Transformed multiple seds to this patch. `MOLMOLHOME` is the runtime variable
that depends on knowledge of paths that I didn't think of how to correctly
pass beyond editing it with sed. For everything else, it is here and changed
to work correctly with build system.
Rolled up sed transformations were to made build system non-parallel,
fix environmental variables, remove sleep and add use right shell and
build dependencies in startup script.
--- a/makedef.lnx
+++ b/makedef.lnx
@@ -11,12 +11,12 @@
 
 XINCL   = -I/usr/X11R6/include
 
-CC=gcc
+CC ?= gcc
 MCPPFLAGS =
-MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686
+MCFLAGS := $(CFLAGS)
 
 RANLIB   = /bin/true
-WAIT     = sleep 2
+WAIT     = sleep 0
 SHELL    = /bin/sh
 CPP      = /lib/cpp
 
--- a/molmol
+++ b/molmol
@@ -1,9 +1,10 @@
-#!/bin/ksh
+#!/bin/sh
 #
 # startup script for MOLMOL
 #
 
-MOLMOLHOME=/opt/group/MOLMOL
+MOLMOLHOME=/;
+MOLMOLDEV="Motif/OpenGL"
 export MOLMOLHOME
 export MOLMOLDEV