Mastodawn

⬆️ Air Force 2
🛩️ Aircraft: 🇺🇸 Boeing C-32A military passenger transport aircraft
🌀 Powerplant: 2x 🇺🇸 Pratt & Whitney PW2000-40 high-bypass turbofan engines
🗂️ S/N: 99-0004
🧑‍✈️Piloted by: United States Air Force
📍Destination: Moffett Federal Airfield KNUQ, California, USA
🧭 Origin: Los Angeles International KLAX, California, USA
🖼️ Prints available 🔗
📷 Fujifilm X-H2
🔭 Fujinon XF500mmF5.6
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#airforce
#usaf
#af2
#airforcetwo
#airforce2
#boeing
#c32
#knuq
#california
#usa
#planespotting
#aviation
#aviationphotography
#fujifilm
#fujixseries

FreddyB Aviation Photography May 17, 2025

USAF C-32A 99-0004 as Air Force 2 with the twilight reflected along her length departs Moffett Field, Sunnyvale, California May 16th, 2025 #USAF #C32A #AF2 #VPOTUS #KNUQ #Moffett #twilight #militaryaviation #AvGeek #spotter #photography #aircraft #milair #nikon

Egor Shkorov May 17, 2025

Air Force 2, a Boeing C-32, carrying Vice President of the United States, on an approach into KNUQ with a guest appearance by N755PA
🛩️ Aircraft 1️⃣: 🇺🇸 Boeing C-32A
🗂️ C-32 S/N: 99-0004
🧑‍✈️C-32 Piloted by: United States Air Force
🛩️ Aircraft 2️⃣: 🇮🇱 IAI LTD Gulfstream G280
💯 G280 Tail number: N755PA
📍Destination: KNUQ: Moffett Federal Airfield, California, USA
🧭 Origin: KLAX: Los Angeles International, California, USA
🖼️ Prints available, link in bio 🔗
📷 Fujifilm X-H2
🔭 Fujinon XF500mmF5
#airforce #usaf #af2 #airforcetwo #airforce2 #boeing #c32 #knuq #california #usa #planespotting #aviation #aviationphotography #fujifilm #fujixseries

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Guillaume Gaullier Oct 10, 2024

After this exhaustive first pass inspecting each residue, I try to clear the biggest problems flagged by #ISOLDE's validation tools (there are always some). Clashes are rare because atoms that are too close strongly repel each other under the MD force field. Ramachandran and rotamer outliers are rare in #AF2 models, but can arise when the simulation distorts the model. These problems often point to regions where the map is ambiguous, and where the model needs more attention.
12/19

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Guillaume Gaullier Oct 10, 2024

During this stage I often get help from two additional sources of information:
1. The model from #model_angelo sometimes helps moving the #AF2 model to the correct location, in these cases where a segment of the AF2 model doesn't match the map. Very often these discrepancies between map and prediction point to regions of the protein involved in conformational change, so I make a note of the chain ID and residue range so I know to take a close look later and compare to related structures.
10/19

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Guillaume Gaullier Oct 10, 2024

At this point, I use #ISOLDE to do manual fitting. If the map has a low resolution, I apply secondary structure restraints to the model. I start with a global simulation to let the model settle, which I let run until the dots in the interactive Ramachandran plot have reached an equilibrium. With #AF2 models, there shouldn't be Ramachandran outliers in the first place, but this is a good overview of how many residues are moving. I want them to settle in the nearest density before I continue.
8/19

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Guillaume Gaullier Oct 10, 2024

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

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Guillaume Gaullier Oct 10, 2024

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

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