The STL file is the geometry of your part. Lets say you wanted to print a hollow box. The STL has the walls and floor of that box as geometric reference coordinates. The Slicer program (usually slic3r or cura or one of the other ones) then takes that STL file and renders a gcode coordinate motion path for your 3d printer extruder. It literally tells the extruder “from your starting point, go 100mm that way and extrude x amount of plastic, then go here, then go here, etc.”. You can see how that coordinate system works if you open up one of the .gco gcode files in a text editor of some sort. From there, your printer control software (in your case matter control) reads that gcode file and applies any printer specific setting information that you have set and executes the file. Since 3d printers almost always print in layers, or slices, thats why generating the gcode file is called slicing the .stl file.
Using slic3r is really easy. You install the program, download a printer configuration file that matches your printer type and most importantly nozzle size and what plastic you will be printing. For example, to print ABS plastic on a Taz 5 you would want a Taz 5 ABS 0.35mm nozzle printing profile, probably the medium quality one. if you wanted to print with a 0.5mm nozzle, you would grab one specific to that nozzle size. PLA plastic you would grab the profile specific for that plastic, etc. The various quality levels refer to print speed and final output quality. A high quality profile is set to make smaller individual layers or slices, so you get better resolution but it will take much much longer to print.
There are a few other options as well. Generally you will have one profile set to generate support material for prints that could not be printed without support, and another without support. You may have one with a Brim layer turned on for better bed adhesion. , or a skirt turned on for printing taller thin walled objects prone to printing.
You will also want to change the settings in the nozzle profile. Basically you just need to tell it what the actual diameter of the fillament you are printing actually measures with calipers (3mm fillament can range anywhere from 2.85 to 3.12mm in diameter and it wildly affects the quality of your final print if that isn’t set correctly)
You will typically have about 5 or 6 different slicing profiles, with one of them being your general go to printing profile. Inside slicer you just drag the model into the positioning area and make sure it is positioned in the middle of the bed and correct side up, rotating or adjusting it as needed (you can also scale it in there). You then go to the slicing section and tell it which profile to use, which nozzle settings file to use (or use the defaults from your last print job) and hit “generate Gcode”
Here’s a video of what most of the slic3r settings do. Its a slightly older version of slic3r but pretty much every setting in there still does the same thing they did in the video https://www.youtube.com/watch?v=o1HPeovBclc He is using the repetier host controller software, which is what I actually use as well. That has Slic3r embedded into it as a module, so you end up with a single gcode generation and control interface. Takes a bit of work to get it set up and tuned in, but I find it to be worth it. The newer versions of repetier host don’t seem to like the TAZ so I am actually using an older version of it, but it worls well.
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