Recent searches

No recent searches

Search options

Only available when logged in.
shakedown.social is one of the many independent Mastodon servers you can use to participate in the fediverse.
A community for live music fans with roots in the jam scene. Shakedown Social is run by a team of volunteers (led by @clifff and @sethadam1) and funded by donations.

Administered by:

Server stats:

270
active users

shakedown.social: AboutStatusProfiles directoryPrivacy policy

Mastodon: AboutGet the appKeyboard shortcutsView source codev4.4.1

#af2

0 posts0 participants0 posts today
FreddyB Aviation Photography<p>USAF C-32A 99-0004 as Air Force 2 with the twilight reflected along her length departs Moffett Field, Sunnyvale, California May 16th, 2025 <a href="https://sfba.social/tags/USAF" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>USAF</span></a> <a href="https://sfba.social/tags/C32A" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>C32A</span></a> <a href="https://sfba.social/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> <a href="https://sfba.social/tags/VPOTUS" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>VPOTUS</span></a> <a href="https://sfba.social/tags/KNUQ" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>KNUQ</span></a> <a href="https://sfba.social/tags/Moffett" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Moffett</span></a> <a href="https://sfba.social/tags/twilight" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>twilight</span></a> <a href="https://sfba.social/tags/militaryaviation" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>militaryaviation</span></a> <a href="https://sfba.social/tags/AvGeek" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AvGeek</span></a> <a href="https://sfba.social/tags/spotter" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>spotter</span></a> <a href="https://sfba.social/tags/photography" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>photography</span></a> <a href="https://sfba.social/tags/aircraft" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>aircraft</span></a> <a href="https://sfba.social/tags/milair" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>milair</span></a> <a href="https://sfba.social/tags/nikon" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>nikon</span></a></p>
Guillaume Gaullier<p>After this exhaustive first pass inspecting each residue, I try to clear the biggest problems flagged by <a href="https://fediscience.org/tags/ISOLDE" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ISOLDE</span></a>'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 <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> 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.<br>12/19</p>
Guillaume Gaullier<p>During this stage I often get help from two additional sources of information:<br>1. The model from <a href="https://fediscience.org/tags/model_angelo" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>model_angelo</span></a> sometimes helps moving the <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> 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.<br>10/19</p>
Guillaume Gaullier<p>At this point, I use <a href="https://fediscience.org/tags/ISOLDE" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ISOLDE</span></a> 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 <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> 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.<br>8/19</p>
Guillaume Gaullier<p>Using <a href="https://fediscience.org/tags/ChimeraX" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ChimeraX</span></a>, I dock these <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> 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 <a href="https://fediscience.org/tags/model_angelo" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>model_angelo</span></a>. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.<br>5/19</p>
Guillaume Gaullier<p>Having identified the proteins, I fetch their <a href="https://fediscience.org/tags/AlphaFold2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AlphaFold2</span></a> predictions from AlphaFold-DB, or compute them if not in the DB. <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> models have excellent geometry and complete sequence correctly numbered, so they are excellent starting models. I rarely use <a href="https://fediscience.org/tags/PDB" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PDB</span></a> 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 <a href="https://fediscience.org/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> models, only the 20 standards amino acids).<br>4/19</p>
Oreo Speedwagon II 🇺🇸 🇺🇦 🇨🇦<p><span class="h-card" translate="no"><a href="https://newsie.social/@stevesilberman" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>stevesilberman</span></a></span> His plane? HIS plane??? Hey J.D. It's the taxpayers' plane. Jerk.</p><p><a href="https://mas.to/tags/Vance" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Vance</span></a> <a href="https://mas.to/tags/AF2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AF2</span></a> <a href="https://mas.to/tags/Harris" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Harris</span></a> <a href="https://mas.to/tags/Trump" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Trump</span></a> <a href="https://mas.to/tags/DictatorInWaiting" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DictatorInWaiting</span></a></p>
TrendingLive feeds
About