From f2525d5e86259dc7316b0b4ac25c608a2ee96e1a Mon Sep 17 00:00:00 2001
From: Pilar Cossio <pcos@phys01.bc.rzg.mpg.de>
Date: Mon, 30 Nov 2015 10:17:58 +0100
Subject: [PATCH] Checks for PSF/CTF correspondance

---
 Tutorial/PrintMAP_CTF_A | 30 ++++++++++++++++++++++++++++++
 Tutorial/PrintMAP_CTF_B | 30 ++++++++++++++++++++++++++++++
 Tutorial/PrintMAP_CTF_C | 30 ++++++++++++++++++++++++++++++
 Tutorial/PrintMAP_PSF_A | 32 ++++++++++++++++++++++++++++++++
 Tutorial/PrintMAP_PSF_B | 31 +++++++++++++++++++++++++++++++
 Tutorial/PrintMAP_PSF_C | 31 +++++++++++++++++++++++++++++++
 6 files changed, 184 insertions(+)
 create mode 100644 Tutorial/PrintMAP_CTF_A
 create mode 100644 Tutorial/PrintMAP_CTF_B
 create mode 100644 Tutorial/PrintMAP_CTF_C
 create mode 100644 Tutorial/PrintMAP_PSF_A
 create mode 100644 Tutorial/PrintMAP_PSF_B
 create mode 100644 Tutorial/PrintMAP_PSF_C

diff --git a/Tutorial/PrintMAP_CTF_A b/Tutorial/PrintMAP_CTF_A
new file mode 100644
index 0000000..ed39cb4
--- /dev/null
+++ b/Tutorial/PrintMAP_CTF_A
@@ -0,0 +1,30 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+BEST_CTF_DEFOCUS 4.8
+BEST_CTF_B_FACTOR 3500. 
+BEST_CTF_AMP 0.9
+
+#USE_PSF
+#BEST_PSF_PHASE 0.00579958170099887 
+#BEST_PSF_ENVELOPE 0.00188373456557911
+#BEST_PSF_AMP 0.11
+
+#WITHNOISE 0.05 
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
diff --git a/Tutorial/PrintMAP_CTF_B b/Tutorial/PrintMAP_CTF_B
new file mode 100644
index 0000000..681b81c
--- /dev/null
+++ b/Tutorial/PrintMAP_CTF_B
@@ -0,0 +1,30 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+BEST_CTF_DEFOCUS 2.8
+BEST_CTF_B_FACTOR 300. 
+BEST_CTF_AMP 0.3
+
+#USE_PSF
+#BEST_PSF_PHASE 0.00579958170099887 
+#BEST_PSF_ENVELOPE 0.00188373456557911
+#BEST_PSF_AMP 0.11
+
+#WITHNOISE 0.05 
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
diff --git a/Tutorial/PrintMAP_CTF_C b/Tutorial/PrintMAP_CTF_C
new file mode 100644
index 0000000..0829ce7
--- /dev/null
+++ b/Tutorial/PrintMAP_CTF_C
@@ -0,0 +1,30 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+BEST_CTF_DEFOCUS 1.8
+BEST_CTF_B_FACTOR 100. 
+BEST_CTF_AMP 0.6
+
+#USE_PSF
+#BEST_PSF_PHASE 0.00579958170099887 
+#BEST_PSF_ENVELOPE 0.00188373456557911
+#BEST_PSF_AMP 0.11
+
+#WITHNOISE 0.05 
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
diff --git a/Tutorial/PrintMAP_PSF_A b/Tutorial/PrintMAP_PSF_A
new file mode 100644
index 0000000..43f905d
--- /dev/null
+++ b/Tutorial/PrintMAP_PSF_A
@@ -0,0 +1,32 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+#EST_CTF_DEFOCUS 5. 
+#BEST_CTF_B_FACTOR 4000. 
+#BEST_CTF_AMP 0.9
+
+#FOR PARAMETERS ABOVE
+USE_PSF
+BEST_PSF_PHASE 0.0062
+BEST_PSF_ENVELOPE 0.0018
+BEST_PSF_AMP 0.71
+#0.993803211198498 FOR 0.2
+
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
+
diff --git a/Tutorial/PrintMAP_PSF_B b/Tutorial/PrintMAP_PSF_B
new file mode 100644
index 0000000..b909ad6
--- /dev/null
+++ b/Tutorial/PrintMAP_PSF_B
@@ -0,0 +1,31 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+#EST_CTF_DEFOCUS 2.8
+#BEST_CTF_B_FACTOR 300. 
+#BEST_CTF_AMP 0.3
+
+#FOR PARAMETERS ABOVE
+USE_PSF
+BEST_PSF_PHASE 0.0113764699661241
+BEST_PSF_ENVELOPE 0.000492672438985998
+BEST_PSF_AMP 0.966025647607897
+
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
+
diff --git a/Tutorial/PrintMAP_PSF_C b/Tutorial/PrintMAP_PSF_C
new file mode 100644
index 0000000..0f24930
--- /dev/null
+++ b/Tutorial/PrintMAP_PSF_C
@@ -0,0 +1,31 @@
+##### Micrograph Parameters #######
+NUMBER_PIXELS 100
+PIXEL_SIZE 2.74
+
+######## Center displacement ################
+BEST_DX 0
+BEST_DY 0
+
+######## Normalization and Offset ################
+BEST_NORM 1. 
+BEST_OFFSET 0.
+
+######## Euler Angles ################
+BEST_ALPHA 0.1122
+BEST_BETA 0.02361
+BEST_GAMMA 1.4586 
+
+######## Using PSF ################
+#EST_CTF_DEFOCUS 2.8
+#BEST_CTF_B_FACTOR 300. 
+#BEST_CTF_AMP 0.3
+
+#FOR PARAMETERS ABOVE
+USE_PSF
+BEST_PSF_PHASE 0.0178
+BEST_PSF_ENVELOPE 0.0005
+BEST_PSF_AMP 0.82
+
+########## Printing the 3d Model rotation ###########
+#PRINT_ROTATED_MODELS
+
-- 
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