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i think chakra refers to the bodys natural psychic glands. there are 3 of them i think....
I know of atleast one, which is commonly reffered to as the 3rd eye because its right above your eyes in the center of your forhead

Look for Robert Monroe's guide to seeing auras on the Astral Pulse site. It should give you all the basics you need. I think its in the 'downloads' section or something.