The orthopedic surgeon gets a lot of diagnostic clues from the history of what happened, how it happened, and the signs and symptoms you developed after the accident. There are some specific tests that can be done to identify which ligaments might have been injured and/or whether or not there was cartilage (or other soft tissue) damage.
In fact, there are actually dozens of tests that can be done. But the surgeon will be able to narrow it down to the most important clinical tests for your particular situation. For example, the clunking that you mentioned is a red flag for possible knee instability. This could be caused by a tear of the anterior cruciate ligament along with injury to other knee structures.
Diagnosing knee problem can be difficult due to the complexity of the structures and anatomical differences from patient to patient. There isn’t one test that provides the answer for each patient.
Scientists studying this problem have new tools and new technology to explore the normal and pathologic biomechanics of the knee and tests for knee instability. In the future, computer systems with the ability to measure and analyze movement will make it possible to identify types and degrees of joint instability. The hope is that it will be possible to plan ACL reconstruction surgery with each individual patient in mind.
For example, knowing the amount and direction of excess rotational movements (not just forward and back instability) is significant. These findings are important for the athlete who needs to jump, stop suddenly, pivot, shift, and cut quickly. Just repairing or reconstructing the torn ACL will not restore stability in the movements that require rotation. All other soft tissue injuries and imbalances must be identified and corrected.