Egyptians lined up Saturday to pick the first president since the ouster of Hosni Mubarak.

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CAIRO — Egyptians lined up Saturday to pick the first president since the ouster of Hosni Mubarak, choosing between a standard-bearer of the old secular autocracy and a veteran of its Islamist opposition, even as a power grab by Egypt’s ruling generals ended the hope the vote would complete Egypt’s transition to democracy.

The runoff election this weekend was to have been the culmination of a nearly 18-month transition since the 18-day uprising that forced out Mubarak, the moment the generals who seized control after his ouster said they were waiting for to hand power to an elected civilian, inaugurate a new democracy, and end six decades of military rule.

Instead, the vote took place in the shadow of the generals’ moves just a day before to shut down the democratically elected, Islamist-led Parliament, take over lawmaking authority and vow to issue their own interim constitution, which would define the role of the leader voters were choosing Saturday.

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“This is the end stage of the whole transition,” said Mahmoud Ismail, 27, a political activist in the town of Menoufia. “To be or not to be.”

The actions by the ruling military council on Friday, acting on a court ruling rushed out on the eve of the vote that dissolved Parliament, foreclosed the possibility the Islamists of the Muslim Brotherhood might immediately take control of both the Parliament and the presidency.

And it raised the likelihood the new president will be either wrestling the military for power or perhaps a collaborator doing its bidding.

Many called it a soft coup, and some voters said they had all but abandoned their hopes for the man they would elect. “The president who is coming will have no powers whatsoever,” said Mohamed Saqr, 51, a bank manager waiting to cast his vote in the working class Cairo neighborhood of Saeda Zeinab.

The two candidates, meanwhile, representing the main opposing forces of the Mubarak era, pushed ahead with their campaigns, mobilizing their respective battle-tested political machines.

The Islamist, Mohammed Morsi of the Muslim Brotherhood, waited in line to cast his vote in the Nile Delta town of Zagazig where he used to teach engineering. “God is greatest,” a throng cried as he emerged.

Morsi saluted those killed demonstrating against Mubarak. “Today is the day of the martyrs,” he declared. “There is no place at all for Mubarak’s helpers.”

The other candidate, Ahmed Shafiq, a former air force general and Mubarak’s last prime minister, cast his ballot in the style of his former boss.

Surrounded by a heavy guard of military and police officers, he visited a school-turned-polling place in an upscale suburb. The lines were pushed aside and guards immediately closed the facility for his private use.

“The Brotherhood is dissolved,” chanted small crowds of his supporters waiting inside and outside the polling place, cheering at the dissolution of the Brotherhood-led Parliament. State media reported a cameraman in a military vehicle filmed Shafiq’s trip to the ballot box, apparently to preserve it for posterity.

Many voters bemoaned the polarizing choice, between a face of the old authoritarianism and the Islamist group that was its principle opposition. In the first round of voting, a narrow majority of voters supported candidates promising a break with the past, and who were sharply critical of both the Brotherhood and the Mubarak government.

The two winners each relied on their organizations — the former ruling party’s network of local power brokers for Shafiq, and the Brotherhood’s vast organization of local cells and charities for Morsi — to muster just under a quarter of the vote.

“I wanted anybody other than these two,” said Kamel el Ghoneim, 50, owner of a small computer-support company.

Perhaps nowhere was the effectiveness of Shafiq’s ground operation, and his reliance on the old order, more evident than in Menoufia, a district Shafiq won by a wide margin during the first round. Mubarak hailed from Menoufia, as did former President Anwar Sadat. So did the disgraced tycoon Ahmed Ezz, whose reputation for corruption became a rallying cry for the revolutionaries last year.

Shafiq’s campaign team there, led by a past chairman of Mubarak’s ruling party, launched a broad attack on the Brotherhood’s credibility in recent weeks, portraying them as liars and hypocrites, in league with both American officials and disgraced cronies of Mubarak.

Tarek al-Warraqui, a campaign staff member who was previously a press officer for the local government, distributed fliers containing those charges, and Shafiq’s accomplishments, throughout the area.

“We don’t have a party,” he said. “We have a network. And our group has experience. We have someone in every village.”

Some saw a vote for Morsi as a last, desperate attempt to save the uprising. Nervana Fouad, a 36-year old teacher, had voted for Amr Moussa in the first round, a former foreign minister who, like Shafiq, had framed his campaign as a more secular alternative to the Brotherhood.

Now she was voting for Morsi. “It’s probably cooked for Shafiq to win,” she said. “I don’t agree with Morsi’s policies, but he’s our only hope that the revolution to survive.”

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