diff --git a/windows/WinCoot_install_masta.nsi b/windows/WinCoot_install_masta.nsi
index 22fe504f5b..63810cf5d4 100644
--- a/windows/WinCoot_install_masta.nsi
+++ b/windows/WinCoot_install_masta.nsi
@@ -171,6 +171,39 @@ FunctionEnd
   Call un.ErrorHandlerFunction
 !macroend
 
+; Macro to move files from INSTDIR to USERPROFILE/COOT
+!macro MoveFileToNewHome File isDir
+  ; to avoid duplicate labels...
+  !define ID ${__LINE__}
+  ; check if file exists
+  ClearErrors
+  MessageBox MB_OK `Is "${File}" a dir?`
+  ${If} ${FileExists} "${INSTDIR}\${File}"
+    # your code here
+    MessageBox MB_OK "Try rename"
+    Rename ${INSTDIR}\${File} $%USERPROFILE%\COOT\${File}
+    IfErrors "" skipit_${ID}
+      # somehow couldnt rename, try to copy to dest and remove src
+      # this may be necessary if on different driveletters
+      ClearErrors
+      CopyFiles /Silent ${INSTDIR}\${File} $%USERPROFILE%\COOT\${File}
+      IfErrors "" remove_src_${ID}
+        # couldnt copy, give message
+        MessageBox MB_ICONINFORMATION `"${File}" couldnt be moved from it's old place in \
+        "${INSTDIR}" to new place "$%USERPROFILE%\COOT". \
+        Consider doing it manually if deemed important.`
+        goto skipit_${ID}
+      remove_src_${ID}:
+        ${IF} isDir == "true"
+          RMDir /r ${INSTDIR}\${File}
+        ${Else}
+          Delete ${INSTDIR}\${File}
+        ${EndIf}
+    skipit_${ID}:
+  ${EndIf}
+  !undef ID
+!macroend
+
 ; MUI end ------
 
 Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"
@@ -279,6 +312,8 @@ Section "!WinCoot" SEC01
   File "${src_dir}\bin\gdk-pixbuf-query-loaders.exe"
   ; render (or more?) from raster3d?!
   File "${src_dir}\bin\render.exe"
+  ; clustalw2
+  File "${src_dir}\bin\clustalw2.exe"
   ;gunzip needed?? dont think so
   File "C:\msys64\home\bernhard\autobuild\extras\gunzip"
   File "C:\msys64\home\bernhard\autobuild\extras\gzip.exe"
@@ -456,11 +491,7 @@ Section -AddIcons
 
  exit:
    SetShellVarContext current
-  ; in case we want to install silently (no user intervention)
-  ; we have to call the finish page function, otherwise runwincoot.bat
-  ; won't be edited.
-  IfSilent 0 +2
-    Call FinishPagePreFunction
+  Call FinishPagePreFunction
   IfErrors 0 +5
     ; ${ErrorHandler} 3 "Error in installation. Could not install icons." 0
     DetailPrint "Error in installation. Could not install icons. Continuing."
@@ -470,6 +501,12 @@ Section -AddIcons
 SectionEnd
 
 Section -Post
+  ; first make COOT_HOME in USERPROFILE if it doesnt exist, then move files
+  IfFileExists "$%USERPROFILE%\COOT\*.*" have_usercoot
+    CreateDirectory "$%USERPROFILE%\COOT"
+    Call MoveUserHomeFiles
+  have_usercoot:
+
   ClearErrors
   WriteUninstaller "$INSTDIR\uninst.exe"
 ;  NO MESSING WITH THE REGISTRY!!!!
@@ -562,6 +599,7 @@ Section Uninstall
   Delete "$INSTDIR\bin\lidia.exe"
   Delete "$INSTDIR\bin\mini-rsr-bin.exe"
   Delete "$INSTDIR\bin\render.exe"
+  Delete "$INSTDIR\bin\clustalw2.exe"
   Delete "$INSTDIR\bin\Microsoft.VC90.CRT.manifest"
   Delete "$INSTDIR\bin\pango-querymodules.exe"
   Delete "$INSTDIR\bin\pango-view.exe"
@@ -706,7 +744,7 @@ Function .onInit
 ; no more examples dir (have data dir now)
 ; so default start dir is $INSTDIR
   ${If} $STARTDIR == ""
-    StrCpy $STARTDIR "$INSTDIR"
+    StrCpy $STARTDIR "$%USERPROFILE%"
   ${EndIf}
   IfErrors 0 +6
     ;${ErrorHandler} 6 "Error in installation. Could not initiate installation." 1
@@ -988,9 +1026,9 @@ ${If} $update = 0
   CreateShortCut "$DESKTOP\WinCoot.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\wincoot.bat"' "$INSTDIR\bin\coot-icon.ico" 0 SW_SHOWMINIMIZED
   CreateShortCut "$SMPROGRAMS\$ICONS_GROUP\WinCoot.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\wincoot.bat"' "$INSTDIR\bin\coot-icon.ico" 0 SW_SHOWMINIMIZED
   Sleep 10
-  SetOutPath "$INSTDIR"
   CreateShortCut "$SMPROGRAMS\$ICONS_GROUP\DynaRama.lnk" "$SYSDIR\cmd.exe" '/c "$INSTDIR\bin\dynarama.bat"' "$INSTDIR\bin\rama_all.ico"
   Sleep 10
+  SetOutPath "$INSTDIR"
   WriteIniStr "$INSTDIR\WinCoot.url" "InternetShortcut" "URL" "${PRODUCT_WEB_SITE}"
   WriteIniStr "$INSTDIR\Coot.url" "InternetShortcut" "URL" "${PRODUCT_WEB_SITE_2}"
   CreateShortCut "$SMPROGRAMS\WinCoot\WinCoot Website.lnk" "$INSTDIR\${PRODUCT_NAME}.url"
@@ -1030,3 +1068,23 @@ Function ErrorHandler
   ${EndIf}
 
 FunctionEnd
+
+; Function to move potentially existing WinCoot files and directories from
+; INSTALLDIR to USERPROFILE\COOT
+Function MoveUserHomeFiles
+  ; what shall we move? preferences, backup, downloads dirs, state and history
+  ; state and history files...
+  !insertmacro "MoveFileToNewHome" ".coot-preferences" "true"
+  !insertmacro "MoveFileToNewHome" "coot-backup" "true"
+  !insertmacro "MoveFileToNewHome" "coot-download" "true"
+  !insertmacro "MoveFileToNewHome" "coot-ccp4" "true"
+  !insertmacro "MoveFileToNewHome" "coot-molprobity" "true"
+  !insertmacro "MoveFileToNewHome" "coot-refmac" "true"
+  !insertmacro "MoveFileToNewHome" "coot-acedrg" "true"
+  !insertmacro "MoveFileToNewHome" "coot-pisa" "true"
+  !insertmacro "MoveFileToNewHome" "0-coot-history.scm" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot.state.py" "false"
+  !insertmacro "MoveFileToNewHome" ".coot.py" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot.state.scm" "false"
+  !insertmacro "MoveFileToNewHome" "0-coot-history.scm" "false"
+FunctionEnd
diff --git a/windows/wincoot.bat b/windows/wincoot.bat
index bc27f6073f..3591e963da 100644
--- a/windows/wincoot.bat
+++ b/windows/wincoot.bat
@@ -3,34 +3,94 @@
 @set LC_NUMERIC=en
 title WinCoot
 
+REM First try to find a dictionary. Search in the registry for a
+REM CCP4 installation and then setup CCP4.
 
-set COOT_PREFIX=yourWinCootdirectory
+if not exist "%CLIBD_MON%" (
+   echo no $CLIBD_MON found trying to setup CCP4
+   call :setup_ccp4
+)
+
+REM main line
+
+set COOT_PREFIX=%~dp0
 set COOT_GUILE_PREFIX=%COOT_PREFIX:\=/%
 
-set COOT_HOME=%COOT_PREFIX%
+REM New COOT_HOME is in User directory now
+set COOT_HOME=%USERPROFILE%\COOT
 set COOT_BACKUP_DIR=%COOT_PREFIX%\coot-backup
 
 set COOT_SHARE=%COOT_PREFIX%\share
+
 if not exist "%CLIBD_MON%" (
   echo no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
-  set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
+  Call :setup_coot_dictionary
 )
+
 set COOT_SCHEME_DIR=%COOT_SHARE%/coot/scheme
 set COOT_STANDARD_RESIDUES=%COOT_SHARE%\coot\standard-residues.pdb
 set COOT_PIXMAPS_DIR=%COOT_SHARE%\coot\pixmaps
 set COOT_RESOURCES_FILE=%COOT_SHARE%\coot\cootrc
 set COOT_DATA_DIR=%COOT_SHARE%\coot
 set COOT_REF_STRUCTS=%COOT_SHARE%\coot\reference-structures
-set COOT_PYTHON_DIR=%COOT_PREFIX%\python27\lib\site-packages\coot
-REM set COOT_REF_SEC_STRUCTS=%COOT_SHARE%\coot\ss-reference-structures
-
-set PYTHONHOME=%COOT_PREFIX%\python27
+set COOT_PYTHON_DIR=%COOT_PREFIX%\lib\python2.7\site-packages\coot
+REM set PYTHONHOME=%COOT_PREFIX%\python27
 
 set GUILE_LOAD_PATH=%COOT_GUILE_PREFIX%/share/guile/1.8;%COOT_GUILE_PREFIX%/share/guile;%COOT_GUILE_PREFIX%/share/guile/gtk-2.0;%COOT_GUILE_PREFIX%/share/guile/gui;%COOT_GUILE_PREFIX%/share/guile/www;%COOT_GUILE_PREFIX%/share/guile/site
 
 set SYMINFO=%COOT_SHARE%\coot\syminfo.lib
 
-set PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\lib;%COOT_PREFIX%\python27;%PATH%;%COOT_PREFIX%\bin\extras
+set PATH=%COOT_PREFIX%\bin;%COOT_PREFIX%\lib;%PATH%;%COOT_PREFIX%\bin\extras
 
 coot-bin.exe %*
 
+Exit /B %ERRORLEVEL%
+
+
+REM function to setup CCP4
+:setup_ccp4
+set /a CCP4_MAJOR=10
+
+:loop_start
+set /a CCP4_MAJOR=CCP4_MAJOR-1
+
+call :find_ccp4 HKCU\SOFTWARE\CCP4-%CCP4_MAJOR%
+if exist "%CLIBD_MON%" (goto :loop_end)
+
+call :find_ccp4 HKLM\SOFTWARE\WOW6432Node\CCP4-%CCP4_MAJOR%
+if exist "%CLIBD_MON%" (goto :loop_end)
+
+if %CCP4_MAJOR% gtr 6 (goto :loop_start)
+:loop_end
+
+Exit /B 0
+
+
+REM Function to find CCP4 in the registry and call ccp4 setup bat
+:find_ccp4
+REM Check in Registry for CCP4 InstallDir
+for /f "skip=1 tokens=3" %%A in (
+  'reg query %1 /v InstallDir 2^>Nul'
+) do set CCP4DIR=%%~A
+if not exist "%CCP4DIR%" (Exit /B 0)
+
+REM find latest dir
+for /f " tokens=*" %%i in (
+  'dir "%CCP4DIR%\%CCP4_MAJOR%.*" /b /ad-h /t:c /od'
+) do set SETUPFILE=%CCP4DIR%\%%i\ccp4.setup.bat
+if not exist "%SETUPFILE%" (Exit /B 0)
+
+REM Finally, setup CCP4
+call "%SETUPFILE%"
+Exit /B 0
+
+:setup_coot_dictionary
+set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
+set WARN=No valid dictionary found, no refinement possible!
+if not exist "%COOT_REFMAC_LIB_DIR%" (
+  REM check for Phenix place too
+  if not exist "%COOT_MONOMER_LIB_DIR%" (
+    msg "%USERNAME%" WinCoot WARNING:: %WARN%
+  )
+)
+Exit /B 0