update get_maps to use curl instead of links to get cutoff

get_maps.sh

 #!/bin/bash
 
 
-bindir=$(dirname $0)
-
+bindir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+rec_gmconvert=${bindir}/recursive_gmconvert.sh
+echo "rec_gmconvert=${rec_gmconvert}"
 source ${bindir}/modules.sh
 
 for f in $(cat)
@@ -10,12 +11,12 @@ do
 	echo $f
 	rsync -a -v -z --delete rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-${f}/ $f
 	cd $f
-	links http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.txt
-	cutoff=$(awk '/contour/{print $4}' < header/map_analysis.txt)
+	curl http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.html
+	cutoff=$(awk '/contour/{print 3}' < header/map_analysis.html)
 	resolution=$(sed -ne 's/[<>/ ]//g' -ne 's/resolutionByAuthor//gp' header/emd-${f}.xml)
 	echo ${cutoff} > cutoff.txt
 	echo ${resolution} > resolution.txt
 	gunzip -c map/emd_${f}.map.gz > emd_${f}.map
-	${bindir}/recursive_gmconvert.sh emd_${f}.map $cutoff $1 $2
+	${rec_gmconvert} -f emd_${f}.map -t $cutoff -n $1 -N $2
 	cd -
 done