#PDB

Six Grandfathers Mountain6G
2025-05-15

@ksaj @heidilifeldman
RE
Why are the always trying to get around their own crimes?

Because they do a lot of criming😭

Like, IMO weakening the security of the US🥶

Allowing, not stopping, looking the other way, Director of National Intelligence to do the presidential daily brief

It was done by the CIA and not done by a Trump cronie "approved" by R Senators.

But, DNI has oversite 🤠of ALL THE OTHER intel agencies (15 of them)

2025-05-12

#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

politico.com/news/2025/05/09/t

2025-05-12

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.

∂𑁨í 🕊 d2i@mk.phreedom.club
2025-04-17

#KOReader
An
#ebook #reader application supporting PDF, DjVu, EPUB, FB2 and many more formats, running on #Cervantes, #Kindle, #Kobo, #PocketBook and #Android devices.
http://koreader.rocks/
#EPUB #PDF #DjVu #XPS #CBT #CBZ #FB2 #PDB #TXT #HTML #RTF #CHM #DOC #MOBI #ZIP

Dave nλ=2dsinθxtaldave@xtaldave.net
2025-04-01

New Presidential executive order on proteins:

All amino acids now to be right w̶i̶n̶g̶ handed.

Leftist amino acids to be outlawed.

(Also, Z-DNA is deemed to be Communist, and is prohibited.)

Trans- and cis- peptide bonds to be banned.

Non-binary amino acid Glycine to be banned.

Proline is not a real amino acid and will be banned immediately.

Phenylalanine looks and sounds a bit like Fentanyl, banned immediately.

@strucbio #StructuralBiology #PDB

Well, I am sad. I’ve been trying to debug code running on a #thread in #Python. I’ve used #PyCharm, #pdb, and #ipdb. Nothing stops at a breakpoint on the thread. So much happening on the thread is invisible to me. Ugh.

Eugene F. Baulinfebos
2025-03-05

Our ARTEMIS tool for aligning 3D structures of nucleic acids is now equipped with a detailed Tutorial, covering structure searches, sub-optimal matches, and even PDB/CIF conversion, check it out:

github.com/david-bogdan-r/ARTE

Prash Singhprash_singh
2024-12-02

Announced: The PDB Molecule of the Month for December is the flagellar motor! An informative article paired with a beautiful artwork by Dr. David Goodsell. pdb101.rcsb.org/motm/300

Bacterial flagellar motor in clockwise orientation, bound to CheY.
@infosec_jcp 🐈🃏 done differentlyinfosec_jcp@infosec.exchange
2024-11-09
Guillaume GaullierGuillawme@fediscience.org
2024-11-07

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.
wwpdb.org/news/news?year=2024#

#StructuralBiology #CryoEM #crystallography #NMR

Guillaume GaullierGuillawme@fediscience.org
2024-10-10

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

Guillaume GaullierGuillawme@fediscience.org
2024-10-10

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

Guillaume GaullierGuillawme@fediscience.org
2024-10-10

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

Dave nλ=2dsinθxtaldave@xtaldave.net
2024-08-30

Handy guide to Post translational modifications in the PDB from @glycojones and colleagues.

@strucbio #StructuralBiology #MX #PDB #Crystallography
Post-translational modifications in the Protein Data Bank journals.iucr.org/paper?pea500

GripNewsGripNews
2024-08-11

🌘 用GDB通過PDB調試運行中的Python腳本
➤ 如何用GDB和PDB調試正在運行的Python腳本
disconnect3d.pl//2024/08/04/de
本文介紹瞭如何使用GDB調試正在運行的Python腳本,透過向Python解釋器進程附加來實現目標。
+ 詳細解釋了在Linux上使用GDB通過PBD來調試正在執行的Python腳本,很具啟發性。
+ 對於想要了解如何在開發中處理已經運行中的程序時有很大幫助。

2024-07-24

#alanine #pymol #pdb
​:blobfoxaww:​

2024-06-27

The leaked files from the disclosure seclists.org/fulldisclosure/20 have since been removed from developercommunity.visualstudi. Someone on Reddit (reddit.com/user/TapAppropriate) posted a direct link to a download from azurewebsites.net that's been taken down now too. The #InternetArchive has the files still at:
web.archive.org/web/2024062421

Unfortunately 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

---

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: 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

---

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

2024-05-31

@mich_waveform yes!

Conventionally, I just use `breakpoint()` in my code - though `import pdb; pdb.set_trace()` was my goto pre #python 3.7 I think?

#pudb is a *fantastic* command line interface for debugging, but regular #pdb is reasonable enough for me.

pudb bridges the gap when I really want that more advanced UI, but those are the kinds of things that a good GUIDE _is_ actually better at.

But that's why I celebrate everyone's approach -- whatever works best for you is what to use! 🥰

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