In San Francisco when it rains, carry an umbrella and do most of what you would do any other day.
However, if you really must be inside, some of the things that you can enjoy are the wonderful museums.
A couple of the good ones to wander through are the Musuem of Modern Art
(appeals to a broad audience....)
Go to the Metreon and wander the stores and see a movie:
Choose a wonderful restaurant and enjoy their taster menu complete with accompanying wines. Perhaps at Jardiniere (very pricey but can take multiple hours for dining):
See if tickets remain and see Jersey Boys
Go to Japantown (as its mostly inside) and wander and enjoy sushi or a Japanese lunch or dinner:
Just a few of the wonderful and varied museums and galleries you can visit: California Academy of Sciences (www.calacademy.org), Asian Art Museum of SF (www.asianart.org), San Francisco Museum of Modern Art (MOMA) (www.sfmoma.org), Fine Arts Museum of San Francisco (www.thinker.org) inc’s the DeYoung Museum and the Legion of Honor, Museum of the City of San Francisco (www.sfmuseum.org), and the Exploratorium (www.exploratorium.edu).
My favorite place to go on a rainy day in San Francisco is the Conservatory of Flowers (www.conservatoryofflowers.org) in Golden Gate Park, a beautiful Victorian light-filled glass building that houses an incredible collection of exotic flowers and water features--and more! Other ideas would be visiting the Grace Cathedral (www.gracecathedral.org) on Nob Hill, which looks magical on a rainy day, and the always delightful and lively Ferry Building (www.ferrybuildingmarketplace.com) at the Embarcadero, where you can browse and eat some of the best local products.
If rain is very light and you happen to be at the de Young, save some time to go to the nearby Japanese Tead Garden. The rain brings out the vividness of the colors, and the crowds will be very light since it is outdoors.
You should go to the tourist attractions that are usually busy in nice weather. You'll have less people around and will probably have a better time of it.
Dress appropriately and take the Ferry over to Alcatraz. Wander around Fort Point, especially the roof in the "windy" corner, which is the NW side. Fishermans Wharf should be quiet as well. Coit Tower, inside and out.
Rain is just clean rain around here - so take advantage of it - dress for fun and enjoy it.
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