P.S. Does anyone else have problems finding Clipper from the COOT ./configure script even when one specifies the path, (c.f. http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT )...or am I overlooking something?
Perhaps you are overlooking the autobuild script, which should do all of this for you?
http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it or http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple
