What gets me is why anybody would use auto junctions in the first place.

I'm guilty of using 4 way junctions, mainly because the circuit makes more
sense (an RC charging node for example) as opposed to staggering components.
If seeing the dots in a printout is a problem, make them bigger. (try faxing
someone an A3 schematic reduced to A4 and see if they can tell the
difference between a cross and a junction 8-)

Within 10 minutes of using P99SE's schematic capture I was on the hunt for a
way to turn it off.
I found that it was inconsistent in placing it's junctions, sometimes it
would place one where you wanted it and other times it wouldn't.

I was aware of the problems associated with 4 way junctions and at school
they told us to use 45 degree offsets on wires approaching a similar net
from opposing sides.... something like this

        |
___/______
         /
        |

and it cone be done quite easily in P99SE

Being a programmer myself, I have very little faith in software and even
less in the people that write it, as such I still worry about different nets
crossing at 90 degrees and resort to placing net labels on and near the
crossing.
Has this ever been known to be a problem? I hate cluttering up schematics,
they're complicated enough without having to worry about the PCB design as
well.

This brings me to another point. Shouldn't the circuit designer concentrate
on the circuit design and the PCB designer on the PCB design? and if so who
is responsible for the intermediate stage of converting the drawing from a
circuit design to a "wiring" schematic?... automated cad software?




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