecurity challenges—war in #Ukraine, a crisis in the #MiddleEast, #China expanding its global #influence, #domestic #security #threats…
https://www.politico.com/news/2025/05/09/trump-intelligence-briefing-frequency-00338946
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Politico’s report…added that the low number of #Trump’s briefings “is troubling to many in & around the #intelligence community….”
…different presidents have approached these briefings in different ways. George W. Bush received intelligence briefings on a nearly daily basis. Obama received briefings every other day, but he was known to be a voracious reader of the written President’s Daily Brief (the #PDB). Biden received an in-person briefing twice a week, but also an avid reader the PDB.
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CW: #uspol #PDB meaning updated #satire
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Since last month, the #wwPDB @PDBeurope considers preprints as publications that trigger release of the corresponding #PDB entries. This is great! It was always frustrating to see new preprints and have to wait for months until being able to look at maps and atomic models.
https://www.wwpdb.org/news/news?year=2024#670d48435697788818ca8c34 -
Once I'm happy, or I abandoned modeling the last remaining bits of unexplained density or fixing the last subtle model errors in places mostly irrelevant to the biological question the model is meant to answer, then I run `phenix.validation_cryoem` on the half-maps and atomic model. This gives me most of the numbers to put in the refinement table. And I deposit the model into the #PDB and maps into the #EMDB. Fin.
Happy to hear any comments or descriptions of how other people do this!
18/19
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This step is important for two reasons. The MD force field will produce a distribution of bond lengths and angles that doesn't quite match the distribution expected by the validation suite run by the #PDB deposition server, so omitting this last refinement will cause many things to be flagged as outliers. The other reason is that #ISOLDE doesn't (yet) refine atomic b-factors, so omitting this last refinement would leave nonsensical b-factors in the model.
15/19 -
Having identified the proteins, I fetch their #AlphaFold2 predictions from AlphaFold-DB, or compute them if not in the DB. #AF2 models have excellent geometry and complete sequence correctly numbered, so they are excellent starting models. I rarely use #PDB entries as starting models anymore. Rare exceptions: a PDB entry I deposited myself, or one containing a post-translational modification or non-natural amino acid I need (never present in #AF2 models, only the 20 standards amino acids).
4/19 -
The leaked files from the disclosure https://seclists.org/fulldisclosure/2024/Jun/7 have since been removed from https://developercommunity.visualstudio.com/t/Incorrect-code-generation-on-warbirded-b/10680249. Someone on Reddit (https://www.reddit.com/user/TapAppropriate1458/) posted a direct link to a download from azurewebsites.net that's been taken down now too. The #InternetArchive has the files still at:
https://web.archive.org/web/20240624211440/https://sendvsfeedback2-download.azurewebsites.net/api/fileBlob/file?name=B0cde770200a945109437927ba3fe4d67638537352993712632_ICE_REPRO.zip&tid=0cde770200a945109437927ba3fe4d67638537352993712632Unfortunately I cannot verify whether those files/the link was the original file or a re-upload. But at least all files within `ICE REPRO.zip/Linker/linkrepro.zip' match the size (in bytes) of the originals as given in the listing on seclists.
The file download from there has the sha256 hash:
d4c1a74f81e5259596466027ebac9f7eb026931c7cef02e5c37d884bbbb7f96f ICE_REPRO.zip
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In addition, the disclosure notes that the MS symbol server does (STILL ONLINE!) leak the PDB of warbird.dll if requested. A backup has been re-upped here: https://files.catbox.moe/8iz2qk.pdb
Again, the sha256 hash. This has been matched against the original served by the MS symbol server:
2e8b5e0c17b4a4693ed494444f347f22a2eed15bcade18a5ac25d370011f8aa5 warbird.dll.pdb
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I provide those hashes just for people to be on the safe side while analyzing the files. Keep in mind that accessing those files may be illegal.
#MSRP #leak #SecLists #Microsoft #WarBird #PlayReady #DRM #PDB #Widevine #PlayFair #Piracy
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Finally the #zalando #postgres #operator for #kubernetes supports a real #PDB, which works for all pods instead of only matching the primary :)
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56142 characters later i have another draft of pDBv1 - an encrypted password database format as a successor to pDBv0
https://github.com/TruncatedDinoSour/armour/blob/main/doc/d/pDB-1.md
#cryptography #database #encryption #passwords #pdb #fileformats
( still a work in progress but yeah )
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PDB molecule of the month: Hyaluronidases! #hyaluronicacid polysaccharides play many roles in the human body (joints, ECM, and more). Somehow these long sugars play a part in diseases from cancer to COVID. At the same time, you find them in creams and many other applications. The hyaluronidase enzymes cut and clip these long #carbohydrates and are crucial for managing HA molecules in the body. Read all about it at the #PDB : https://pdb101.rcsb.org/motm/291
#structuralbiology #glycotime -
A commentary by Derek Lowe (https://www.science.org/content/blog-post/alphafold-s-place-world) explaining the significance of our article,
"AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023) (https://www.nature.com/articles/s41592-023-02087-4)
#Crystallography #MX #CryoEM #PDB #Alphafold #StructuralBiology @strucbio
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Hi Structural biologists!
Here is our article that helps you make the case that the experiment is still very much needed: https://www.nature.com/articles/s41592-023-02087-4
"AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023)
#Crystallography #MX #PDB #Alphafold #StructuralBiology @strucbio
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@lucas_nivon Thanks for sharing it Lucas, certainly worth reading to see how far one can get with 6k #protein - small molecule complexes in #PDB. I guess more people have something similar on their TODO lists...
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#AsmResolver 5.2.0 is out now.
This version includes read support for many more #PDB symbols, #dotnet AppHost patching, .NET TypeSignature::IsAssignableTo(type), QoL improvements and bug fixes.
👉 Full changelog and download links:
https://github.com/Washi1337/AsmResolver/releases/tag/v5.2.0 -
#AsmResolver 5.2.0 is out now.
This version includes read support for many more #PDB symbols, #dotnet AppHost patching, .NET TypeSignature::IsAssignableTo(type), QoL improvements and bug fixes.
👉 Full changelog and download links:
https://github.com/Washi1337/AsmResolver/releases/tag/v5.2.0 -
#Funfact #structuralbiology The #PDB code for the crystal structure of the active form of the MAP #kinase ERK2 is 2ERK 😬 (and the inactive form was 1ERK)
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#AlphaFold predictions solve the #Crystallographic #PhaseProblem problem with an 85% success rate
(187 of 215 #PDB entries originally determined with experimental phasing automatically redetermined with iterative AlphaFold prediction and rebuilding)
https://www.biorxiv.org/content/10.1101/2022.11.18.517112v1 -
#Checkliste für #Vim als #IDE für #Python
#Checkliste für die #Vervollständigung der #Datei #Vimrc
Bezüglich #Debugging sagt der Vortragende er benutze dafür nicht Vim, sondern #iPython und #ipdb (#IPython #pdb).
I will insert breakpoints with a shortkey, open another terminal window and start my program, waiting until the breakpoint is hit and then inspect the scope.
