Truthfully the best way is to clear you crystals on a regular schedule. If you think you have been exposed to a lot of negative energy this will insure you don't get an overload of harmful energy in the crystal that can stress or discolor the crystal. If the crystal had a lot of inclusions this is really important as heat and excess energy will act to active the inclusions to discolor the clear crystals. No natural crystal even clear quartz is pure quartz. The other elements need an input of heat or energy to act as if it has been irradiated causing color to appear. Clearing will keep the excess energy from building up. I have incorporated a link below on different ways you can cleanse your crystals.
Master Crystal Healer
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