X and Y axis perpendicularity

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It all started when I was looking under the bed at the Y axes belt, this was not looking straight, the belt was bended down at the pulley on the stepper motor.
So I loosened the pulley and moved it 3 mm up and straightened the belt. This had a direct result, when moving the bed I felt less resistance.
After this was done I looked at the X belt, this was off also and more the X axis were not parallel to the frame. I decided to fix this problem as well.
By loosening the 8 hex bolts that connects the U frame to the bottom part of the printer you will find the there is a lot of play, you can shear your U frame quite a bit. Used my eyes to shear the frame so the X axis were parallel to the frame and fastened the hex bolts and, checking that the frame did not move. After that I aligned the X belt by loosening the pulley of the X stepper motor so I could make the belt parallel to the X rods and frame.
This also resulted in a lot less resistance moving the print head.
After that I wanted to check if my efforts worked. I printed a large rectangle and measured the sides and diagonal.
As you all now they must be 1 : 1 x √2, in my case 144.4 mm and 204.2 mm.
It all worked just fine now my X and Y axis are perpendicular.

Thanks! I had a similar issue, at least with my Y axis. Only had this printer for two weeks but from new it was making an odd clunking/cracking noise. Googling mostly returned issues of extruder clunk, which I knew this not the case with my printer. Even with the printer off if I slid the bed slowly front and back it would make the noise, right about at the center position. In addition, my Ultrabase was not perfectly level: it was domed in the center. Print quality was okay, but not what I felt at the level this printer should be capable of producing.

After reading your thread I immediately checked my Y belt, and it indeed was off my several mm (didn't remove bed). Corrected that and also loosened the 8 u-frame screws, and re-tightened making sure all was true. At first the printer seemed better, but that cracking noise was still there, and I was sure it was affecting print results.

So I came back again and this time removed the bed, in preparation for removing the Y rods. (Noticed that the Ultrabase, free from the metal plater, was perfectly flat, and not domed in center.) While loosening the set screws on the right rod, there was a noise: like a snap or crack having to do with tension suddenly being released (not actually cracking or snapping a part). But my rods were straight, and best I could measure, the mounting brackets were true. So I reassembled everything, being careful to make sure there was no binding, and everything was as true as I could manage.

First thing I noticed was that the Ultrabase was not nearly as domed in the center. Finally could level this thing to at least an acceptable level. Then I tried a quick print and there was zero clunking/cracking. Then a longer print and still no noise. Better yet, I am seeing a much more consistent print quality.

Still having checked the X axis, since things are looking good at the moment. But I know I will eventually succumb to the temptation to try and dial this thing even more.

Did check the X axis and sure enough, it was a bit off. Corrected that but, dang, one of the set screws on the pulley was nearly impossible to remove. Had to use a hardened allen wrench with pliers to loosen it.

Wasn't quite sure, at first, what HansvG meant my U frame shearing. Now I get it and will run through it all again and check that too.

I have noticed a similar problem, but was not able to correct it. It does seem your solution works however not everything is clear to me. If possible, could you please upload a few pictures with highlights of the parts/screws/etc with a step by step description? Thank you for your work!

I have the same issue on Y axis... but the pulley is a press-pulley :( I cannot move it. Maybe I should get a new pulley and change this one...

X belt adjustment helped, it was a bit off. One thing I've noticed though, Y belt adjustment is not that straight forward. You shouldn't adjust the pulleys to be level with each other. They should be level with the bed holder, because its height cannot be adjusted.

This I know, just loosen the pulley on the stepper motor then move your bed back and forth slowly, checking if the belt stays straight on the pulleys, it is kind of self adjusting, when the belt stays on the same position on the pulleys tighten the screws on the pulley.

This is great and much better than I expected! Thank you very much!

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I noticed a similar problem on my printer, it even have this grinding noise before I adjusted the front pulley on the Y axis. The edge of the belt is having more friction on the pulley producing grinding noise. However, I did not do any adjustment on the motor side pulley that the belt remains not totally straight after that. Now I adjusted the pulley on the motor side and the belt stays straight as it is moving. Did the same checking on the U frame, indeed there is a huge chance that the frame is not totally vertical so I adjusted it also. The belt on the X axis is also not in parallel with the rods so I loosened the two screws on the motor side pulley and did the adjustment then manually moved the hotend left to right for the pulley to position better while it is still not tightened and it did aligned better. Tightened the screws back and the belt is now in parallel with the rods. The grinding noise on the pulley on the x-axis at the opposite side of the motor is now gone. Anycubic3d support was aware of the problem on the noise on the pulley but did not suggested any solution. What you're sharing today is a big help for everyone with the same printer and I thank you for that. Let me report this back to Anycubic3d support that they can make sure all printers from factory have this alignment on the pulleys done already and people should only do the frame part alignment during assembly.

Thanks for your reply. It feels good that my findings and adjustments help other people fine tuning their printer. I think the Anycubic is a printer well worth the money but it needs a little tweaking and adjusting. I also did some upgrades like better fans, TMC2208 stepper drivers etc.
People should read petrzmax's post on how to improve the i3 Mega: https://www.thingiverse.com/thing:2901190
They helped me a lot improving and upgrading my printer. When I encountered this alignment problem I searched if other people had the same problem, did not find any, so I decided to post my findings.

Anycubic I3 Mega ULTIMATE Upgrade Guide