Here’s how to solve Marek’s Trunk in Nancy Drew: Mystery of the Seven Keys.
After you open the glass cylinder and see the three gems, you unlock the ability to take the Haunted Prague tour by clicking on the A-frame board just outside the museum door in the hallway.
Talk to Marek about Rezidente and about Alchemy, and you can then try and open his puzzle trunk. When you step up to it, click when your cursor turns into a magnifying glass. The arrows that appear on your screen will let you examine the left and right sides of the trunk.
On the left side, find the circular button and press it. Then move to the right and find another circular button to press. When you are centered, notice the 8 pins that extrude from the edges. Press them down one by one until all are pressed. This is not a randomized puzzle, nor does it change each time. Figure out the order to press to keep each pin down. (Answer shown in the video, below.)
When the lid opens, take out the marionette and notice the centered design of a familiar symbol. Only once you see this in the trunk can you return to the glass artifact (at night, during the haunted tour when Oskar is not around). Open the glass cylinder and take the three gems. Exit the tour and return to Marek’s trunk.
Place the blue diamond in the slot on the right. A tray lifts out. Place the red square gem in the top slot, and the green triangle in the lower slot. Another tray lifts out.
Notice the painted shapes – these areas indicate where the gems need to be. Slide the oval gem into the center wheel and click to drag-rotate to the bottom center position, hovering over the green triangle gem. Next, slide the blue diamond into the center wheel, and the red square down. Click any gem to rotate all of them together and align them to where they need to go.
At this point, you may think you need to slide them OUT of the wheel, but instead, bring in the green triangle. The center design on the box will pop up and you can press it, which pushes all gems outward and a drawer to the trunk opens.