diff --git a/data/result2structprofile.sh b/data/result2structprofile.sh
index 37668d39..41883a07 100644
--- a/data/result2structprofile.sh
+++ b/data/result2structprofile.sh
@@ -1,29 +1,33 @@
 #!/bin/sh -e
 
-if [ -e "${IN1}.dbtype" ]; then
+INPUT="$1"
+RESULT="$3"
+OUT="$4"
+
+if [ -e "${INPUT}.dbtype" ]; then
     # shellcheck disable=SC2086
-    "$MMSEQS" base:result2profile "${IN1}" "${IN2}" "${RESULT}" "${OUT}" ${PROFILE_PAR} \
+    $RUNNER "$MMSEQS" base:result2profile "${INPUT}" "${TARGET}${INDEXEXT}" "${RESULT}" "${OUT}" ${PROFILE_PAR} \
         || fail "result2profile died"
 fi
 
-if [ -e "${IN1}_ss.dbtype" ]; then
+if [ -e "${INPUT}_ss.dbtype" ]; then
     # shellcheck disable=SC2086
-    "$MMSEQS" base:result2profile "${IN1}_ss" "${IN2}_ss" "${RESULT}" "${OUT}_ss" ${PROFILE_SS_PAR} \
+    $RUNNER "$MMSEQS" base:result2profile "${INPUT}_ss" "${TARGET}_ss${INDEXEXT}" "${RESULT}" "${OUT}_ss" ${PROFILE_SS_PAR} \
         || fail "result2profile died"
 fi
 
-if [ -e "${IN1}_ca.dbtype" ]; then
+if [ -e "${INPUT}_ca.dbtype" ]; then
     # shellcheck disable=SC2086
-    "$MMSEQS" lndb "${IN1}_ca" "${OUT}_ca" ${VERBOSITY} \
+    "$MMSEQS" lndb "${INPUT}_ca" "${OUT}_ca" ${VERBOSITY} \
         || fail "Create lndb died"
 fi
 
-if [ -e "${IN1}_h.dbtype" ]; then
+if [ -e "${INPUT}_h.dbtype" ]; then
     # shellcheck disable=SC2086
-    "$MMSEQS" lndb "${IN1}_h" "${OUT}_h" ${VERBOSITY} \
+    "$MMSEQS" lndb "${INPUT}_h" "${OUT}_h" ${VERBOSITY} \
         || fail "Create lndb died"
 fi
 
-if [ -e "${OUT}.sh" ]; then
+if [ -e "${INPUT}.sh" ]; then
     rm -f -- "${OUT}.sh"
 fi
diff --git a/data/structureiterativesearch.sh b/data/structureiterativesearch.sh
index a6ba1d66..b2e81931 100644
--- a/data/structureiterativesearch.sh
+++ b/data/structureiterativesearch.sh
@@ -92,7 +92,7 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
     if [ $STEP -ne $((NUM_IT - 1)) ]; then
         if notExists "$TMP_PATH/profile_${STEP}.dbtype"; then
             # shellcheck disable=SC2086
-            $RUNNER "$MMSEQS" result2profile "${QUERYDB}" "${TARGET_ALIGNMENT}${INDEXEXT}" "$TMP_PATH/aln_${STEP}" "$TMP_PATH/profile_${STEP}" ${PROFILE_PAR} \
+            "$MMSEQS" result2profile "${QUERYDB}" "${TARGET_ALIGNMENT}${INDEXEXT}" "$TMP_PATH/aln_${STEP}" "$TMP_PATH/profile_${STEP}" ${PROFILE_PAR} \
                 || fail "Create profile died"
         fi
     fi
diff --git a/src/strucclustutils/result2structprofile.cpp b/src/strucclustutils/result2structprofile.cpp
index 78a90742..b68c419f 100644
--- a/src/strucclustutils/result2structprofile.cpp
+++ b/src/strucclustutils/result2structprofile.cpp
@@ -4,41 +4,41 @@
 #include "CommandCaller.h"
 #include "Util.h"
 #include "LocalParameters.h"
+#include "PrefilteringIndexReader.h"
 #include "result2structprofile.sh.h"
 
 int result2structprofile(int argc, const char **argv, const Command &command) {
     LocalParameters &par = LocalParameters::getLocalInstance();
     par.parseParameters(argc, argv, command, true, Parameters::PARSE_VARIADIC, 0);
 
-    std::string program = par.db4 + ".sh";
-
-    FileUtil::writeFile(program, result2structprofile_sh, result2structprofile_sh_len);
 
     CommandCaller cmd;
-    cmd.addVariable("OUT", par.filenames.back().c_str());
-    par.filenames.pop_back();
-    cmd.addVariable("RESULT", par.filenames.back().c_str());
-    par.filenames.pop_back();
-    cmd.addVariable("IN2", par.filenames.back().c_str());
-    par.filenames.pop_back();
-    cmd.addVariable("IN1", par.filenames.back().c_str());
-    par.filenames.pop_back();
-
+    std::string db2NoIndexName = PrefilteringIndexReader::dbPathWithoutIndex(par.db2);
+    if (db2NoIndexName != par.db2) {
+        cmd.addVariable("TARGET", db2NoIndexName.c_str());
+        cmd.addVariable("INDEXEXT", ".idx");
+    } else {
+        cmd.addVariable("TARGET", par.db2.c_str());
+        cmd.addVariable("INDEXEXT", "");
+    }
     par.scoringMatrixFile = "blosum62.out";
     par.seedScoringMatrixFile = "blosum62.out";
     cmd.addVariable("PROFILE_PAR", par.createParameterString(par.result2structprofile).c_str());
-        par.pca = 1.4;
-        par.pcb = 1.5;
-        par.scoringMatrixFile = "3di.out";
-        par.seedScoringMatrixFile = "3di.out";
-        par.maskProfile = 0;
-        par.compBiasCorrection = 0;
-        if(par.PARAM_E_PROFILE.wasSet == false){
-            par.evalProfile = 0.1;
-            par.evalThr = 0.1;
-        }
+    par.pca = 1.4;
+    par.pcb = 1.5;
+    par.scoringMatrixFile = "3di.out";
+    par.seedScoringMatrixFile = "3di.out";
+    par.maskProfile = 0;
+    par.compBiasCorrection = 0;
+    if (par.PARAM_E_PROFILE.wasSet == false) {
+        par.evalProfile = 0.1;
+        par.evalThr = 0.1;
+    }
     cmd.addVariable("PROFILE_SS_PAR", par.createParameterString(par.result2structprofile).c_str());
     cmd.addVariable("VERBOSITY", par.createParameterString(par.onlyverbosity).c_str());
+
+    std::string program = par.db4 + ".sh";
+    FileUtil::writeFile(program, result2structprofile_sh, result2structprofile_sh_len);
     cmd.execProgram(FileUtil::getRealPathFromSymLink(program).c_str(), par.filenames);
 
     // Should never get here