This gist shows how to loop throw and alter/update an individual uniquely identified document.

updating_docs.py

from pymongo import MongoClient
import sys

# code example to show updating individual records in a loop

# initialize the database with:
# mongoimport -d school -c scores --type json grades.js

# verify no records with "added"
# db.scores.find({"added":{$exists:true}})  // returns nothing

# run this program
# python updating_docs.py

# use the command below in the mongo shell to see the records that were altered:
# use school
# db.scores.find({"added":{$exists:true}})
# db.scores.find({"added":{$exists:true}}).count()  // should be 800

# in the series of posts here:
# https://groups.google.com/forum/?fromgroups=#!topic/mongodb-user/0bCEb7vcUvg
# Brendan has a good explanation of why we need the doesn't exist query

connection = MongoClient("mongodb://localhost", safe=True)
scores = connection.school.scores

# give me records that don't have the added field
query = {'added': {'$exists': False}}
counter = 0

try:
    cursor = scores.find(query)

except:
    print("Unexpected error:", sys.exc_info()[0])

for doc in cursor:
    counter += 1
    doc['added'] = counter
    scores.update({"_id": doc['_id']}, {'$set': {'added': counter}})
    print counter

connection.disconnect()