New Tutorial and Manual

Tutorial_BioEM/Euler_Angle_List

+2
+    0.836000    1.369000    2.640000
+   -1.375000    0.400000    3.018000

Tutorial_BioEM/ListMRC

+OneImage.mrc
+TwoImages.mrc

Tutorial_BioEM/MODEL_COMPARISION/Compare_LogP

+   0  -70910.9000  -70904.7000      -6.2000      -6.2000
+   1  -70625.1000  -70607.9000     -17.2000     -23.4000
+   2  -70838.0000  -70812.7000     -25.3000     -48.7000
+   3  -70742.2000  -70751.8000       9.6000     -39.1000
+   4  -70582.3000  -70691.6000     109.3000      70.2000
+   5  -70756.7000  -70823.8000      67.1000     137.3000
+   6  -70565.9000  -70556.2000      -9.7000     127.6000
+   7  -70737.6000  -70742.0000       4.4000     132.0000
+   8  -70312.2000  -70464.9000     152.7000     284.7000
+   9  -70880.0000  -70880.4000       0.4000     285.1000
+  10  -70645.1000  -70645.5000       0.4000     285.5000
+  11  -70816.3000  -70814.3000      -2.0000     283.5000
+  12  -70759.3000  -70755.2000      -4.1000     279.4000
+  13  -70636.6000  -70638.0000       1.4000     280.8000
+  14  -70567.5000  -70638.3000      70.8000     351.6000
+  15  -70593.5000  -70579.6000     -13.9000     337.7000
+  16  -70785.1000  -70800.9000      15.8000     353.5000
+  17  -70548.2000  -70585.2000      37.0000     390.5000
+  18  -70856.3000  -70876.7000      20.4000     410.9000
+  19  -70764.9000  -70763.5000      -1.4000     409.5000

Tutorial_BioEM/MODEL_COMPARISION/Param_Input_ModelComparision

+NUMBER_PIXELS 224
+PIXEL_SIZE 1.32
+GRIDPOINTS_ENVELOPE 3 
+START_ENVELOPE 0.000
+END_ENVELOPE 0.001
+GRIDPOINTS_PSF_PHASE 3
+START_PSF_PHASE 0.004
+END_PSF_PHASE 0.024
+GRIDPOINTS_PSF_AMP 1
+START_PSF_AMP 1.
+END_PSF_AMP 1.
+MAX_D_CENTER 20
+PIXEL_GRID_CENTER 2
+NO_PROJECT_RADIUS
+QUATERNIONS

Tutorial_BioEM/Param_Input_ExtraFeatures

+NUMBER_PIXELS 220
+PIXEL_SIZE 1.77
+GRIDPOINTS_ALPHA 4 
+GRIDPOINTS_BETA  2
+GRIDPOINTS_ENVELOPE 4
+START_ENVELOPE 0.0002
+END_ENVELOPE 0.0012
+GRIDPOINTS_PSF_PHASE 4
+START_PSF_PHASE 0.004
+END_PSF_PHASE 0.016
+GRIDPOINTS_PSF_AMP 1
+START_PSF_AMP 1.
+END_PSF_AMP 1.
+MAX_D_CENTER 25
+PIXEL_GRID_CENTER 2
+WRITE_PROB_ANGLES
+WRITE_CROSSCOR
+CROSSCOR_NOTBAYESIAN 
+FLIPPED

Tutorial_BioEM/Param_Input_Quaternions

+NUMBER_PIXELS 220
+PIXEL_SIZE 1.77
+QUATERNIONS 4
+GRIDPOINTS_ENVELOPE 4
+START_ENVELOPE 0.0002
+END_ENVELOPE 0.0012
+GRIDPOINTS_PSF_PHASE 4
+START_PSF_PHASE 0.004
+END_PSF_PHASE 0.016
+GRIDPOINTS_PSF_AMP 1
+START_PSF_AMP 1.
+END_PSF_AMP 1.
+MAX_D_CENTER 25
+PIXEL_GRID_CENTER 2
+PROJECT_RADIUS
+WRITE_PROB_ANGLES

Tutorial_BioEM/Param_Input_Short

+NUMBER_PIXELS 220
+PIXEL_SIZE 1.77
+GRIDPOINTS_ALPHA 10 
+GRIDPOINTS_BETA  5
+GRIDPOINTS_ENVELOPE 4
+START_ENVELOPE 0.0002
+END_ENVELOPE 0.0012
+GRIDPOINTS_PSF_PHASE 4
+START_PSF_PHASE 0.004
+END_PSF_PHASE 0.016
+GRIDPOINTS_PSF_AMP 1
+START_PSF_AMP 1.
+END_PSF_AMP 1.
+MAX_D_CENTER 25
+PIXEL_GRID_CENTER 2

Tutorial_BioEM/Param_Print_MAP

+NUMBER_PIXELS 220
+PIXEL_SIZE 1.77
+BEST_AMP 1
+BEST_DX -10
+BEST_DY 5
+BEST_NORM 1
+BEST_OFFSET 0
+BEST_PHASE 0.00068
+BEST_ENVELOPE 0.03
+WITHNOISE 5.476
+BEST_ALPHA -0.464793
+BEST_GAMMA -0.409391
+BEST_BETA 1.97283
+#PRINT_ROTATED_MODELS

bioem.cpp

@@ -1006,6 +1006,10 @@ if(param.printrotmod) {
 
       for(int n = 0; n < Model.nPointsModel; n++)
 	{
+	 if(Model.points[n].radius < param.pixelSize){
+		cout << "Error: Radius less than Pixel size: use keyword NO_PROJECT_RADIUS in inputfile\n";
+		exit(1);
+		}
 	  //Getting Centers of Sphere
 	  i = floor(RotatedPointsModel[n].pos[0] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
 	  j = floor(RotatedPointsModel[n].pos[1] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
@@ -1016,7 +1020,8 @@ if(param.printrotmod) {
 	 if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
             {
               if (DebugOutput >= 0) cout << "WARNING::: Model Point out of Projection map: " << i << ", " << j << "\n";
-              continue;
+//              continue;
+		exit(1);
             }
 
 
@@ -1048,7 +1053,8 @@ if(param.printrotmod) {
 	  if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
 	    {
 	      if (DebugOutput >= 0) cout << "WARNING:::: Model Point out of Projection map: " << i << ", " << j << "\n";
-	      continue;
+//	      continue;
+		exit(1);
 	    }
 
 	  localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density;//Model.NormDen;