diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
index fcb6c626..13f191b9 100644
--- a/src/commons/LocalParameters.cpp
+++ b/src/commons/LocalParameters.cpp
@@ -90,11 +90,14 @@ LocalParameters::LocalParameters() :
     tmalign.push_back(&PARAM_V);
 
     structurerescorediagonal.push_back(&PARAM_TMSCORE_THRESHOLD);
+    structurerescorediagonal.push_back(&PARAM_LDDT_THRESHOLD);
+    structurerescorediagonal.push_back(&PARAM_ALIGNMENT_TYPE);
     structurerescorediagonal = combineList(structurerescorediagonal, align);
 
     structurealign.push_back(&PARAM_TMSCORE_THRESHOLD);
     structurealign.push_back(&PARAM_LDDT_THRESHOLD);
     structurealign.push_back(&PARAM_SORT_BY_STRUCTURE_BITS);
+    structurealign.push_back(&PARAM_ALIGNMENT_TYPE);
     structurealign = combineList(structurealign, align);
 //    tmalign.push_back(&PARAM_GAP_OPEN);
 //    tmalign.push_back(&PARAM_GAP_EXTEND);
@@ -105,13 +108,11 @@ LocalParameters::LocalParameters() :
     strucclust.push_back(&PARAM_REMOVE_TMP_FILES);
     strucclust.push_back(&PARAM_RUNNER);
     // structuresearchworkflow
-    // structuresearchworkflow
     structuresearchworkflow = combineList(structurealign, prefilter);
     structuresearchworkflow = combineList(tmalign, structuresearchworkflow);
     structuresearchworkflow.push_back(&PARAM_EXHAUSTIVE_SEARCH);
     structuresearchworkflow.push_back(&PARAM_PREF_MODE);
     structuresearchworkflow.push_back(&PARAM_NUM_ITERATIONS);
-    structuresearchworkflow.push_back(&PARAM_ALIGNMENT_TYPE);
     structuresearchworkflow.push_back(&PARAM_REMOVE_TMP_FILES);
     structuresearchworkflow.push_back(&PARAM_RUNNER);
     structuresearchworkflow.push_back(&PARAM_REUSELATEST);
@@ -122,7 +123,7 @@ LocalParameters::LocalParameters() :
     easystructuresearchworkflow.push_back(&PARAM_GREEDY_BEST_HITS);
 
     structureclusterworkflow = combineList(prefilter, structurealign);
-    structureclusterworkflow = combineList(structureclusterworkflow, rescorediagonal);
+    structureclusterworkflow = combineList(structureclusterworkflow, structurerescorediagonal);
     structureclusterworkflow = combineList(structureclusterworkflow, tmalign);
     structureclusterworkflow = combineList(structureclusterworkflow, clust);
     structureclusterworkflow.push_back(&PARAM_CASCADED);
diff --git a/src/strucclustutils/structurealign.cpp b/src/strucclustutils/structurealign.cpp
index f1f2ae65..abfa41f3 100644
--- a/src/strucclustutils/structurealign.cpp
+++ b/src/strucclustutils/structurealign.cpp
@@ -31,6 +31,7 @@ static bool compareHitsByStructureBits(const Matcher::result_t &first, const Mat
 
 static void structureAlignDefault(LocalParameters & par) {
     par.compBiasCorrectionScale = 0.5;
+    par.alignmentType = LocalParameters::ALIGNMENT_TYPE_3DI_AA;
 }
 
 int alignStructure(StructureSmithWaterman & structureSmithWaterman,
@@ -219,7 +220,8 @@ int structurealign(int argc, const char **argv, const Command& command) {
             break;
         }
     }
-    SubstitutionMatrix subMatAA(blosum.c_str(), 1.4, par.scoreBias);
+    float aaFactor = (par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA) ? 1.4 : 0.0;
+    SubstitutionMatrix subMatAA(blosum.c_str(), aaFactor, par.scoreBias);
     //temporary output file
     Debug::Progress progress(resultReader.getSize());
 
diff --git a/src/strucclustutils/structurerescorediagonal.cpp b/src/strucclustutils/structurerescorediagonal.cpp
index 3df927c6..9b4d69fd 100644
--- a/src/strucclustutils/structurerescorediagonal.cpp
+++ b/src/strucclustutils/structurerescorediagonal.cpp
@@ -221,7 +221,8 @@ int structureungappedalign(int argc, const char **argv, const Command& command)
             break;
         }
     }
-    SubstitutionMatrix subMatAA(blosum.c_str(), 1.4, par.scoreBias);
+    float aaFactor = (par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA) ? 1.4 : 0.0;
+    SubstitutionMatrix subMatAA(blosum.c_str(), aaFactor, par.scoreBias);
     //temporary output file
     Debug::Progress progress(resultReader.getSize());
 
diff --git a/src/workflow/StructureCluster.cpp b/src/workflow/StructureCluster.cpp
index 3f547532..5cd587ca 100644
--- a/src/workflow/StructureCluster.cpp
+++ b/src/workflow/StructureCluster.cpp
@@ -107,14 +107,10 @@ int structurecluster(int argc, const char **argv, const Command& command) {
     CommandCaller cmd;
     cmd.addVariable("REMOVE_TMP", par.removeTmpFiles ? "TRUE" : NULL);
     std::string alnParam;
-    if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI) {
-        cmd.addVariable("ALIGNMENT_ALGO", "align");
-        cmd.addVariable("ALN_EXTENSION", "_ss");
-        alnParam = par.createParameterString(par.align);
-    } else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN) {
+    if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN) {
         cmd.addVariable("ALIGNMENT_ALGO", "tmalign");
         alnParam = par.createParameterString(par.tmalign);
-    } else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA) {
+    } else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA || par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI) {
         cmd.addVariable("ALIGNMENT_ALGO", "structurealign");
         alnParam = par.createParameterString(par.structurealign);
     }
diff --git a/src/workflow/StructureSearch.cpp b/src/workflow/StructureSearch.cpp
index 243fc70d..14b77f6e 100644
--- a/src/workflow/StructureSearch.cpp
+++ b/src/workflow/StructureSearch.cpp
@@ -119,12 +119,7 @@ int structuresearch(int argc, const char **argv, const Command &command) {
     if(par.exhaustiveSearch){
         cmd.addVariable("PREFMODE", "EXHAUSTIVE");
     }
-    if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI){
-        cmd.addVariable("ALIGNMENT_ALGO", "align");
-        cmd.addVariable("QUERY_ALIGNMENT", (query+"_ss").c_str());
-        cmd.addVariable("TARGET_ALIGNMENT", (target+"_ss").c_str());
-        cmd.addVariable("ALIGNMENT_PAR", par.createParameterString(par.align).c_str());
-    }else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN){
+   if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_TMALIGN){
         cmd.addVariable("ALIGNMENT_ALGO", "tmalign");
         cmd.addVariable("QUERY_ALIGNMENT", query.c_str());
         cmd.addVariable("TARGET_ALIGNMENT", target.c_str());
@@ -133,7 +128,7 @@ int structuresearch(int argc, const char **argv, const Command &command) {
         par.sortByStructureBits = 0;
         //par.evalThr = 10; we want users to adjust this one. Our default is 10 anyhow.
         cmd.addVariable("STRUCTUREALIGN_PAR", par.createParameterString(par.structurealign).c_str());
-    }else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA){
+    }else if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI_AA || par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI){
         cmd.addVariable("ALIGNMENT_ALGO", "structurealign");
         cmd.addVariable("QUERY_ALIGNMENT", query.c_str());
         cmd.addVariable("TARGET_ALIGNMENT", target.c_str());