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Hold your guitar up at eye level and gaze down the neck. Look for signs of warpage or other issues that could be affecting your guitar's intonation. When you look down the neck of your guitar, it should be perfectly straight. If you see any cracks or separation at the neck joint, or notice any warping along the width of the neck, take your guitar to an experienced luthier. This repair requires work beyond simple adjustments. Your guitar's "neck relief" is the amount it curves along its length. Too much neck relief can cause problems with intonation because it means that your strings are further away from the neck at some frets than at others.  You can make minor adjustments to correct neck relief by tightening or loosening the truss rod. This is something that you can do at home, but if you feel at all uncomfortable doing it, go ahead and take it to a luthier. If your neck is curved to the point of being bowed, you risk breaking it if you adjust the truss rod. Take it to an experienced luthier for an assessment. Your guitar has a truss rod, accessible either through the sound hole of your guitar or behind a panel just above the nut. The rod can be adjusted either with a regular Allen wrench or a socket wrench.  Turn the rod to the left to loosen it, or to the right to tighten it. Go extremely slowly, and only turn it a maximum of a quarter-inch (about 6 millimeters) at a time. Never turn it more than a complete turn. Loosening will add relief (greater distance between the string and the neck), while tightening the truss rod takes away relief. The action is the space between the strings and the frets. A lot of action will make the strings more difficult to press down, and can affect your guitar's intonation. Not enough action and the strings will buzz, damaging your sound quality.  Hold the neck of your guitar at eye level. One at a time, press down each string between the second and third frets and look at the clearance of the string over the first fret. If you can see just a sliver of light between the string and the first fret, that tells you that the strings are sitting correctly in the nut. If there's too much space, the intonation will be off. You can fix this by filing down the string slots just a little so that the string sits lower. If there's no space between the first fret and the string, this is going to cause the string to buzz against the first fret when you strum the open string, which can also affect the sound of your guitar. You can fix this by raising the nut so the string sits higher. If you noticed that you had too much action at the nut, you can file the string slots yourself if you have the right tools. You'll need a nut file to get the slot in the right shape. Otherwise, take your guitar to a luthier.  On the other hand, you also can raise the nut yourself if there isn't enough action. Simply glue a piece of material similar to the nut to the bottom of the nut to increase its thickness. When raising your nut, start with the smallest sliver – if you raise your nut too high you could adversely affect the tone of your instrument. Keep the same thing in mind when filing the string slots – once the nut is filed away, you can't put it back. Swapping out your old nut with a prefabricated nut that will correct the action may be the easiest thing for you to do. Prefabricated nuts aren't too expensive, and you don't run the risk of ruining the original nut.  You can find prefabricated compensated nuts at your local guitar shop, or you can order one online. Make sure the nut you choose is designed to fit on your guitar. If you have trouble installing it yourself or find you don't have the right tools to do it correctly, take your guitar to a luthier. Installing a prefabricated compensated nut also may remedy intonation problems that were caused either by the shape of your nut, or the shapes of the string slots.
Sight the neck of your guitar. Evaluate neck relief. Adjust the truss rod. Check action at the nut. Try to file or raise the nut yourself. Install a prefabricated compensated nut instead of filing the nut yourself.