diff --git a/bioem.cpp b/bioem.cpp
index ee6c264e307a27c06b43949cfcb09363844c4e2a..79625bba8260fa1ec477ab67ce083ee1232ffaa9 100755
--- a/bioem.cpp
+++ b/bioem.cpp
@@ -57,8 +57,8 @@ int bioem::configure(int ac, char* av[])
 	param.writeAngles = false;
 	param.dumpMap = false;
 	param.loadMap = false;
-	RefMap.readMRC = false;
-	RefMap.readMultMRC = false;
+	RefMap.readMRC = false;
+	RefMap.readMultMRC = false;
 
 	// *************************************************************************************
 	cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
@@ -68,17 +68,17 @@ int bioem::configure(int ac, char* av[])
 
 	try {
 		po::options_description desc("Command line inputs");
-		desc.add_options()
-		("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
-		("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
-		("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
-		("ReadPDB", "(Optional) If reading model file in PDB format")
-		("ReadMRC", "(Optional) If reading particle file in MRC format")
-		("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
-		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
-		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
-		("help", "(Optional) Produce help message")
-		;
+		desc.add_options()
+		("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
+		("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
+		("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
+		("ReadPDB", "(Optional) If reading model file in PDB format")
+		("ReadMRC", "(Optional) If reading particle file in MRC format")
+		("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
+		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
+		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
+		("help", "(Optional) Produce help message")
+		;
 
 
 		po::positional_options_description p;
@@ -86,8 +86,8 @@ int bioem::configure(int ac, char* av[])
 		p.add("Modelfile", -1);
 		p.add("Particlesfile", -1);
 		p.add("ReadPDB", -1);
-		p.add("ReadMRC", -1);
-		p.add("ReadMultipleMRC", -1);
+		p.add("ReadMRC", -1);
+		p.add("ReadMultipleMRC", -1);
 		p.add("DumpMaps", -1);
 		p.add("LoadMapDump", -1);
 
@@ -125,17 +125,17 @@ int bioem::configure(int ac, char* av[])
 			Model.readPDB = true;
 		}
 
-		if (vm.count("ReadMRC"))
-		{
-			cout << "Reading particle file in MRC format.\n";
-			RefMap.readMRC=true;
-		}
-
-		if (vm.count("ReadMultipleMRC"))
-		{
-			cout << "Reading Multiple MRCs.\n";
-			RefMap.readMultMRC=true;
-		}
+		if (vm.count("ReadMRC"))
+		{
+			cout << "Reading particle file in MRC format.\n";
+			RefMap.readMRC=true;
+		}
+
+		if (vm.count("ReadMultipleMRC"))
+		{
+			cout << "Reading Multiple MRCs.\n";
+			RefMap.readMultMRC=true;
+		}
 
 		if (vm.count("DumpMaps"))
 		{
@@ -379,8 +379,8 @@ int bioem::run()
 
 int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
 {
-	//***************************************************************************************
-	//***** BioEM routine for comparing reference maps to convoluted maps *****
+	//***************************************************************************************
+	//***** BioEM routine for comparing reference maps to convoluted maps *****
 	if (FFTAlgo)
 	{
 		//With FFT Algorithm
@@ -405,8 +405,8 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
 
 inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC)
 {
-	//***************************************************************************************
-	//***** Calculating cross correlation in FFTALGOrithm *****
+	//***************************************************************************************
+	//***** Calculating cross correlation in FFTALGOrithm *****
 
 	const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
 	for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
diff --git a/include/map.h b/include/map.h
index 796a5e3e3be93150cb6f5ae9f72fd0d307d6aa7e..05a11ed894f01802734daf375619ed4785e7232c 100755
--- a/include/map.h
+++ b/include/map.h
@@ -34,16 +34,16 @@ public:
 	int precalculate(bioem_param& param, bioem& bio);
 	int PreCalculateMapsFFT(bioem_param& param);
 
-	int  read_int(int *currlong, FILE *fin, int swap);
-	int  read_float(float *currfloat, FILE *fin, int swap);
-	int  read_float_empty (FILE *fin);
-	int  read_char_float (float *currfloat, FILE *fin) ;
-	int  test_mrc (const char *vol_file, int swap);
-	int  read_MRC(const char* filename,bioem_param& param);
+	int  read_int(int *currlong, FILE *fin, int swap);
+	int  read_float(float *currfloat, FILE *fin, int swap);
+	int  read_float_empty (FILE *fin);
+	int  read_char_float (float *currfloat, FILE *fin) ;
+	int  test_mrc (const char *vol_file, int swap);
+	int  read_MRC(const char* filename,bioem_param& param);
 
 	mycomplex_t* RefMapsFFT;
 
-	bool readMRC,readMultMRC;
+	bool readMRC,readMultMRC;
 
 	int ntotRefMap;
 	int numPixels;
diff --git a/map.cpp b/map.cpp
index a22e1cd9d15db40bcdb4fafadf2ca1dc57374eb5..789243583c3f3ee5b1f522759ba2dcd2058df889 100755
--- a/map.cpp
+++ b/map.cpp
@@ -35,54 +35,54 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 
 		cout << "Particle Maps read from Map Dump\n";
 	}
-	else if(readMRC)
-	{
-		ntotRefMap=0;
-
-		if(readMultMRC)
-		{
-			ifstream input(filemap);
-
-			if (!input.good())
-			{
-				cout << "Failed to open file contaning MRC names: " << filemap << "\n";
-				exit(0);
-			}
-
-			char line[512] = {0};
-			char mapname[100];
-			char tmpm[10] = {0};
-			const char* indifile;
-
-			while (!input.eof())
-			{
-				input.getline(line,512);
-				char tmpVals[100]  = {' '};
-
-				strncpy (tmpVals,line,100);
-				sscanf (tmpVals,"%99c",mapname);
-
-				// Check for last line
-				strncpy (tmpm,mapname,3);		
-				if(strcmp(tmpm,"XXX")!=0)
-				{
-					indifile = mapname;  
-					//Reading Multiple MRC
-					read_MRC(indifile,param);
-
-				}
-				for(int i=0;i<3;i++)mapname[i] = 'X';	
-				for(int i=3;i<100;i++)mapname[i] = {0};	
-
-			}
-			cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
-		} else {
-			read_MRC(filemap,param);
-			cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
-			cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
-		}
-	}
+	else if(readMRC)
+	{
+		ntotRefMap=0;
+
+		if(readMultMRC)
+		{
+			ifstream input(filemap);
+
+			if (!input.good())
+			{
+				cout << "Failed to open file contaning MRC names: " << filemap << "\n";
+				exit(0);
+			}
+
+			char line[512] = {0};
+			char mapname[100];
+			char tmpm[10] = {0};
+			const char* indifile;
+
+			while (!input.eof())
+			{
+				input.getline(line,512);
+				char tmpVals[100]  = {' '};
+
+				strncpy (tmpVals,line,100);
+				sscanf (tmpVals,"%99c",mapname);
+
+				// Check for last line
+				strncpy (tmpm,mapname,3);		
+				if(strcmp(tmpm,"XXX")!=0)
+				{
+					indifile = mapname;  
+					//Reading Multiple MRC
+					read_MRC(indifile,param);
+
+				}
+				for(int i=0;i<3;i++)mapname[i] = 'X';	
+				for(int i=3;i<100;i++)mapname[i] = {0};	
+
+			}
+			cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
+			cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
+		} else {
+			read_MRC(filemap,param);
+			cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
+			cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
+		}
+	}
 	else
 	{
 		int nummap = -1;
@@ -177,7 +177,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 	}
 
 	cout << "Total Number of particles: " << ntotRefMap;
-	cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
+	cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
 
 	sum_RefMap = (myfloat_t*) mallocchk(sizeof(myfloat_t) * ntotRefMap);
 	sumsquare_RefMap = (myfloat_t*) mallocchk(sizeof(myfloat_t) * ntotRefMap);
@@ -265,266 +265,266 @@ void bioem_Probability::init(size_t maps, size_t angles, bioem& bio)
 	set_pointers();
 }
 
-int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
-{
-	myfloat_t st,st2; 
-	unsigned long count;
-	FILE *fin;
-	float currfloat;
-	int nc, nr, ns, swap, header_ok = 1;
-	float xlen, ylen, zlen;
-	int mode, ncstart, nrstart, nsstart, ispg, nsymbt, lskflg;
-	float a_tmp, b_tmp, g_tmp;
-	int  mx, my, mz,mapc, mapr, maps;
-	float dmin, dmax, dmean;
-	int n_range_viol0, n_range_viol1;
-
-	fin = fopen(filename, "rb");
-	if( fin == NULL ) {
-		cout << "ERROR opening MRC: " << filename;
-		exit(1);
-	}
-	n_range_viol0 = test_mrc(filename,0);
-	n_range_viol1 = test_mrc(filename,1);
-
-
-	if (n_range_viol0 < n_range_viol1) { //* guess endianism 
-		swap = 0;
-		if (n_range_viol0 > 0) {
-			printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0,filename);
-		}
-	} else {
-		swap = 1;
-		if (n_range_viol1 > 0) {
-			printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1,filename);
-		}
-	}
-	printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
-	printf("Reading Information from MRC: %s \n", filename);
-	header_ok *= read_int(&nc,fin,swap);
-	header_ok *= read_int(&nr,fin,swap);
-	header_ok *= read_int(&ns,fin,swap);
-	header_ok *= read_int(&mode,fin,swap);
-	header_ok *= read_int(&ncstart,fin,swap);
-	header_ok *= read_int(&nrstart,fin,swap);
-	header_ok *= read_int(&nsstart,fin,swap);
-	header_ok *= read_int(&mx,fin,swap);
-	header_ok *= read_int(&my,fin,swap);
-	header_ok *= read_int(&mz,fin,swap);
-	header_ok *= read_float(&xlen,fin,swap);
-	header_ok *= read_float(&ylen,fin,swap);
-	header_ok *= read_float(&zlen,fin,swap);
-	header_ok *= read_float(&a_tmp,fin,swap);
-	header_ok *= read_float(&b_tmp,fin,swap);
-	header_ok *= read_float(&g_tmp,fin,swap);
-	header_ok *= read_int(&mapc,fin,swap);
-	header_ok *= read_int(&mapr,fin,swap);
-	header_ok *= read_int(&maps,fin,swap);
-	header_ok *= read_float(&dmin,fin,swap);
-	header_ok *= read_float(&dmax,fin,swap);
-	header_ok *= read_float(&dmean,fin,swap);
-	header_ok *= read_int(&ispg,fin,swap);
-	header_ok *= read_int(&nsymbt,fin,swap);
-	header_ok *= read_int(&lskflg,fin,swap);
-
-	printf("Number Columns  = %8d \n",nc);
-	printf("Number Rows     = %8d \n",nr);
-	printf("Number Sections = %8d \n",ns);
-	printf("MODE = %4d (only data type mode 2: 32-bit)\n",mode);
-	printf("NSYMBT = %4d (# bytes symmetry operators)\n",nsymbt);
-
-	/* printf("  NCSTART = %8d  (index of first column, counting from 0)\n",ncstart);
-	printf(">  NRSTART = %8d  (index of first row, counting from 0)\n",nrstart);
-	printf("  NSSTART = %8d  (index of first section, counting from 0)\n",nsstart);
-	printf("       MX = %8d  (# of X intervals in unit cell)\n",mx);
-	printf("       MY = %8d  (# of Y intervals in unit cell)\n",my);
-	printf("       MZ = %8d  (# of Z intervals in unit cell)\n",mz);
-	printf(" X length = %8.3f  (unit cell dimension)\n",xlen);
-	printf(" Y length = %8.3f  (unit cell dimension)\n",ylen);
-	printf(" Z length = %8.3f  (unit cell dimension)\n",zlen);
-	printf("    Alpha = %8.3f  (unit cell angle)\n",a_tmp);
-	printf("     Beta = %8.3f  (unit cell angle)\n",b_tmp);
-	printf("    Gamma = %8.3f  (unit cell angle)\n",g_tmp);
-	printf("     MAPC = %8d  (columns axis: 1=X,2=Y,3=Z)\n",mapc);
-	printf("     MAPR = %8d  (rows axis: 1=X,2=Y,3=Z)\n",mapr);
-	printf("     MAPS = %8d  (sections axis: 1=X,2=Y,3=Z)\n",maps);
-	printf("     DMIN = %8.3f  (minimum density value - ignored)\n",dmin);
-	printf("     DMAX = %8.3f  (maximum density value - ignored)\n",dmax);
-	printf("    DMEAN = %8.3f  (mean density value - ignored)\n",dmean);
-	printf("     ISPG = %8d  (space group number - ignored)\n",ispg);
-	printf("   NSYMBT = %8d  (# bytes storing symmetry operators)\n",nsymbt);
-	printf("   LSKFLG = %8d  (skew matrix flag: 0:none, 1:follows)\n",lskflg);*/
-
-	if (header_ok == 0) {
-		cout << "ERROR reading MRC header: " << filename;
-		exit(1);
-	}
-
-	if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
-	{
-		cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
-		exit(1);
-	}
-
-	if(mode!=2)
-	{
-		cout << "ERROR with MRC mode " << mode << "\n";
-		cout << "Currently mode 2 is the only one allowed" << "\n";
-		exit(1);
-
-	} else
-	{  
-		rewind (fin);
-		for (count=0; count<256; ++count) if (read_float_empty(fin)==0) {
-			cout << "ERROR Converting Data: " <<  filename;
-			exit(1);
-		}
-
-		for (count=0; count<(unsigned long)nsymbt; ++count) if (read_char_float(&currfloat,fin)==0) {
-			cout << "ERROR Converting Data: " <<  filename;
-			exit(1);    
-		}
-
-		for ( int nmap = 0 ; nmap < ns ; nmap ++ )
-		{
-			st=0.0;
-			st2=0.0;
-			for ( int j = 0 ; j < nr ; j ++ )
-				for ( int i = 0 ; i < nc ; i ++ )
-				{
-					if (read_float(&currfloat,fin,swap)==0) {
-						cout << "ERROR Converting Data: " <<  filename;
-						exit(1);
-					} else {
-						Ref[nmap+ntotRefMap].points[i][j] = currfloat;
-						st += currfloat;
-						st2 += currfloat*currfloat;
-					}
-				}	
-
-				//Normaling maps to zero mean and unit standard deviation
-				st /= float(nr*nc);
-				st2 = sqrt(st2/float(nr*nc)-st*st); 
-				for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
-					Ref[nmap+ntotRefMap].points[i][j] =  Ref[nmap+ntotRefMap].points[i][j]/st2 - st/st2;
-					//    if(nmap+ntotRefMap==300)cout << i << " " << j << " " << nmap+ntotRefMap << " " <<  Ref[nmap+ntotRefMap].points[i][j]  << "\n";                          
-				}
-		}
-		ntotRefMap += ns ;
-		//  cout << ntotRefMap << "\n";
-	}
-	fclose (fin);
-
-	return(0);
-}
-
-int bioem_RefMap::read_float(float *currfloat, FILE *fin, int swap) {
-	unsigned char *cptr, tmp;
-
-	if (fread(currfloat,4,1,fin)!=1) return 0;
-	if (swap == 1) {
-		cptr = (unsigned char *)currfloat;
-		tmp = cptr[0];
-		cptr[0]=cptr[3];
-		cptr[3]=tmp;
-		tmp = cptr[1];
-		cptr[1]=cptr[2];
-		cptr[2]=tmp;
-	}
-	return 1;
-}
-
-int  bioem_RefMap::read_int(int *currlong, FILE *fin, int swap) {
-	unsigned char *cptr, tmp;
-
-	if (fread(currlong,4,1,fin)!=1) return 0;
-	if (swap == 1) {
-		cptr = (unsigned char *)currlong;
-		tmp = cptr[0];
-		cptr[0]=cptr[3];
-		cptr[3]=tmp;
-		tmp = cptr[1];
-		cptr[1]=cptr[2];
-		cptr[2]=tmp;
-	}
-	return 1;
-}
-int  bioem_RefMap::read_float_empty (FILE *fin) {
-	float currfloat;
-
-	if (fread(&currfloat,4,1,fin)!=1) return 0;
-	return 1;
-}
-
-int  bioem_RefMap::read_char_float (float *currfloat, FILE *fin) {
-	char currchar;
-
-	if (fread(&currchar,1,1,fin)!=1) return 0;
-	*currfloat=(float)currchar;
-	return 1;
-}
-
-int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
-	FILE *fin;
-	int nc, nr, ns, mx, my, mz;
-	int mode, ncstart, nrstart, nsstart;
-	float xlen, ylen, zlen;
-	int i, header_ok = 1, n_range_viols = 0;
-	int mapc, mapr, maps;
-	float alpha, beta, gamma;
-	float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;
-
-	fin = fopen(vol_file, "rb");
-	if( fin == NULL ) {
-		cout << "ERROR opening MRC: " << vol_file;
-		exit(1);
-	}
-
-	//* read header info 
-	header_ok *= read_int(&nc,fin,swap);
-	header_ok *= read_int(&nr,fin,swap);
-	header_ok *= read_int(&ns,fin,swap);
-	header_ok *= read_int(&mode,fin,swap);
-	header_ok *= read_int(&ncstart,fin,swap);
-	header_ok *= read_int(&nrstart,fin,swap);
-	header_ok *= read_int(&nsstart,fin,swap);
-	header_ok *= read_int(&mx,fin,swap);
-	header_ok *= read_int(&my,fin,swap);
-	header_ok *= read_int(&mz,fin,swap);
-	header_ok *= read_float(&xlen,fin,swap);
-	header_ok *= read_float(&ylen,fin,swap);
-	header_ok *= read_float(&zlen,fin,swap);
-	header_ok *= read_float(&alpha,fin,swap);
-	header_ok *= read_float(&beta,fin,swap);
-	header_ok *= read_float(&gamma,fin,swap);
-	header_ok *= read_int(&mapc,fin,swap);
-	header_ok *= read_int(&mapr,fin,swap);
-	header_ok *= read_int(&maps,fin,swap);
-	header_ok *= read_float(&dmin,fin,swap);
-	header_ok *= read_float(&dmax,fin,swap);
-	header_ok *= read_float(&dmean,fin,swap);
-	for (i=23; i<50; ++i) header_ok *= read_float(&dummy,fin,swap);
-	header_ok *= read_float(&xorigin,fin,swap);
-	header_ok *= read_float(&yorigin,fin,swap);
-	header_ok *= read_float(&zorigin,fin,swap);
-	fclose (fin);
-	if (header_ok == 0) {
-		cout << "ERROR reading MRC header: " << vol_file;
-		exit(1);
-	}
-
-	n_range_viols += (nc>5000); n_range_viols += (nc<0);
-	n_range_viols += (nr>5000); n_range_viols += (nr<0);
-	n_range_viols += (ns>5000); n_range_viols += (ns<0);
-	n_range_viols += (ncstart>5000); n_range_viols += (ncstart<-5000);
-	n_range_viols += (nrstart>5000); n_range_viols += (nrstart<-5000);
-	n_range_viols += (nsstart>5000); n_range_viols += (nsstart<-5000);
-	n_range_viols += (mx>5000); n_range_viols += (mx<0);
-	n_range_viols += (my>5000); n_range_viols += (my<0);
-	n_range_viols += (mz>5000); n_range_viols += (mz<0);
-	n_range_viols += (alpha>360.0f); n_range_viols += (alpha<-360.0f);
-	n_range_viols += (beta>360.0f); n_range_viols += (beta<-360.0f);
-	n_range_viols += (gamma>360.0f); n_range_viols += (gamma<-360.0f);
-
-	return n_range_viols;
-}
+int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
+{
+	myfloat_t st,st2; 
+	unsigned long count;
+	FILE *fin;
+	float currfloat;
+	int nc, nr, ns, swap, header_ok = 1;
+	float xlen, ylen, zlen;
+	int mode, ncstart, nrstart, nsstart, ispg, nsymbt, lskflg;
+	float a_tmp, b_tmp, g_tmp;
+	int  mx, my, mz,mapc, mapr, maps;
+	float dmin, dmax, dmean;
+	int n_range_viol0, n_range_viol1;
+
+	fin = fopen(filename, "rb");
+	if( fin == NULL ) {
+		cout << "ERROR opening MRC: " << filename;
+		exit(1);
+	}
+	n_range_viol0 = test_mrc(filename,0);
+	n_range_viol1 = test_mrc(filename,1);
+
+
+	if (n_range_viol0 < n_range_viol1) { //* guess endianism 
+		swap = 0;
+		if (n_range_viol0 > 0) {
+			printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0,filename);
+		}
+	} else {
+		swap = 1;
+		if (n_range_viol1 > 0) {
+			printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1,filename);
+		}
+	}
+	printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
+	printf("Reading Information from MRC: %s \n", filename);
+	header_ok *= read_int(&nc,fin,swap);
+	header_ok *= read_int(&nr,fin,swap);
+	header_ok *= read_int(&ns,fin,swap);
+	header_ok *= read_int(&mode,fin,swap);
+	header_ok *= read_int(&ncstart,fin,swap);
+	header_ok *= read_int(&nrstart,fin,swap);
+	header_ok *= read_int(&nsstart,fin,swap);
+	header_ok *= read_int(&mx,fin,swap);
+	header_ok *= read_int(&my,fin,swap);
+	header_ok *= read_int(&mz,fin,swap);
+	header_ok *= read_float(&xlen,fin,swap);
+	header_ok *= read_float(&ylen,fin,swap);
+	header_ok *= read_float(&zlen,fin,swap);
+	header_ok *= read_float(&a_tmp,fin,swap);
+	header_ok *= read_float(&b_tmp,fin,swap);
+	header_ok *= read_float(&g_tmp,fin,swap);
+	header_ok *= read_int(&mapc,fin,swap);
+	header_ok *= read_int(&mapr,fin,swap);
+	header_ok *= read_int(&maps,fin,swap);
+	header_ok *= read_float(&dmin,fin,swap);
+	header_ok *= read_float(&dmax,fin,swap);
+	header_ok *= read_float(&dmean,fin,swap);
+	header_ok *= read_int(&ispg,fin,swap);
+	header_ok *= read_int(&nsymbt,fin,swap);
+	header_ok *= read_int(&lskflg,fin,swap);
+
+	printf("Number Columns  = %8d \n",nc);
+	printf("Number Rows     = %8d \n",nr);
+	printf("Number Sections = %8d \n",ns);
+	printf("MODE = %4d (only data type mode 2: 32-bit)\n",mode);
+	printf("NSYMBT = %4d (# bytes symmetry operators)\n",nsymbt);
+
+	/* printf("  NCSTART = %8d  (index of first column, counting from 0)\n",ncstart);
+	printf(">  NRSTART = %8d  (index of first row, counting from 0)\n",nrstart);
+	printf("  NSSTART = %8d  (index of first section, counting from 0)\n",nsstart);
+	printf("       MX = %8d  (# of X intervals in unit cell)\n",mx);
+	printf("       MY = %8d  (# of Y intervals in unit cell)\n",my);
+	printf("       MZ = %8d  (# of Z intervals in unit cell)\n",mz);
+	printf(" X length = %8.3f  (unit cell dimension)\n",xlen);
+	printf(" Y length = %8.3f  (unit cell dimension)\n",ylen);
+	printf(" Z length = %8.3f  (unit cell dimension)\n",zlen);
+	printf("    Alpha = %8.3f  (unit cell angle)\n",a_tmp);
+	printf("     Beta = %8.3f  (unit cell angle)\n",b_tmp);
+	printf("    Gamma = %8.3f  (unit cell angle)\n",g_tmp);
+	printf("     MAPC = %8d  (columns axis: 1=X,2=Y,3=Z)\n",mapc);
+	printf("     MAPR = %8d  (rows axis: 1=X,2=Y,3=Z)\n",mapr);
+	printf("     MAPS = %8d  (sections axis: 1=X,2=Y,3=Z)\n",maps);
+	printf("     DMIN = %8.3f  (minimum density value - ignored)\n",dmin);
+	printf("     DMAX = %8.3f  (maximum density value - ignored)\n",dmax);
+	printf("    DMEAN = %8.3f  (mean density value - ignored)\n",dmean);
+	printf("     ISPG = %8d  (space group number - ignored)\n",ispg);
+	printf("   NSYMBT = %8d  (# bytes storing symmetry operators)\n",nsymbt);
+	printf("   LSKFLG = %8d  (skew matrix flag: 0:none, 1:follows)\n",lskflg);*/
+
+	if (header_ok == 0) {
+		cout << "ERROR reading MRC header: " << filename;
+		exit(1);
+	}
+
+	if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
+	{
+		cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
+		exit(1);
+	}
+
+	if(mode!=2)
+	{
+		cout << "ERROR with MRC mode " << mode << "\n";
+		cout << "Currently mode 2 is the only one allowed" << "\n";
+		exit(1);
+
+	} else
+	{  
+		rewind (fin);
+		for (count=0; count<256; ++count) if (read_float_empty(fin)==0) {
+			cout << "ERROR Converting Data: " <<  filename;
+			exit(1);
+		}
+
+		for (count=0; count<(unsigned long)nsymbt; ++count) if (read_char_float(&currfloat,fin)==0) {
+			cout << "ERROR Converting Data: " <<  filename;
+			exit(1);    
+		}
+
+		for ( int nmap = 0 ; nmap < ns ; nmap ++ )
+		{
+			st=0.0;
+			st2=0.0;
+			for ( int j = 0 ; j < nr ; j ++ )
+				for ( int i = 0 ; i < nc ; i ++ )
+				{
+					if (read_float(&currfloat,fin,swap)==0) {
+						cout << "ERROR Converting Data: " <<  filename;
+						exit(1);
+					} else {
+						Ref[nmap+ntotRefMap].points[i][j] = currfloat;
+						st += currfloat;
+						st2 += currfloat*currfloat;
+					}
+				}	
+
+				//Normaling maps to zero mean and unit standard deviation
+				st /= float(nr*nc);
+				st2 = sqrt(st2/float(nr*nc)-st*st); 
+				for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
+					Ref[nmap+ntotRefMap].points[i][j] =  Ref[nmap+ntotRefMap].points[i][j]/st2 - st/st2;
+					//    if(nmap+ntotRefMap==300)cout << i << " " << j << " " << nmap+ntotRefMap << " " <<  Ref[nmap+ntotRefMap].points[i][j]  << "\n";                          
+				}
+		}
+		ntotRefMap += ns ;
+		//  cout << ntotRefMap << "\n";
+	}
+	fclose (fin);
+
+	return(0);
+}
+
+int bioem_RefMap::read_float(float *currfloat, FILE *fin, int swap) {
+	unsigned char *cptr, tmp;
+
+	if (fread(currfloat,4,1,fin)!=1) return 0;
+	if (swap == 1) {
+		cptr = (unsigned char *)currfloat;
+		tmp = cptr[0];
+		cptr[0]=cptr[3];
+		cptr[3]=tmp;
+		tmp = cptr[1];
+		cptr[1]=cptr[2];
+		cptr[2]=tmp;
+	}
+	return 1;
+}
+
+int  bioem_RefMap::read_int(int *currlong, FILE *fin, int swap) {
+	unsigned char *cptr, tmp;
+
+	if (fread(currlong,4,1,fin)!=1) return 0;
+	if (swap == 1) {
+		cptr = (unsigned char *)currlong;
+		tmp = cptr[0];
+		cptr[0]=cptr[3];
+		cptr[3]=tmp;
+		tmp = cptr[1];
+		cptr[1]=cptr[2];
+		cptr[2]=tmp;
+	}
+	return 1;
+}
+int  bioem_RefMap::read_float_empty (FILE *fin) {
+	float currfloat;
+
+	if (fread(&currfloat,4,1,fin)!=1) return 0;
+	return 1;
+}
+
+int  bioem_RefMap::read_char_float (float *currfloat, FILE *fin) {
+	char currchar;
+
+	if (fread(&currchar,1,1,fin)!=1) return 0;
+	*currfloat=(float)currchar;
+	return 1;
+}
+
+int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
+	FILE *fin;
+	int nc, nr, ns, mx, my, mz;
+	int mode, ncstart, nrstart, nsstart;
+	float xlen, ylen, zlen;
+	int i, header_ok = 1, n_range_viols = 0;
+	int mapc, mapr, maps;
+	float alpha, beta, gamma;
+	float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;
+
+	fin = fopen(vol_file, "rb");
+	if( fin == NULL ) {
+		cout << "ERROR opening MRC: " << vol_file;
+		exit(1);
+	}
+
+	//* read header info 
+	header_ok *= read_int(&nc,fin,swap);
+	header_ok *= read_int(&nr,fin,swap);
+	header_ok *= read_int(&ns,fin,swap);
+	header_ok *= read_int(&mode,fin,swap);
+	header_ok *= read_int(&ncstart,fin,swap);
+	header_ok *= read_int(&nrstart,fin,swap);
+	header_ok *= read_int(&nsstart,fin,swap);
+	header_ok *= read_int(&mx,fin,swap);
+	header_ok *= read_int(&my,fin,swap);
+	header_ok *= read_int(&mz,fin,swap);
+	header_ok *= read_float(&xlen,fin,swap);
+	header_ok *= read_float(&ylen,fin,swap);
+	header_ok *= read_float(&zlen,fin,swap);
+	header_ok *= read_float(&alpha,fin,swap);
+	header_ok *= read_float(&beta,fin,swap);
+	header_ok *= read_float(&gamma,fin,swap);
+	header_ok *= read_int(&mapc,fin,swap);
+	header_ok *= read_int(&mapr,fin,swap);
+	header_ok *= read_int(&maps,fin,swap);
+	header_ok *= read_float(&dmin,fin,swap);
+	header_ok *= read_float(&dmax,fin,swap);
+	header_ok *= read_float(&dmean,fin,swap);
+	for (i=23; i<50; ++i) header_ok *= read_float(&dummy,fin,swap);
+	header_ok *= read_float(&xorigin,fin,swap);
+	header_ok *= read_float(&yorigin,fin,swap);
+	header_ok *= read_float(&zorigin,fin,swap);
+	fclose (fin);
+	if (header_ok == 0) {
+		cout << "ERROR reading MRC header: " << vol_file;
+		exit(1);
+	}
+
+	n_range_viols += (nc>5000); n_range_viols += (nc<0);
+	n_range_viols += (nr>5000); n_range_viols += (nr<0);
+	n_range_viols += (ns>5000); n_range_viols += (ns<0);
+	n_range_viols += (ncstart>5000); n_range_viols += (ncstart<-5000);
+	n_range_viols += (nrstart>5000); n_range_viols += (nrstart<-5000);
+	n_range_viols += (nsstart>5000); n_range_viols += (nsstart<-5000);
+	n_range_viols += (mx>5000); n_range_viols += (mx<0);
+	n_range_viols += (my>5000); n_range_viols += (my<0);
+	n_range_viols += (mz>5000); n_range_viols += (mz<0);
+	n_range_viols += (alpha>360.0f); n_range_viols += (alpha<-360.0f);
+	n_range_viols += (beta>360.0f); n_range_viols += (beta<-360.0f);
+	n_range_viols += (gamma>360.0f); n_range_viols += (gamma<-360.0f);
+
+	return n_range_viols;
+}
diff --git a/param.cpp b/param.cpp
index 58b544ad5fbc039fd176f40ba14b23a38997836b..6e514d2704c4ece391ebde21e6128a8db9df0517 100755
--- a/param.cpp
+++ b/param.cpp
@@ -42,22 +42,22 @@ int bioem_param::readParameters()
 	// ***************************** Reading Input Parameters ******************************
 	// **************************************************************************************
 
-	// Control for Parameters
-	bool yesPixSi = false;
-	bool yesNumPix = false;
-	bool yesGPal = false;
-	bool yesGPbe = false;
-	bool yesGPEnv = false;
-	bool yesGPamp = false;
-	bool yesGPpha = false;
-	bool yesSTEnv = false;
-	bool yesSTamp = false;
-	bool yesSTpha = false;
-	bool yesGSPamp = false ;
-	bool yesGSPEnv = false ;
-	bool yesGSPpha = false ;
-	bool yesMDC = false ;
-	bool yesGCen = false ;	
+	// Control for Parameters
+	bool yesPixSi = false;
+	bool yesNumPix = false;
+	bool yesGPal = false;
+	bool yesGPbe = false;
+	bool yesGPEnv = false;
+	bool yesGPamp = false;
+	bool yesGPpha = false;
+	bool yesSTEnv = false;
+	bool yesSTamp = false;
+	bool yesSTpha = false;
+	bool yesGSPamp = false ;
+	bool yesGSPEnv = false ;
+	bool yesGSPpha = false ;
+	bool yesMDC = false ;
+	bool yesGCen = false ;	
 
 	ifstream input(fileinput);
 	if (!input.good())
@@ -87,116 +87,116 @@ int bioem_param::readParameters()
 		{
 			token = strtok(NULL, " ");
 			pixelSize = atof(token);
-			if (pixelSize < 0 ) { cout << "*** Error: Negative pixelSize "; exit(1);}
-			cout << "Pixel Sixe " << pixelSize << "\n";
-			yesPixSi= true;
+			if (pixelSize < 0 ) { cout << "*** Error: Negative pixelSize "; exit(1);}
+			cout << "Pixel Sixe " << pixelSize << "\n";
+			yesPixSi= true;
 		}
 		else if (strcmp(token, "NUMBER_PIXELS") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.NumberPixels = int(atoi(token));
-			if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
-			cout << "Number of Pixels " << param_device.NumberPixels << "\n";			
-			yesNumPix= true ;
+			if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
+			cout << "Number of Pixels " << param_device.NumberPixels << "\n";			
+			yesNumPix= true ;
 		}
 		else if (strcmp(token, "GRIDPOINTS_ALPHA") == 0)
 		{
 			token = strtok(NULL, " ");
 			angleGridPointsAlpha = int(atoi(token));
-			if (angleGridPointsAlpha < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ALPHA "; exit(1);}
-			cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
-			yesGPal= true;
+			if (angleGridPointsAlpha < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ALPHA "; exit(1);}
+			cout << "Grid points alpha " << angleGridPointsAlpha << "\n";
+			yesGPal= true;
 		}
 		else if (strcmp(token, "GRIDPOINTS_BETA") == 0)
 		{
 			token = strtok(NULL, " ");
 			angleGridPointsBeta = int(atoi(token));
-			if (angleGridPointsBeta < 0 ) { cout << "*** Error: Negative GRIDPOINTS_BETA "; exit(1);}
-			cout << "Grid points beta " << angleGridPointsBeta << "\n";
-			yesGPbe= true;
+			if (angleGridPointsBeta < 0 ) { cout << "*** Error: Negative GRIDPOINTS_BETA "; exit(1);}
+			cout << "Grid points beta " << angleGridPointsBeta << "\n";
+			yesGPbe= true;
 		}
 
 		else if (strcmp(token, "GRIDPOINTS_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			numberGridPointsEnvelop = int(atoi(token));
-			if (numberGridPointsDisplaceCenter < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ENVELOPE "; exit(1);}
-			cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
-			yesGPEnv = true;
+			if (numberGridPointsDisplaceCenter < 0 ) { cout << "*** Error: Negative GRIDPOINTS_ENVELOPE "; exit(1);}
+			cout << "Grid points envelope " << numberGridPointsEnvelop << "\n";
+			yesGPEnv = true;
 		}
 		else if (strcmp(token, "START_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			startGridEnvelop = atof(token);
-			if (startGridEnvelop < 0 ) { cout << "*** Error: Negative START_ENVELOPE "; exit(1);}
-			cout << "Start Envelope " << startGridEnvelop << "\n";
-			yesSTEnv = true ;
+			if (startGridEnvelop < 0 ) { cout << "*** Error: Negative START_ENVELOPE "; exit(1);}
+			cout << "Start Envelope " << startGridEnvelop << "\n";
+			yesSTEnv = true ;
 		}
 		else if (strcmp(token, "GRIDSPACE_ENVELOPE") == 0)
 		{
 			token = strtok(NULL, " ");
 			gridEnvelop = atof(token);
-			if (gridEnvelop < 0 ) { cout << "*** Error: Negative GRIDSPACE_ENVELOPE "; exit(1);}
-			cout << "Grid spacing Envelope " << gridEnvelop << "\n";
-			yesGSPEnv = true ;
+			if (gridEnvelop < 0 ) { cout << "*** Error: Negative GRIDSPACE_ENVELOPE "; exit(1);}
+			cout << "Grid spacing Envelope " << gridEnvelop << "\n";
+			yesGSPEnv = true ;
+		}
+		else if (strcmp(token,"GRIDPOINTS_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			numberGridPointsCTF_phase=int(atoi(token));
+			cout << "Grid points PSF " << numberGridPointsCTF_phase << "\n";
+			yesGPpha = true;
+		}
+		else if (strcmp(token,"START_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			startGridCTF_phase=atof(token);
+			cout << "Start PSF " << startGridCTF_phase << "\n";
+			yesSTpha = true ;
+		}
+		else if (strcmp(token,"GRIDSPACE_PSF_PHASE")==0)
+		{
+			token = strtok(NULL," ");
+			gridCTF_phase=atof(token);
+			cout << "Grid Space PSF " << gridCTF_phase << "\n";
+			yesGSPpha = true ;
+		}
+		else if (strcmp(token,"GRIDPOINTS_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			numberGridPointsCTF_amp=int(atoi(token));
+			cout << "Grid points PSF " << numberGridPointsCTF_amp << "\n";
+			yesGPamp = true ;
+		}
+		else if (strcmp(token,"START_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			startGridCTF_amp=atof(token);
+			cout << "Start PSF " << startGridCTF_amp << "\n";
+			yesSTamp = true ;
+		}
+		else if (strcmp(token,"GRIDSPACE_PSF_AMP")==0)
+		{
+			token = strtok(NULL," ");
+			gridCTF_amp=atof(token);
+			cout << "Grid Space PSF " << gridCTF_amp << "\n";
+			yesGSPamp = true ;
 		}
-		else if (strcmp(token,"GRIDPOINTS_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			numberGridPointsCTF_phase=int(atoi(token));
-			cout << "Grid points PSF " << numberGridPointsCTF_phase << "\n";
-			yesGPpha = true;
-		}
-		else if (strcmp(token,"START_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			startGridCTF_phase=atof(token);
-			cout << "Start PSF " << startGridCTF_phase << "\n";
-			yesSTpha = true ;
-		}
-		else if (strcmp(token,"GRIDSPACE_PSF_PHASE")==0)
-		{
-			token = strtok(NULL," ");
-			gridCTF_phase=atof(token);
-			cout << "Grid Space PSF " << gridCTF_phase << "\n";
-			yesGSPpha = true ;
-		}
-		else if (strcmp(token,"GRIDPOINTS_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			numberGridPointsCTF_amp=int(atoi(token));
-			cout << "Grid points PSF " << numberGridPointsCTF_amp << "\n";
-			yesGPamp = true ;
-		}
-		else if (strcmp(token,"START_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			startGridCTF_amp=atof(token);
-			cout << "Start PSF " << startGridCTF_amp << "\n";
-			yesSTamp = true ;
-		}
-		else if (strcmp(token,"GRIDSPACE_PSF_AMP")==0)
-		{
-			token = strtok(NULL," ");
-			gridCTF_amp=atof(token);
-			cout << "Grid Space PSF " << gridCTF_amp << "\n";
-			yesGSPamp = true ;
-		}
 		else if (strcmp(token, "MAX_D_CENTER") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.maxDisplaceCenter = int(atoi(token));
-			if (param_device.maxDisplaceCenter < 0 ) { cout << "*** Error: Negative MAX_D_CENTER "; exit(1);}
-			cout << "Maximum displacement Center " <<  param_device.maxDisplaceCenter << "\n";
-			yesMDC = true;
+			if (param_device.maxDisplaceCenter < 0 ) { cout << "*** Error: Negative MAX_D_CENTER "; exit(1);}
+			cout << "Maximum displacement Center " <<  param_device.maxDisplaceCenter << "\n";
+			yesMDC = true;
 		}
 		else if (strcmp(token, "PIXEL_GRID_CENTER") == 0)
 		{
 			token = strtok(NULL, " ");
 			param_device.GridSpaceCenter = int(atoi(token));
-			if (param_device.GridSpaceCenter < 0 ) { cout << "*** Error: Negative PIXEL_GRID_CENTER "; exit(1);}
-			cout << "Grid space displacement center " <<   param_device.GridSpaceCenter << "\n";
-			yesGCen = true;
+			if (param_device.GridSpaceCenter < 0 ) { cout << "*** Error: Negative PIXEL_GRID_CENTER "; exit(1);}
+			cout << "Grid space displacement center " <<   param_device.GridSpaceCenter << "\n";
+			yesGCen = true;
 		}
 		else if (strcmp(token, "WRITE_PROB_ANGLES") == 0)
 		{
@@ -206,41 +206,41 @@ int bioem_param::readParameters()
 	}
 	input.close();
 
-	// Checks for ALL INPUT 
-	if( not ( yesPixSi ) ){ cout << "**** INPUT MISSING: Please provide PIXEL_SIZE\n" ; exit (1);};
-	if( not ( yesNumPix ) ){ cout << "**** INPUT MISSING: Please provide NUMBER_PIXELS \n" ; exit (1);};
-	if( not ( yesGPal ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA \n" ; exit (1);};
-	if( not ( yesGPbe ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_BETA \n" ; exit (1);};
-	if( not (  yesGPEnv ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE \n" ; exit (1);};
-	if( not (  yesGPamp ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP \n" ; exit (1);};
-	if( not (  yesGPpha ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE \n" ; exit (1);};
-	if( not (  yesSTEnv  ) ) { cout << "**** INPUT MISSING: Please provide START_ENVELOPE \n" ; exit (1);};
-	if( not (  yesSTamp  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_AMP \n" ; exit (1);};
-	if( not (  yesSTpha  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_PHASE \n" ; exit (1);};
-	if( not (  yesGSPamp  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP \n" ; exit (1);};
-	if( not ( yesGSPEnv  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE \n" ; exit (1);};
-	if( not ( yesGSPpha  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_PHASE \n" ; exit (1);};
-	if( not (  yesMDC  ) ) { cout << "**** INPUT MISSING: Please provide MAX_D_CENTER \n" ; exit (1);};
-	if( not (  yesGCen  ) ) { cout << "**** INPUT MISSING: Please provide PIXEL_GRID_CENTER \n" ; exit (1);};
-
-	//More checks with input parameters
-
-	// Envelope should not have a standard deviation greater than Npix/2 
-	if(sqrt(1./( (myfloat_t) numberGridPointsDisplaceCenter  * gridEnvelop + startGridEnvelop))> float(param_device.NumberPixels)/2.0) {
-		cout << "MAX Standar deviation of envelope is larger than Allowed KERNEL Length " ;
-		exit(1);
-	}
-	// Envelop param should be positive
-	if( startGridCTF_amp < 0 || startGridCTF_amp > 1){
-		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
-		exit(1);
-	}
-
-	if( (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp < 0 || (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp > 1){
-		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
-		exit(1);
-	}
-
+	// Checks for ALL INPUT 
+	if( not ( yesPixSi ) ){ cout << "**** INPUT MISSING: Please provide PIXEL_SIZE\n" ; exit (1);};
+	if( not ( yesNumPix ) ){ cout << "**** INPUT MISSING: Please provide NUMBER_PIXELS \n" ; exit (1);};
+	if( not ( yesGPal ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA \n" ; exit (1);};
+	if( not ( yesGPbe ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_BETA \n" ; exit (1);};
+	if( not (  yesGPEnv ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE \n" ; exit (1);};
+	if( not (  yesGPamp ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP \n" ; exit (1);};
+	if( not (  yesGPpha ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE \n" ; exit (1);};
+	if( not (  yesSTEnv  ) ) { cout << "**** INPUT MISSING: Please provide START_ENVELOPE \n" ; exit (1);};
+	if( not (  yesSTamp  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_AMP \n" ; exit (1);};
+	if( not (  yesSTpha  ) ) { cout << "**** INPUT MISSING: Please provide START_PSF_PHASE \n" ; exit (1);};
+	if( not (  yesGSPamp  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP \n" ; exit (1);};
+	if( not ( yesGSPEnv  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE \n" ; exit (1);};
+	if( not ( yesGSPpha  ) ) { cout << "**** INPUT MISSING: Please provide GRIDSPACE_PSF_PHASE \n" ; exit (1);};
+	if( not (  yesMDC  ) ) { cout << "**** INPUT MISSING: Please provide MAX_D_CENTER \n" ; exit (1);};
+	if( not (  yesGCen  ) ) { cout << "**** INPUT MISSING: Please provide PIXEL_GRID_CENTER \n" ; exit (1);};
+
+	//More checks with input parameters
+
+	// Envelope should not have a standard deviation greater than Npix/2 
+	if(sqrt(1./( (myfloat_t) numberGridPointsDisplaceCenter  * gridEnvelop + startGridEnvelop))> float(param_device.NumberPixels)/2.0) {
+		cout << "MAX Standar deviation of envelope is larger than Allowed KERNEL Length " ;
+		exit(1);
+	}
+	// Envelop param should be positive
+	if( startGridCTF_amp < 0 || startGridCTF_amp > 1){
+		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
+		exit(1);
+	}
+
+	if( (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp < 0 || (myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp > 1){
+		cout << "PSF Amplitud should be between 0 and 1  \n" ;	   
+		exit(1);
+	}
+
 
 
 	cout << " +++++++++++++++++++++++++++++++++++++++++ \n";