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How to adjust nozzle height in Repetier on 1.0A
I've tried everything and looked at every menu in Host and Slic3r a dozen times as well as read a million guides to setting the Z axis, But for some reason, even with Z probe running before each print, I am getting just barely too big of a gap. My first layer isn't pressing onto the glass, it just looks very...... textured.[Image: IMG_20150129_002202.jpg]
Look at extruder offset in slicer. Hover over it and u should see a description. From what I recall, positive values move the nozzle further from the bed, negative moves closer. Really though with bed manually calibrated with a piece of paper, you should be close enough to get a good first layer. The idea is to calibrate the bed so that zhome is just a papers width from the nozzle.
The problem I'm having is that no matter how I level the bed with paper, The first layer prints X mm above the bed exactly, where X is what I have the first layer height set to. I can't get it to squish into the bed unless I use a Z offset in slic3r. I feel like I'm missing something here, because everywhere I read, once the bed is homed and leveled with the paper, it should print just fine. Is using Z offset just the way to do it?
what Z min do you have in EEPROM ? should be 0
That's exactly what is expected happen. If your layer height is 0.2mm then the bed will go down (from the Z end-stop position) exactly 0.2mm when you begin to print. If you want the first layer to be more squished in the bed then you can either set a negative Z offset in the firmware or in the slicer, or simply rise the bed a bit more using the leveling screws (so if you are using the paper method then let the tip of the nozzle grip the paper more).
...OR you can increase the amount of extrusion for the first layer in slic3r, so that even though the height is 0.2mm it pushes out enough plastic for a height of say 0.25 or 0.3mm (effectively squishing).
Yes. This.

I typically run 150%-200% width for first layer [setting in Slic3r] Doing this just pushes more material out and gives you thicker lines, which leads to a very nicely filled/flat first layer...and good adhesion.

However, if your issue is really not enough material being extruded, this will only fix the problem for the first you may still see adhesion issues between layers and improperly filled top surfaces.
Also, if you ever tried to use the auto level, you will need to turn it back off or it will screw up any manual leveling you do.

Go to the menu and choose Printer -> EEPROM Settings.

Verify that Autolevel Active is off. Doing a Manual level from the front panel of the printer doesn't turn off Autolevel. I just realized I should ping Luc to see if that's a bug or not.

When first trying to get the print to stick, you can use 0.2 or 0.3 for the first layer height and then set the extrusion width to 175 to 200% for the first layer. Once you've got things starting ok consistently, then you can start messing with the settings more.
I have tried ALL OF THE ABOVE and I'm still getting the same result on multiple filaments. I've tried extrusion width and percentage in slic3r, setting the Z offset until it should be printing with the nozzle almost touching the glass, I've even tried turning off autoleveling, setting the bed to 0.2mm from home, and raising the bed until it is leveled to the nozzle within the width of a piece of paper. Everything I try, no matter how close it is to the glass during a dry run, when it comes to the print it just won't squish enough. Any ideas?
Well, I went on a hunch and upped the first layer temperature from 231 to 239 and now it squishes. Seems I made a newbie mistake. Thanks toneveryone who responded, I've learned a lot about the first layer.

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