When I print a part without a raft the nozzle gets very close to the build plate, close enough that the build material will not extrude. When I print with a raft there is no issue and the raft goes down as it should with the part on top of it. I have mucked with the offset with no change, run through recommissioning with no change. I have also messed around with some of the settings in Simplify3D also to no avail. I am looking for any suggestions as to what to try next. I am running RC6 on a stock BigBox. Issues started after nozzle ran into bed during a print when there was an issue with gcode. Thanks in advance.
I guess it's back to basics. Commissioning followed by bed levelling, followed by testing, importantly one step at a time. A. From memory during the build various set-screws are left loose and then various things checked/measured/tightened in a specific sequence. B. At some stage after this (memory weak and not looking at the old WiKi as yet) you do bed levelling. C. Once the above is done then either a test print (like Benchy) or some tests say printing a single layer over most of the bed. D. Actual print having reset Simplify3D "A" is going to be tedious (but necessary) unless you find the source of the problem some other way. "B" is vital "C" is very useful and a way to see what Z adjustments you can make (People here make micro adjustments immediately prior to printing to get this very first layer right.) Critical is if you just knocked something out of kilter, something that can be put back/re-adjusted etc. OR if something was permanently bent when you had the crash. Permanently bent like one of the Z lead screws bent, or one of the couplers to the Z motors bent/twisted out of alignment. If you can get back to a stage where you know the BB is square (part of commissioning and for which you can do separately) and the bed is levelled and the settings saved, then you are back to adjustment (in S3D and micro adjustments which depend on if on Rumba or other controllers) for which I am NOT the expert but you will get some good help here from others. Is S3D up to date, I seemed magically to have less problems after the last update.
also, recheck your first layer height. If that's too small, a raft can be more forgiving. Some discussion of a similar issue here https://forum.simplify3d.com/viewtopic.php?t=2567
I second what JFB said. The raft uses isolated strands so the nozzle being too close doesn't quite stall the extruder but the infill on a regular layer one builds up too much pressure.