diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4e9da0a435d5a49ea8a91eac9432ca49b3b8e786..e052dd2ca83100aa39e4995fc4dc306e88049368 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,9 +2,9 @@ cmake_minimum_required(VERSION 2.6)
 project(BioEM)
 
 ###Set up options
-option (INCLUDE_CUDA "Build BioEM with CUDA support" OFF)
-option (INCLUDE_OPENMP "Build BioEM with OpenMP support" ON)
-option (INCLUDE_MPI "Build BioEM with MPI support" ON)
+option (USE_CUDA "Build BioEM with CUDA support" OFF)
+option (USE_OPENMP "Build BioEM with OpenMP support" ON)
+option (USE_MPI "Build BioEM with MPI support" ON)
 option (PRINT_CMAKE_VARIABLES "List all CMAKE Variables" OFF)
 option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" ON)
 
diff --git a/Manual/BioEM_Manual.pdf b/Manual/BioEM_Manual.pdf
index a16950399296506231497dc285eb0cb491cd7b38..68e16d600801902a3b1699879c3f5c66b40fce54 100644
Binary files a/Manual/BioEM_Manual.pdf and b/Manual/BioEM_Manual.pdf differ
diff --git a/Manual/BioEM_Manual.tex b/Manual/BioEM_Manual.tex
index fabec4d7b1fefebbf58d89c6bd9afd0eebad1ca8..55ae8872379c677ff0da5996547e9e01442a17a1 100644
--- a/Manual/BioEM_Manual.tex
+++ b/Manual/BioEM_Manual.tex
@@ -119,7 +119,7 @@ However, analyzing the images individually is challenging because the signal-to-
 This has so far limited EM to study a small subset of static biomolecules, because, 
 for it to be effective, it requires most particles to be in the same conformation.
 
-Here, we present a computing tool to harness the single-molecule caracter of EM for studying dynamic biomolecules.
+Here, we present a computing tool to harness the single-molecule character of EM for studying dynamic biomolecules.
 With our method, we can categorize and classify models of flexible biomolecules from individual EM images.
 Bayesian inference of electron microscopy images, BioEM \cite{CossioHummerJSB_2013,BioEM_server}, allows us to
 compute the posterior probability of a model given experimental data. 
@@ -132,7 +132,7 @@ the variability and dynamics of the biological system.
 In this chapter, we briefly describe the mathematical background of the BioEM method.
 Then, we present the necessary tools and procedures to install the BioEM software. We describe the prerequisite programs 
 that should be preinstalled on the compute node. Then, we explain the BioEM download files and directories. Lastly, 
-we describe the steps to install BioEM using the CMake program.
+we describe the steps to install BioEM using the CMake program. The commandline executions are using the bash scripting language.
 
 \section{Theoretical background}
 \label{theory}
@@ -184,6 +184,7 @@ In this manual, it is assumed that the user has sufficient comprehension
 of the BioEM theory. Therefore, it is encouraged to read refs.~\cite{CossioHummerJSB_2013,BioEM_server} thoroughly. 
 
 \section{Installation}
+
 \subsection{Prerequisite programs and libraries}
 
 Before installation, there are several programs and libraries that should be preinstalled on the compute node. 
@@ -223,6 +224,8 @@ www.nvidia.com.
 \item {\it MPI:} Message Passing Interface is a standardized and portable message-passing system designed to function on a wide variety of parallel computers, with and without shared-memory.
 Any MPI platform (either openMPI or MPICH) can be used with BioEM. The minimal version of {\it impi} is {\bf 5.0}.
 
+\item {\it Git:} is a system that is used for project development (see https://git-scm.com/). Git can be used to clone the BioEM software into a local directory.
+
 \end{itemize}
 
 
@@ -237,17 +240,26 @@ libraries is also used to compile BioEM.
 \subsection{Download}
 \label{download}
 
-A compressed directory of the BioEM software can be downloaded from [{\bf PC: mpi biophys or RZG?}].
-After downloading the {\it tar.gz} file, uncompress it by executing
+The BioEM software can be cloned using {\it git} from https://gitlab.rzg.mpg.de/BioEM/BioEM with
+\vspace{0.5cm}
+
+\fbox{%
+\parbox{12cm}{
+{ \texttt{git clone https://gitlab.rzg.mpg.de/BioEM/BioEM}}}}
+
+\vspace{0.5cm}
+
+In addition, a compressed directory of the BioEM software can be downloaded from https://gitlab.rzg.mpg.de/BioEM/BioEM.
+After downloading the {\it zip} file, uncompress it by executing
 \vspace{0.5cm}
 
 \fbox{%
 \parbox{12cm}{
-{ \texttt{tar -zxvf BioEM.tar.gz}}}}
+{ \texttt{unzip BioEM.zip}}}}
 
 \vspace{0.5cm}
 
-In the uncompressed {\bf BioEM} directory, there are:
+In the {\bf BioEM} directory there are:
 \begin{itemize}
 \item[--]the source code {\it .cpp} and {\it .cu} files.
 \item[--]the {\bf include} directory with corresponding header files.
@@ -280,9 +292,9 @@ These options can be enabled or disabled by executing cmake with:
 \\
 \fbox{%
 \parbox{12cm}{
-{\texttt{cmake -DINCLUDE\_CUDA=ON CMakeLists.txt}}}}\\
+{\texttt{cmake -DUSE\_CUDA=ON CMakeLists.txt}}}}\\
 
-It is also possible to modify these options directly in the CMakeLists.txt file. At the begining of this file, the
+It is also possible to modify these options directly in the CMakeLists.txt file. At the beginning of this file, the
 keywords and ON/OFF options are presented.
 
 \begin{table}[h]
@@ -292,11 +304,11 @@ keywords and ON/OFF options are presented.
 \hline
 {\bf Keyword} & {\bf Option}\\
 \hline
-\texttt{INCLUDE\_OPENMP} & Enable/Disable OpenMP \\
+\texttt{USE\_OPENMP} & Enable/Disable OpenMP \\
 \hline
-\texttt{INCLUDE\_MPI} & Enable/Disable MPI \\
+\texttt{USE\_MPI} & Enable/Disable MPI \\
 \hline
-\texttt{INCLUDE\_CUDA} & Enable/Disable CUDA \\
+\texttt{USE\_CUDA} & Enable/Disable CUDA \\
 \hline
  \texttt{PRINT\_CMAKE\_VARIABLES} & Printout CMake variables\\
 \hline
@@ -326,7 +338,7 @@ standard host compiler is incompatible with CUDA)\\
 \parbox{12cm}{
 {\texttt{mkdir build \&\& cd build}}}}
 
-\item[--] Run CMake with the desired options and the {\it CMakeLists.txt} file {\bf PC: This is not working for me, I'm getting in-source builds?}
+\item[--] Run CMake with the desired options and the {\it CMakeLists.txt} file %{\bf PC: This is not working for me, I'm getting in-source builds?}
 
 \fbox{%
 \parbox{12cm}{
@@ -383,7 +395,7 @@ Command line inputs:
 In this chapter, we describe the BioEM input commands and keywords. BioEM has two 
 main sources of input: from the commandline and from the input-parameter file. In the first section, we describe  each commandline item from Listing \ref{tableBioEM}. 
 In the second section, we describe the keywords that should be specified in the input-parameter file. Lastly, we describe the specific formats of the model, particle-image,
-and input-paramter files that are used in the BioEM software.
+and input-parameter files that are used in the BioEM software.
 
 
 \section{Commandline Input}
@@ -589,7 +601,7 @@ integration of uniformly distributed model orientations.
 To uniformly sample {\it SO3}, we recommend using a list of quaternions generated with the successive orthonormal images method from ref.~\cite{Yershova2010}.
 In the directory {\bf Quaternions}, we provide lists of quaternions that have been generated
 using this method. Here, it is necessary to follow section \ref{ortfile} because a list of quaternions is read from a separate file. To use quaternions
-the keyword \texttt{USE\_sQUATERNIONS} in the input-parameter file is also required.
+the keyword \texttt{USE\_QUATERNIONS} in the input-parameter file is also required.
 
 \subsubsection{Non-uniform sampling}
 
@@ -620,7 +632,7 @@ keywords
 where \texttt{(int)} is the grid spacing in each dimension $[-1,1]$.
 
 \item {\it Non-uniform sampling of orientations from a file:} We note that with the option of reading the orientations from a file (section \ref{ortfile}) the user has 
-great freedom to sample, also non-uniformly, the orientational space.
+great freedom to sample, also non-uniformly, the orientation space.
 
 
 \end{itemize}
@@ -644,9 +656,9 @@ The envelope function is
 \begin{equation}
 \mathrm{Env}(s)=e^{-bs^2/2},
 \end{equation}
-where parameter $b$ controlls the Gaussian width and modulates the CTF. 
+where parameter $b$ controls the Gaussian width and modulates the CTF. 
 
-To calculate the BioEM posterior probability, we integrate numerically the three parametes $\Delta f$, $b$ and $A$.
+To calculate the BioEM posterior probability, we integrate numerically the three parameters $\Delta f$, $b$ and $A$.
 To do so, one should include in the input-parameter file the keyword for each parameter, its integration limits, and number of grid points:
 \vspace{0.3cm}
 
@@ -923,7 +935,7 @@ The integral over Euler angle $\gamma$ is identical to that of $\alpha$.
 \item \texttt{GRIDPOINTS\_BETA (int)}: (Integration of Orientations) Number of grid points used in the integration
 over $\cos(\beta) \in [-1,1]$. 
 
-\item \texttt{USE\_QUATERNIONS}: (Integration of Orientations) If using quaternions to the describe the orientations. {\it Recommened} for uniformly sampling of $SO3$ with the  
+\item \texttt{USE\_QUATERNIONS}: (Integration of Orientations) If using quaternions to the describe the orientations. {\it Recommended} for uniformly sampling of $SO3$ with the  
 quaternions lists available in the {\bf Quaternions} directory. 
 
 \item \texttt{GRIDPOINTS\_QUATERNION (int)}: (Integration of Orientations) For a hypercubic grid quaternion sampling. Each quaternion is within $[-1,1]$. 
@@ -960,14 +972,14 @@ quaternions lists available in the {\bf Quaternions} directory.
 \begin{itemize}
 \item \texttt{ELECTRON\_WAVELENGTH (float)}: To change the default value of the electron wavelength \texttt{(float)} used to calculate the CTF phase with the defocus. 
 Default 0.019688 $\AA$. 
-\item \texttt{PRIOR\_MODEL (float)}: Prior probability of model. Default 1.
+\item \texttt{PRIOR\_MODEL (float)}: Prior probability of model. {\bf Default} 1.
 \item \texttt{PRIOR\_ANGLES}: To read the prior of each orientation in the input file of orientations.
 
-\item \texttt{SIGMA\_PRIOR\_B\_CTF (float)}: To change the Gaussian width of the prior probability of the CTF envelope parameter $b$ (section \ref{priorsec}).
+\item \texttt{SIGMA\_PRIOR\_B\_CTF (float)}: To change the Gaussian width of the prior probability of the CTF envelope parameter $b$ (section \ref{priorsec}). {\bf Default} 100 \AA.
 
-\item \texttt{SIGMA\_PRIOR\_DEFOCUS (float)}: To change the Gaussian width of the prior of the defocus $\sigma_{\Delta f}$ (section \ref{priorsec}).
+\item \texttt{SIGMA\_PRIOR\_DEFOCUS (float)}: To change the Gaussian width of the prior of the defocus $\sigma_{\Delta f}$ (section \ref{priorsec}). {\bf Default} 1 $\mu$m.
 
-\item \texttt{PRIOR\_DEFOCUS\_CENTER (float)}: To change the Gaussian center of the prior of the deocus $\Delta f_c$ (section \ref{priorsec}).
+\item \texttt{PRIOR\_DEFOCUS\_CENTER (float)}: To change the Gaussian center of the prior of the defocus $\Delta f_c$ (section \ref{priorsec}). {\bf Default} 3 $\mu$m.
 
 \item \texttt{NO\_MAP\_NORM}: Condition to not normalize to zero mean and unit variance the input maps.
 
@@ -1104,7 +1116,8 @@ The format for this file is
 \label{perfparm}
 
 The BioEM performance variables enhance or modify the code's computational performance without modifying the numerical results. 
-They should be tuned for the specific computing node characteristics where BioEM is executed. They are passed via environment variables. 
+They should be tuned for the specific computing node characteristics where BioEM is executed. They are passed via environment variables
+using the bash scripting language. 
 
 In the following chapter, we explain the types of parallelization used within the BioEM software, list all relevant
 environment variables, and provide some suggestions for runtime configurations in different
@@ -1233,7 +1246,7 @@ particle-images the innermost loop.
 
 For parallelization over the CPU cores: 
 \begin{itemize}
-\item[--] On a single node, one can  use OpenMP to parallelize over the particle images, and optionally using the enviormental variable 
+\item[--] On a single node, one can  use OpenMP to parallelize over the particle images, and optionally using the environmental variable 
 \texttt{BIOEM\_PROJECTIONS\_AT\_ONCE=[x]}.
 \item[--] One can use MPI with as many MPI processes as there are CPU cores $\times$ nodes, and with \texttt{OMP\_NUM\_THREAD=1}.
 In this case, the parallelization is done only over the orientations.
@@ -1243,8 +1256,8 @@ In this case, the parallelization is done only over the orientations.
 For instance, on a single node, \texttt{OMP\_NUM\_THREADS=[x]} can be set to \texttt{x = 1/4 N}, where  \texttt{N} is the number of CPU cores on the system,
 and BioEM can be called with \texttt{'mpirun'}, and 4 MPI processes. In this case, four
 orientations are processed in parallel using MPI, and  \texttt{x} particle-images are processed in parallel using OpenMP.
-\item[--] If multiple nodes are used MPI is mandatory, and should be combined with OpenMP. Optimal work distribution will depend on the number of orientations (parallization with MPI) compared 
-to the number of particle-images (parallization with openMP). 
+\item[--] If multiple nodes are used MPI is mandatory, and should be combined with OpenMP. Optimal work distribution will depend on the number of orientations (parallelization with MPI) compared 
+to the number of particle-images (parallelization with openMP). 
 \item[--] The Fourier-algorithm can be combined (and is by default combined) with any chosen option
 automatically.
 \end{itemize}
@@ -1678,7 +1691,7 @@ Several additional features using the commandline are available with BioEM:
 
 \item {\it Dump particle-images:}
 This feature writes out the particle-images in binary format.
-This allows a faster to readput in a further BioEM execution.
+This allows a faster to readout in a further BioEM execution.
 
 {\bf New Command:}\texttt{ --DumpMaps}
 
@@ -1872,9 +1885,9 @@ can simply run in terminal the bash script {\it subtract\_LogP.sh}:\\
 \vspace{0.5cm}
 
 This script prints out the particle number, log-posterior of {\it Model 1}, log-posterior of {\it Model 2},
-difference in log-posteriors ({\it Model 1- Model 2}), and cumulative difference. In Figure \ref{fig:ModelComp}A, we compare the output from this analysis by graphing 
-the BioEM log-posterior of {\it Model 1} versus {\it Model 2} (output columns 4 and 6 from the script execution). In Figure \ref{fig:ModelComp}A, we show the cumulative
-diference of ({\it Model 1- Model 2}) (column 10) as a function of the image number. From these results, one can conclude that {\it Model 1} is more probable. 
+difference in log-posteriors ({\it Model 1- Model 2}), and cumulative difference. In Figure \ref{fig:ModelComp}(top), we compare the output from this analysis by graphing 
+the BioEM log-posterior of {\it Model 1} versus {\it Model 2} (output columns 4 and 6 from the script execution). In Figure \ref{fig:ModelComp}(bottom), we show the cumulative
+difference of ({\it Model 1- Model 2}) (column 10) as a function of the image number. From these results, one can conclude that {\it Model 1} is more probable. 
 Lastly, we note that the analysis of the posterior probabilities can be done in many different manners, as in ref.~\cite{CossioHummerJSB_2013}. 
 The final interpretation of the results is left to the individual user. 
 
@@ -1882,7 +1895,7 @@ The final interpretation of the results is left to the individual user.
  \begin{centering}
 \includegraphics[width=8cm]{ModComp.eps}
  \par\end{centering}
- \caption{ {\it Example of model comparison using BioEM.} A) Natural logarithm of the BioEM Posterior probability of {\it Model\_1} versus {\it Model\_2} for 20 particle-images. B)
+ \caption{ {\it Example of model comparison using BioEM.} (top) Natural logarithm of the BioEM Posterior probability of {\it Model\_1} versus {\it Model\_2} for 20 particle-images. (bottom)
  Cumulative difference of {\it Model 1- Model 2} as a function of the image number.
  Example files of models, particle-images and input-parameters
  are in the {\bf MODEL\_COMPARISON} directory.}
@@ -1895,7 +1908,7 @@ The final interpretation of the results is left to the individual user.
 
 
 \bibliographystyle{plain}
-\bibliography{Biblio_BioEM.bib}
+\bibliography{bib_manual.bib}
 
 
 
diff --git a/Manual/ModComp.eps b/Manual/ModComp.eps
index 0bd8630a4e97adf18d6e6df3f7de5c8aab6c20bc..cd6630f35bef9862e445809398cb75c2befed2de 100755
--- a/Manual/ModComp.eps
+++ b/Manual/ModComp.eps
@@ -1,7 +1,7 @@
 %!PS-Adobe-2.0 EPSF-2.0
 %%Title: ModComp.eps
 %%Creator: gnuplot 4.2 patchlevel 3 
-%%CreationDate: Tue Jan 19 13:37:18 2016
+%%CreationDate: Wed Jun  8 14:14:44 2016
 %%DocumentFonts: (atend)
 %%BoundingBox: 50 50 410 554
 %%EndComments
@@ -48,7 +48,7 @@ SDict begin [
   /Author (Pilar Cossio,MBP, ,)
 %  /Producer (gnuplot)
 %  /Keywords ()
-  /CreationDate (Tue Jan 19 13:37:18 2016)
+  /CreationDate (Wed Jun  8 14:14:44 2016)
   /DOCINFO pdfmark
 end
 } ifelse
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+49 2 V
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 stroke
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diff --git a/Manual/title_Manual.tex b/Manual/title_Manual.tex
new file mode 100644
index 0000000000000000000000000000000000000000..4308c831cf86f7118af7db89d8316b4ce0a1722b
--- /dev/null
+++ b/Manual/title_Manual.tex
@@ -0,0 +1,44 @@
+\begin{titlepage}
+
+\begin{center}
+
+\thispagestyle{empty}
+
+
+
+\vfill
+% Title
+\vspace{0.8 in}
+\centerline{\textit{}}
+\vspace{1 in}
+ \HRule \\[0.5in]
+{\fontsize{50}{60}\selectfont BioEM Manual}
+\vspace{0.5 in}
+\HRule \\[0.5in]
+
+\vspace{0.4 in}
+\centerline{\textit{}}
+
+\vspace{0.7 in}
+
+\centerline{\Large \textit{A software for Bayesian analysis of EM images}}
+
+\vspace{2 in}
+%\centerline{\large \textit{Theoretical Biophysics}}
+\centerline{\small \textbf{Max Planck Institute of Biophysics}}
+\vspace{0.1 in}
+\centerline{\small \textbf{Frankfurt Institute for Advanced Studies}}
+\vspace{0.1 in}
+\centerline{\small \textbf{Max Planck Computing and Data Facility}}
+\vspace{0.2 in}
+\centerline{\Large 2016}
+
+\vfill
+
+% Bottom of the page
+%{\large \today}
+
+\end{center}
+
+\end{titlepage}
+
diff --git a/README.md b/README.md
index 3a52b6a219f38311bd71c9d348e81543f55a793a..13f0554540d6e21d9e6bee1f468ee397ec90f4fe 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # BioEM:  Bayesian inference of Electron Microscopy
-# PRE-ALPHA VERSION: June, 2016
+# 1.0 VERSION: June, 2016
 
 
 ## Contributors