Atticus asks Tom why he ran because he wants to understand Tom's actions and gain insight into how Tom perceives the situation. Atticus believes in giving everyone a fair chance to explain themselves and wants to ensure that Tom's perspective is heard in the courtroom.
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When Mayella is on the stand the question Atticus asks that makes her furious is "How?" She has just described how Tom Robinson choked and beat her, and Atticus asks Tom to stand up. This draws the jury's attention to the fact that Tom's left arm is useless, making it highly unlikely he was Mayella's attacker. When Tom stands, Atticus asks Mayella if Tom is the man who attacked. When she responds that he is, Atticus asks, "How?"
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This is specific to your particular edition of the book.
Just about the time Scout decides that she prefers the company of men, Atticus interrupts the meeting with the news that Tom Robinson has been killed in an attempted escape. In the kitchen, Atticus asks Calpurnia to accompany him to give the news to Tom's wife, Helen.
Atticus was showing the Ewell was left handed and that he could have beaten Mayella.
Atticus asks Tom to catch a glass cup to test his injured arm's mobility and strength. This incident symbolizes Atticus's respect for Tom's dignity and humanity, challenging racist attitudes that dehumanize black individuals. It also shows Atticus's belief in fairness and justice for all, regardless of race.
Atticus is sitting in front of the jail that contains Tom
Atticus has Tom Robinson stand to prove his innocence. Due to Tom Robinson's stature, he was incapable of punching the opposing variable talked about in court due to the twelve inches of difference between each of his arms.
Calpurnia's note to Atticus says that Tom Robinson has been given the death penalty and that there is trouble at the jail. She asks him to come to the jailhouse to help protect Tom from a lynch mob.
Judge Taylor assigns Atticus to defend Tom Robinson.