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Comments below this answer tell us that the Space Shuttle always remained in Earth's atmosphere. When it visited the Hubble Space Telescope or the ISS or Mir it was still in the thermosphere and simultaneously the ionosphere.

Of course the crew of any spacecraft in LEO will need to understand the impact of atmospheric drag since it has a continuous and significant effect on orbit altitude and phasing, and spacecraft attitude and tilt of solar panels can have a significant impact on that.

Question: But what (if anything) were crew taught about the ionosphere and its interaction with the Space Shuttle? Did they have to worry about spacecraft charging? Were there interactions between the ionosphere and communications systems they needed to understand? Were they briefed before launch on the effect of solar activity and space weather on the ionosphere and how that could impact aspects of a mission?

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    $\begingroup$ Can't recall much ever being said about this for any purposes beyond informational... $\endgroup$
    – Digger
    Oct 6, 2020 at 18:46
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    $\begingroup$ I know that spacecraft charging was a concern in the 1960s when docking was being considered, and Wikipedia reports that the Gemini 8 thruster incident may have been due to a static discharge en.wikipedia.org/wiki/… $\endgroup$ Oct 6, 2020 at 19:59
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    $\begingroup$ @DaveGremlin ISS has this gizmo and I'm assuming it mostly runs itself and generates a status report that crew and ground monitor. Shuttle is earlier and it's possible there were more uncertainties and/or surprises. There's one mission with these curious things and that might be a notable special case here and the basis of an answer (not sure), but what about all the others? Sadly though, there was no St. Elmo's fire. $\endgroup$
    – uhoh
    Oct 6, 2020 at 21:45
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    $\begingroup$ The words 'ionosphere' or 'charging' don't appear in the Shuttle Crew Training Catalog. The phrase 'space weather' appears once, in the description of a class the crew got on the Tissue Equivalent Proportional Counter. The context was expected radiation dosage. $\endgroup$ Oct 8, 2020 at 23:32
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    $\begingroup$ Unfortunately a lot of the natural environments stuff was run out of Marshal so I can't be definitive. $\endgroup$ Oct 9, 2020 at 0:15

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Combining a couple comments into an answer -- community wiki as none of this is my contribution.

Per user OrganicMarble, who worked in training for the shuttle:

The words 'ionosphere' or 'charging' don't appear in the Shuttle Crew Training Catalog. The phrase 'space weather' appears once, in the description of a class the crew got on the Tissue Equivalent Proportional Counter. The context was expected radiation dosage. – Organic Marble Oct 8 '20 at 23:32

Per user Digger, who actually flew on the shuttle:

Can't recall much ever being said about this for any purposes beyond informational... – Digger Oct 6 '20 at 18:46

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