diff --git a/src/DiagramWindow.h b/src/DiagramWindow.h
index 379f749..d4fe479 100755
--- a/src/DiagramWindow.h
+++ b/src/DiagramWindow.h
@@ -21,7 +21,7 @@
 #include "RNAStructure.h"
 #include "BranchTypeIdentification.h"
 
-#define IMAGE_DIM                    (550)
+#define IMAGE_DIM                    (485)
 #define IMAGE_WIDTH                  (IMAGE_DIM)
 #define IMAGE_HEIGHT                 (IMAGE_DIM)
 #define IMAGE_DEPTH                  (3)
@@ -29,7 +29,7 @@
 #define PNG_FOOTER_HEIGHT            (100)
 
 #define GLWIN_TRANSLATEX             (35)
-#define GLWIN_TRANSLATEY             (90)
+#define GLWIN_TRANSLATEY             (110)
 
 #define WIDGET_SPACING               (35)
 #define EXPORT_BUTTON_WIDTH          (115)
diff --git a/src/FolderWindow.cpp b/src/FolderWindow.cpp
index 9377fb6..a288b4c 100755
--- a/src/FolderWindow.cpp
+++ b/src/FolderWindow.cpp
@@ -153,8 +153,10 @@ void FolderWindow::AddStructure(const char* filename, const int index)
     size_t fileNameBytes = strlen(filename);
     snprintf(filePrefix, MAX_BUFFER_SIZE, "%-.20s%s", filename, 
 	     fileNameBytes > MAX_FOLDER_LABEL_CHARS ? "..." : "");
-    snprintf(labelWithIcon, MAX_BUFFER_SIZE - 1, "@filenew   %s%s@|>", 
-	     filePrefix, spaceBuffer.substr(0, MAX_FOLDER_LABEL_CHARS - strlen(filePrefix)).c_str());
+    snprintf(labelWithIcon, MAX_BUFFER_SIZE - 1, "@filenew   %s%s", 
+	     filePrefix, spaceBuffer.substr(0, 
+             MAX(0, MAX_FOLDER_LABEL_CHARS - ((int ) strlen(filePrefix)))).c_str());
+    strcat(labelWithIcon, "   @|>");
     label->copy_label(labelWithIcon); 
     
     Fl_Button* removeButton = new Fl_Button(pack->x() + pack->w() - 20, vertPosn + 5, 20, 20);
diff --git a/src/FolderWindow.h b/src/FolderWindow.h
index 1993c36..ad273b1 100755
--- a/src/FolderWindow.h
+++ b/src/FolderWindow.h
@@ -17,7 +17,7 @@
 
 #include "ConfigOptions.h"
 
-#define MAX_FOLDER_LABEL_CHARS           (20)
+#define MAX_FOLDER_LABEL_CHARS           (25)
 
 class FolderWindow : public Fl_Group
 {
diff --git a/src/InputWindow.cpp b/src/InputWindow.cpp
index 168e09a..8784c84 100755
--- a/src/InputWindow.cpp
+++ b/src/InputWindow.cpp
@@ -83,23 +83,23 @@ InputWindow::InputWindow(int w, int h, const char *label,
 	    button->set_active();
 	    input->callback(InputCallback, (void*)0);
 	    input->labelcolor(GUI_TEXT_COLOR);
-	    /*const char *cbText = " Use only default names for structure folders";
+	    const char *cbText = " Use only default names for structure folders";
 	    cbUseDefaultNames = new Fl_Check_Button(30, 100, 325, 30, cbText);
 	    cbUseDefaultNames->box(FL_ROUND_UP_BOX);
 	    cbUseDefaultNames->color(GUI_BGCOLOR);
 	    cbUseDefaultNames->labelcolor(GUI_BTEXT_COLOR);
 	    cbUseDefaultNames->down_color(GUI_WINDOW_BGCOLOR);
-	    cbUseDefaultNames->align(FL_ALIGN_LEFT | FL_ALIGN_INSIDE | FL_ALIGN_CENTER);*/
+	    cbUseDefaultNames->align(FL_ALIGN_LEFT | FL_ALIGN_INSIDE | FL_ALIGN_CENTER);
 	    callback(CloseCallback);
 	}
         show();
-        /*if(type == InputWindow::FILE_INPUT || !GUI_USE_DEFAULT_FOLDER_NAMES) { 
+        if(type == InputWindow::FILE_INPUT || !GUI_USE_DEFAULT_FOLDER_NAMES) { 
             show();
 	}
 	else {
 	    show();
 	    InputCallback((Fl_Widget *) cbUseDefaultNames, (void *) NULL);
-	}*/
+	}
 }
 
 InputWindow::~InputWindow() {
@@ -131,9 +131,9 @@ void InputWindow::InputCallback(Fl_Widget *widget, void *userdata)
 	    return;
 	}
 	window->name = window->inputText;
-        //if(window->cbUseDefaultNames->value()) {
-        //    GUI_USE_DEFAULT_FOLDER_NAMES = true;
-        //}
+        if(window->cbUseDefaultNames->value()) {
+            GUI_USE_DEFAULT_FOLDER_NAMES = true;
+        }
     }    
     free(window->string);
     window->hide();
@@ -151,15 +151,5 @@ std::string InputWindow::ExtractStructureNameFromCTName(const char *ctPath) {
     char suggestedShortName[MAX_BUFFER_SIZE];
     snprintf(suggestedShortName, MAX_BUFFER_SIZE, "Structure #% 2d\0", ++InputWindow::distinctStructureCount);
     return std::string(suggestedShortName);
-    /*std::string structName(ctPath);
-    int structureNameNoPrefix = structName.find_first_of('_');
-    if(structureNameNoPrefix >= 0) {
-        structName = structName.substr(structureNameNoPrefix + 1);;
-    }
-    int dotIndexPtr = structName.find_last_of('.');
-    if(dotIndexPtr >= 0) {
-        structName = structName.substr(0, dotIndexPtr);
-    }
-    return structName;*/ 
 }