Commit af0a4c90 authored by Pilar Cossio's avatar Pilar Cossio
Browse files

BackupManual

parent ab64ae14
\documentclass[12pt, psamsfonts]{book} \documentclass[a4paper,10pt]{report}
\usepackage[english]{babel} \usepackage[british,activeacute]{babel}
\usepackage[latin1]{inputenc} \usepackage[latin1]{inputenc}
\usepackage[reqno]{amsmath} \usepackage[reqno]{amsmath}
\usepackage{threeparttable,rotating,fancybox}
\usepackage[colorlinks=true]{hyperref} %Insert hyperlinks in latex files
\usepackage{graphicx} \usepackage{graphicx}
\usepackage{amsfonts} \usepackage{amsfonts}
\usepackage{latexsym} \usepackage{latexsym}
\usepackage[dvips]{color} \usepackage[dvips]{color}
%% \usepackage{amssymb, amsmath, amsfonts} \usepackage{layout}
%% \usepackage{latin1} \usepackage{setspace}
%% \usepackage{color}
%% \usepackage[dvips]{graphics}
%\documentclass[12pt, psamsfonts]{report}
%\usepackage[english]{babel}
%\usepackage[latin1]{inputenc}
%\usepackage[reqno]{amsmath}
\usepackage{threeparttable,rotating,fancybox}
%\usepackage[colorlinks=true]{hyperref} %Insert hyperlinks in latex files
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{xspace}
\usepackage{xcolor}
\usepackage{listings}
\usepackage{bm}
\usepackage{geometry}
\usepackage{fancyhdr} \usepackage{fancyhdr}
\setlength{\headheight}{15.2pt} \usepackage{mathptmx}
\pagestyle{fancy} %\setlength{\headheight}{15.2pt}
%\pagestyle{fancy}
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
%\usepackage[utf8]{inputenc} %\usepackage[utf8]{inputenc}
\pagenumbering{roman} \pagenumbering{roman}
\newcommand*{\titleGM}{\begingroup % Create the command for including the title page in the document \newcommand*{\titleGM}{\begingroup
\hbox{ % Horizontal box \hbox{
\hspace*{0.1\textwidth} % Whitespace to the left of the title page \hspace*{0.1\textwidth}
\rule{3pt}{\textheight} % Vertical line \rule{6pt}{\textheight}
\hspace*{0.05\textwidth} % Whitespace between the vertical line and title page text \hspace*{0.1\textwidth}
\parbox[b]{0.75\textwidth}{ % Paragraph box which restricts text to less than the width of the page \parbox[b]{0.95\textwidth}{
{\noindent\Huge BioEM Manual}\\[2\baselineskip] % Title {\noindent \Huge BioEM Manual}\\[2\baselineskip] % Title
{\large \textit{A software for bayesian analysis of EM images}}\\[4\baselineskip] % Tagline or further description \rule{10.5cm}{0.4pt}\\
{\large \textit{A software for Bayesian analysis of EM images}}\\[4\baselineskip]
{\Large \textsc{ }}%Pilar Cossio \\ David Rohr \\ Volker Linderstruth \\ Gerhard Hummer}} % Author name {\Large \textsc{ }}%Pilar Cossio \\ David Rohr \\ Volker Linderstruth \\ Gerhard Hummer}} % Author name
\vspace{0.5\textheight} % Whitespace between the title block and the publisher \vspace{0.5\textheight} % Whitespace between the title block and the publisher
...@@ -45,89 +57,170 @@ ...@@ -45,89 +57,170 @@
\title{BioEM Manual} \title{BioEM Manual}
\author{P.Cossio, D. Rohr, V. Lindestruth, G. Hummer } \author{P.Cossio, D. Rohr, V. Lindestruth, G. Hummer }
\date{March 2015} \date{December 2015}
\begin{document} \begin{document}
\pagestyle{plain} \pagestyle{plain}
\include{title_Manual}
%\titleGM
\section*{Preface \& Disclaimer}
This manual is a preliminary guide for installation and use of the BioEM software. It
is not intended to be complete. As the BioEM code is improved and developed, the manual will be updated.
For any comments or questions please contact: {\it pilar.cossio@biophys.mpg.de}.
\section*{Copyright}
\titleGM $<${\bf BioEM} software for Bayesian inference of Electron Microscopy images$>$
Copyright (C) 2016 Pilar Cossio, David Rohr, Volker Linderstruth and Gerhard Hummer.
The BioEM program is a free software, under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License. This program is distributed in the hope that it will be useful,
but {\bf without any warranty}. See the
GNU General Public License for more details.
\section*{Citation}
For scientific results from usage of the BioEM program please cite refs. \cite{CossioHummerJSB_2013,BioEM_server}.
\tableofcontents \tableofcontents
%\pagestyle{fancy} %\pagestyle{fancy}
\chapter{The BioEM software} \chapter{The BioEM software}
\pagenumbering{arabic} \pagenumbering{arabic}
\section{Introduction} \section{Introduction}
The BioEM method calculates the posterior probability Electron microscopy (EM) experiments can provide structural details of biomolecules in a near-native environment.
of a model to multiple experimental EM images, using Bayesian analysis. Each particle-image contains structural information of the single-molecule trapped in a given conformational state.
The key idea is not to modify the raw images but to create a calculated image, from the original model, as similar as possible to the observed experimental image. Many relevant biomolecules do not
The calculated image takes into account the relevant factors in the experiment and image formation, such as the molecule orientation, interference effects, uncertainties in the particle center, offset in the intensities, etc., and, importantly, noise. have an unique stable state but have alternative metastable conformations that play functional roles.
The individual EM images are an excellent tool to assess the structural details of these dynamic conformations.
Here, we present a computing tool to categorize and classify models of flexible biomolecules from individual EM images.
Our method of Bayesian inference of electron microscopy images, BioEM \cite{CossioHummerJSB_2013,BioEM_server},
computes the posterior probability of a model given the experimental data.
By comparing the BioEM posterior probabilities it is possible to discriminate and rank structural models, allowing to characterize
the variability and dynamics of biomolecular systems when standard cryo-EM techniques fail to generate high-resolution
3D reconstructions.
The BioEM posterior probability is computed by solving a multidimensional integral over many nuisance parameters that account for
the experimental factors in the image formation, such as molecular orientation and interference effects.
The BioEM software computes this integral via numerical grid sampling over a portable CPU/GPU computing platform.
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.
\section{Theoretical background}
\label{theory}
The BioEM method calculates the posterior probability of a model, $m$, given a set of experimental images.
The key idea in BioEM is to create a calculated image, from the original model, as similar as possible to the experimental image.
The factors that influence the experiment are modeled with
nuisance parameters, $\boldsymbol \theta$, that describe the molecule orientation, interference effects, uncertainties
in the particle center, etc., and, importantly, noise.
Figure \ref{fig:likeliCons} exemplifies how a calculated image from a model, with a given set of nuisance parameters, is created.
Technically, the model is first rotated to a given orientation, then projected along the $z$-axis, Technically, the model is first rotated to a given orientation, then projected along the $z$-axis,
then it is convoluted with a point spread function in Fourier space to cope with imaging artefacts, then it is convoluted with a Point Spread Function (PSF) to cope with imaging artifacts,
next it is shifted by a certain number of pixels to account for the center displacement, next it is shifted by a certain number of pixels to account for the uncertainties in the particle center.
and finally this modified projection is compared to a reference particle-image. Normalization, and offset in the intensity, as well as noise, are taken implicitly into account.
The similarity between the calculated projection and the experimental image, for a given parameter set, is assessed through a likelihood function. The calculated image is compared to an experimental particle-image, $\omega$, through a likelihood function, $L(\omega|m,\boldsymbol\theta)$.
The posterior probability of the model is obtained by integrating the likelihood function, and prior probabilities, over a all parameter ranges. Eq. 7 of ref. \cite{CossioHummerJSB_2013} shows its analytical formulation.
The BioEM software is used to perform this integration numerically. A detailed description of the BioEM method is found in Refs. \cite{CossioHummer_2013,BioEM_server}.
\begin{figure}[h]
\section{Installation} \begin{centering}
\includegraphics[width=14cm]{Fig1_10Dec.eps}
\par\end{centering}
\caption{ {\it Steps in building a realistic image starting from a 3D model:} rotation,
projection, point spread function convolution, center displacement, and integrated-out parameters of normalization, offset and noise.
The likelihood function establishes the similarity between the calculated image and the observed experimental image.}
\label{fig:likeliCons}
\end{figure}
The Bayesian posterior probability of a model, given an experimental image, is a weighted integral over the product of prior probabilities and likelihood, over all nuisance parameters,
\begin{equation}
P_{m\omega} \propto \int
L(\omega|m,\boldsymbol\theta)p_M(m)p(\boldsymbol\theta)
d\boldsymbol\theta~,
\label{eq:Pmom}
\end{equation}
where $p_M(m)$, $p(\boldsymbol\theta)$ are the prior probabilities of model and parameters, respectively.
The BioEM software is used to perform the integrals in Eq. \ref{eq:Pmom} over orientation, PSF parameters, and center displacement using numerical grid sampling.
The remaining integrals over the intensity normalization, offset, and noise are performed analytically following ref. \cite{CossioHummerJSB_2013}.
The posterior probability of a single model given a set of images, $\omega \in \Omega$, becomes
\begin{equation}
P(m|\Omega) \propto \prod_{\omega=1}^{\Omega}P_{m\omega}~.
\label{eq:pb2}
\end{equation}
The main result of the BioEM software is the computation of Eq. \ref{eq:pb2}. This can be used for model comparison and discrimination, {\it e.g.} to rank the best model, or
to calculate the posterior probability of a full set of models, $m \in M$, following Eq. 2 of ref. \cite{CossioHummerJSB_2013}.
Before installation, there are several programs or libraries that
should be installed on the compute node. In the following,
we will give a brief explanation of the mandatory, and the optional prerequisite programs.
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} \subsection{Prerequisite programs and libraries}
Before installation, there are several programs and libraries that should be preinstalled on the compute node. In the following,
we give a brief explanation of the mandatory, and optional prerequisite programs.
\subsubsection{Mandatory preinstalled libraries/programs}
\begin{itemize} \begin{itemize}
\item {\it FFTW library:} is a subroutine library for computing the discrete Fourier transform. \item {\it FFTW library:} is a subroutine library for computing the discrete Fourier transform.
It is specifically used in BioEM, to calculate the convolution of the ideal image with the point spread function (PSF), and It is specifically used in BioEM, to calculate the convolution of the ideal image with the PSF, and
the cross-correlation of the calculated image to the experimental image. FFTW can be downloaded from the webpage www.fftw.org. the cross-correlation of the calculated image to the experimental image. FFTW can be downloaded from the webpage www.fftw.org.
\item {\it BOOST library:} provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, \item {\it BOOST library:} provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading,
image processing, and unit testing. In particular, they are used in the code to access and organize input-data. image processing, and unit testing. In particular, this library is used to access and organize input-data in the BioEM code.
BOOST can be downloaded from www.boost.org. BOOST can be downloaded from www.boost.org.
\item {\it OpenMP:} is a programming interface that supports multi-platform shared memory parallel programming. \item {\it OpenMP:} is a programming interface that supports shared memory parallel programming.
It is normally, included in the standard GNU or Intel c++ compliers (so no downloading should be necessary). For more information see http://openmp.org/. It is normally, included in the standard GNU or Intel c++ compliers, so no downloading should be necessary. For more information see http://openmp.org/.
\end{itemize} \end{itemize}
The optional (but \subsubsection{Optional preinstalled programs}
{\bf encouraged} to use) programs for an easy compilation, and optimal performance, are described bellow. The optional but {\it encouraged} to use programs for an easy compilation, and optimal performance, are described bellow:
\begin{itemize} \begin{itemize}
\item {\it CMake:} is a cross-platform software for managing the build process of software using a compiler-independent method ({\it i.e.} creating a Makefile). \item {\it CMake:} is a cross-platform software for managing the build process of software using a compiler-independent method ({\it i.e.} creating a Makefile).
CMake can be downloaded from www.cmake.org. CMake can be downloaded from www.cmake.org.
\item {\it CUDA:} is a parallel computing platform implemented by the graphics processing units (GPUs) that NVIDIA\cite{} produce. \item {\it CUDA:} is a parallel computing platform implemented by the graphics processing units (GPUs) that NVIDIA produce.
Thus, NVIDIA graphics cards are necessary for running BioEM with the CUDA implementation. For more information see Thus, NVIDIA graphics cards are necessary for running BioEM with the CUDA implementation. For more information see
www.nvidia.com. 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. \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.
{\bf PC:} Difference between openMPI and MPICH (?). Is one recommend over the other? Any MPI platform (either openMPI or MPICH) can be used with BioEM.
\end{itemize} \end{itemize}
After these programs are successfully installed in your compute node, After these programs are successfully installed on your compute node,
it will be possible to install BioEM. it will be possible to install BioEM.
\vspace{0.5cm}
{\it Note:} It is recommended that the same complier that is used for the {\it Note:} It is recommended that the same complier that is used for the
libraries, is also used BioEM. libraries is also used to compile BioEM.
\subsection{Download} \subsection{Download}
\label{download}
A compressed directory of the BioEM software can be downloaded from [mpi biophys]. A compressed directory of the BioEM software can be downloaded from [{\it mpi biophys}].
After downloading the {\it tar} file, uncompress by executing After downloading the {\it tar.gz} file, uncompress it by executing
\vspace{0.5cm} \vspace{0.5cm}
\fbox{% \fbox{%
...@@ -136,27 +229,27 @@ After downloading the {\it tar} file, uncompress by executing ...@@ -136,27 +229,27 @@ After downloading the {\it tar} file, uncompress by executing
\vspace{0.5cm} \vspace{0.5cm}
In the uncompressed {\it BioEM} directory, there are In the uncompressed {\bf BioEM} directory, there are:
\begin{itemize} \begin{itemize}
\item[--]the source code {\it cpp} files, and {\it include} directory with corresponding header files. \item[--]the source code {\it .cpp} and {\it .cu} files.
\item[--]the copyright license, and README file. \item[--]the {\bf include} directory with corresponding header files.
\item[--]the {\it CMakeLists.txt} file that is necessary for CMake (see section bellow). \item[--]the copyright license, and {\it README} file.
\item[--]the {\it Tutorial} directory that includes the example files used in the tutorial (see chapter \ref{tutorial}). Inside this directory, \item[--]the {\it CMakeLists.txt} file that is necessary for installation with CMake (see section bellow).
there is also a directory called {\it MODEL\_COMPARISON}. \item[--]the {\bf Tutorial\_BioEM} directory that includes the example files used in the tutorial (see chapter \ref{tutorial}). Inside this directory,
\item[--]the {\it Quaternions} directory that includes list files of quaternions that sample uniformly there is also a directory called {\bf MODEL\_COMPARISON}.
the rotational group (see section \ref{intor}). \item[--]the {\bf Quaternions} directory that includes files with lists of quaternions that sample uniformly
the rotational group {\it SO3} (see section \ref{intor}).
\end{itemize} \end{itemize}
\subsection{Installing with CMake} \subsection{Installing BioEM with CMake}
The easiest installation is done with the CMake program The easiest installation of BioEM is done with the CMake program.
that generates automatically a Makefile, according to the CMake contains all the instructions to generate automatically a {\it Makefile}
specific CPU/GPU architecture, and desired features. CMake according to the specific architecture of the computing node, and the desired features of parallelization.
uses the {\it CMakeLists.txt} file, that contains all the instructions to generate the Makefile. CMake uses the {\it CMakeLists.txt} file. This file is provided in the uncompressed {\bf BioEM} directory.
This file is provided in the uncompressed BioEM directory.
At the beginning of the {\it CMakeLists.txt} the modifiable options are provided. At the beginning of the {\it CMakeLists.txt} the modifiable options are provided.
These options should be enabled/disabled ({\bf ON}/{\bf OFF}) according to the desired functionalities. These options should be enabled/disabled ({\bf ON}/{\bf OFF}, respectively) according to the desired functionalities:
\begin{itemize} \begin{itemize}
...@@ -195,40 +288,42 @@ standard host compiler is incompatible with CUDA)" ON/OFF)}}}} ...@@ -195,40 +288,42 @@ standard host compiler is incompatible with CUDA)" ON/OFF)}}}}
\end{itemize} \end{itemize}
{\it Note:} For certain architectures, additional files ({\it e.g.} FindFFTW.cmake) could also be needed for successful CMake {\it Note:} For certain architectures, additional files ({\it e.g.} FindFFTW.cmake) may be required.
execution. For more information, on specific CMake features ({\it e.g.} changing compiler) see www.cmake.org. For more information on specific CMake features see www.cmake.org.
\subsubsection{Steps for basic installation} \subsubsection{Steps for basic installation}
\begin{itemize} \begin{itemize}
\item[--] Setup the desired features in the CMakeLists.txt file. \item[--] Setup the desired features in the {\it CMakeLists.txt} file.
\item[--] Generate a build directory in the main BioEM directory %\item[--] Generate a build directory in the main {\bf BioEM} directory
\fbox{% %\fbox{%
\parbox{10cm}{ %\parbox{10cm}{
{\footnotesize \texttt{mkdir build}}}} %{\footnotesize \texttt{mkdir build}}}}
\item[--]Access the build directory, and run CMake with the {\it CMakeLists.txt} file \item[--] Run CMake with the {\it CMakeLists.txt} file
%Access the build directory, and run CMake with the {\it CMakeLists.txt} file
\fbox{% \fbox{%
\parbox{10cm}{ \parbox{10cm}{
{\footnotesize \texttt{cd build \\ {\footnotesize \texttt{%cd build \\
cmake ../CMakeLists.txt}}}} cmake CMakeLists.txt}}}}
\item[--] If this process is successful, a Makefile and CMakeFiles directory should be generated in the build directory. \item[--] If this process is successful, a {\it Makefile} and {\bf CMakeFiles} directory should be generated.
If this is not the case, turn on the \texttt{PRINT\_CMAKE\_VARIABLES} option in the CMakeLists.txt file, and re-run If this is not the case, enable the variable
CMake with verbosity. \texttt{PRINT\_CMAKE\_VARIABLES} in the {\it CMakeLists.txt} file, and re-run
\item[--] After generating the Makefile, run it in the build directory CMake with verbosity to debug.
\item[--] After generating the {\it Makefile}, execute it% in the build directory
\fbox{% \fbox{%
\parbox{10cm}{ \parbox{10cm}{
{\footnotesize \texttt{make}}}} {\footnotesize \texttt{make}}}}
\item[--] If this process is successful a bioEM executable should be generated. \item[--] If this process is successful a \texttt{bioEM} executable should be generated.
\end{itemize} \end{itemize}
For a simple test, run For a simple test, run the BioEM executable
\vspace{0.5cm} \vspace{0.5cm}
\fbox{% \fbox{%
...@@ -237,9 +332,16 @@ For a simple test, run ...@@ -237,9 +332,16 @@ For a simple test, run
\vspace{0.5cm} \vspace{0.5cm}
The output on the screen should be If the code runs successfully, the output on the terminal screen should be as that shown in Table \ref{tableBioEM}.
In the following chapter, we will describe each of the commandline input options for BioEM.
\vspace{0.5cm} \vspace{0.5cm}
\begin{table}[h]
\begin{center}
\begin{tabular}{l}
\fbox{% \fbox{%
\parbox{12cm}{ \parbox{12cm}{
{\footnotesize \texttt{ {\footnotesize \texttt{
...@@ -258,69 +360,78 @@ Command line inputs:\\ ...@@ -258,69 +360,78 @@ Command line inputs:\\
--LoadMapDump (Optional) Read Maps from dump instead of maps file\\ --LoadMapDump (Optional) Read Maps from dump instead of maps file\\
--OutputFile arg (Optional) For changing the outputfile name\\ --OutputFile arg (Optional) For changing the outputfile name\\
--help (Optional) Produce help message\\ --help (Optional) Produce help message\\
}}}} }}}
}
\end{tabular}
\end{center}
\caption{BioEM commandline input options.}
\label{tableBioEM}
\end{table}
\vspace{1cm}
\chapter{BioEM input} \chapter{BioEM Input}
In this chapter, we describe the BioEM input commands and keywords. BioEM has two
main sources of input: from the commandline or from the input-parameter file. In the first section, we describe in detail each commandline item from Table \ref{tableBioEM}.
In the second section, we describe the keywords that should be specified in the input-parameter file.
The BioEM software's main input is from the command line. Here the filenames
of the model, particle-images and parameter file should be provided.
We will now give a detailed description of each input item.
\section{Model file} \section{Commandline Input}
The BioEM software requires a model, a set of experimental images and a input-parameter file.
The names of these files are passed to the \texttt{bioEM} executable via the commandline, as well as their format specifications.
We now give a detailed description of each input from in Table \ref{tableBioEM}, and the possible formats for each file.
The model is represented as spheres (or points) in 3-dimensional space, with corresponding radius and density. \subsection{Model file}
%either in PDB or
% txt format.
Through the command line one has to provide the name of the file
that contains these items:
The structural model is represented as spheres in 3-dimensional space. The position of the center of the sphere should be specified in the model file, as well
as its corresponding radius and number of electrons. These spheres can represent atoms, coarse-grained residues or multi-scale blobs.
The radius size approximately determines the resolution of the model. Spheres with radius less than the pixel size are projected on to a single pixel.
The name of the file containing the model has to be provided in the commandline when \texttt{bioEM} is executed:
\vspace{0.5cm} \vspace{0.5cm}
\fbox{% \fbox{%
\parbox{12cm}{ \parbox{12cm}{
{\footnotesize \texttt{ --Modelfile arg}}}} {\footnotesize \texttt{./bioEM --Modelfile arg}}}}
\vspace{0.5cm} \vspace{0.5cm}
Where \texttt{arg} is the filename. There are two types of model file formats that are read by BioEM: \noindent where \texttt{arg} is the model filename.
\subsubsection*{Format}
There are two types of model file formats that are read by BioEM:
\begin{itemize} \begin{itemize}
\item[--] {\it *.txt *.dat file:} \item[--] {\it Text file:}
Useful for all atom representation or 3D voxel representation of density maps. A simple text file with format "\%f \%f \%f \%f \%f".
With format "\%f \%f \%f \%f \%f", The first three columns are the coordinates of the sphere centers in $\AA$, the fourth column is the radius in $\AA$, and the
the first three columns are the coordinates of atoms or last column is the corresponding number of electrons.
voxels, the fourth column is the radius or voxel side length ($\AA$) and the
last column is the corresponding electron density (Format: {\footnotesize \texttt{ x --- y --- z --- radius --- number electrons }}).
(Format: {\footnotesize \texttt{ x --- y --- z --- radius --- density }}).
This format is useful for all atom, mixed or coarse-grained representations of the density maps.
\item[--] {\it pdb file:} BioEM reads only the C$_\alpha$ atom positions from standard {\it pdb} files, with
their corresponding residue type. The residues are modeled as a sphere, centered at the \item[--] {\it pdb file:} BioEM reads the C$_\alpha$ atom positions with
C$_\alpha$ with corresponding van-der-Waals radii, and electron density (as in ref. their corresponding residue type from standard {\it pdb} files. A residue is modeled as a sphere, centered at the
\cite{CossioHummer_2013}). To read pdb files the following commandline keyword is needed: C$_\alpha$, with van-der-Waals radii and number of electrons corresponding to the specific amino acid type (as in ref.
\cite{CossioHummerJSB_2013}). To read pdb files the following commandline keyword is needed:
\fbox{% \fbox{%
\parbox{12cm}{ \parbox{12cm}{
{\footnotesize \texttt{--ReadPDB}}}} {\footnotesize \texttt{--ReadPDB}}}}
{\it Note:} the .pdb extension is not mandatory.
\end{itemize} \end{itemize}
{\it Additional Feature:} It is possible to model the elements simply as points
(instead of spheres) by projecting only the density of each element. For this, add the keyword \texttt{"NO\_PROJECT\_RADIUS"},
in the input parameter file (see section \ref{Physparm}).
\section{Particle-image file} \subsection{Particle-image file}
\label{partimag}
The name of the experimental image file is needed, as a commandline input in BioEM: The name of the experimental particle-image file is passed to the BioEM executable using the commandline:
\vspace{0.5cm} \vspace{0.5cm}
\fbox{% \fbox{%
...@@ -329,19 +440,19 @@ The name of the experimental image file is needed, as a commandline input in Bio ...@@ -329,19 +440,19 @@ The name of the experimental image file is needed, as a commandline input in Bio
\vspace{0.5cm} \vspace{0.5cm}
Where \texttt{arg} is the name of the file containing the experimental particle images. \noindent where \texttt{arg} is the file name.
Two format options are allowed for the these files:
\subsubsection*{Format}
Two format options are allowed for the the particle-image file:
\begin{itemize} \begin{itemize}
\item[--] {\it *.txt or .dat file:} Data are formatted as \item[--] {\it Text file:} Data are formatted as
"\%8d\%8d\%16.8f" where the first two columns are "\%8d\%8d\%16.8f" where the first two columns are
the pixel indexes, and the third column is the image intensity. the pixel indexes, and the third column is the intensity at that pixel.
Multiple particles are read in the same file with the Multiple particles are read in the same file with the
separator \texttt{"PARTICLE"