Commit 263b0ce0 authored by Pilar Cossio's avatar Pilar Cossio
Browse files

Additional Info README.md

parent 419cb2ee
Pipeline #4480 passed with stage
# BioEM: Bayesian inference of Electron Microscopy
# PRE-ALPHA VERSION: April 25, 2014
# PRE-ALPHA VERSION: June, 2016
## Contributors
......@@ -12,76 +12,55 @@ Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, Volker Lindenstruth and G
* Cossio, P., Rohr, D., Baruffa, F., Rampp, M., Lindenstruth, V. and Hummer, G. "BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images" (in preparation)
## DESCRIPTION:
## Description
The BioEM code compares one Model to multiple experimental EM images.
The BioEM code calculates the posterior probability of a structural model given multiple experimental EM images.
The posterior is calculated 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.
By comparing the BioEM posterior probabilities it is possible to discriminate and rank structural models, allowing to characterize
the variability and dynamics of the biological system.
See the BioEM_Maunal.pdf for a detailed description of the BioEM software.
### Command line input & help is found by just running the compiled executable ./bioEM
++++++++++++ FROM COMMAND LINE +++++++++++
Command line inputs:
--Inputfile arg (Mandatory) Name of input parameter file
--Modelfile arg (Mandatory) Name of model file
--Particlesfile arg (Mandatory) Name of paricles file
--Particlesfile arg if BioEM (Mandatory) Name of particle-image file
--Inputfile arg if BioEM (Mandatory) Name of input parameter file
--PrintBestCalMap arg (Optional) Only print best calculated map. NO BioEM (!)
--ReadOrientation arg (Optional) Read file name containing orientations
--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
--DumpMaps (Optional) Dump maps after they were read from
particle-image file
--LoadMapDump (Optional) Read Maps from dump option
--OutputFile arg (Optional) For changing the outputfile name
--help (Optional) Produce help message
Details for the inputfiles and formats are provided in chapters 1 and 2 of the BioEM_Manual.pdf.
### OUTPUT:
### Output
* Main output file: "Output_Probabilities" with
* Main output file with, default name "Output_Probabilities" has
RefMap #(number Particle Map) Probability #(log(P))
RefMap #(number Particle Map) Maximizing Param: #(Euler Angles) #(PSF parameters) #(center displacement)
**Important: It is recommended to compare log(P) with respect to other Models or to Noise as in [1].
* (Optional) Write the probabilities for each triplet of Euler Angles (key word: WRITE_PROB_ANGLES in InputFile).
* (Optional) Write the posterior probabilities as a function of the orientations (key word: WRITE_PROB_ANGLES in InputFile, see BioEM_Manual.pdf).
### EXAMPLE DIRECTORY:
### TUTORIAL DIRECTORY:
A directory with example EM particles, c-alpha PDB & simple Model, and the corresponding launch scripts are provided. Standard input file parameters are provided and recommened.
### REMARKS:
#### EXPERIMENTAL IMAGE FORMAT:
Two options are allowed for the map-particle files:
* Simple *.txt or .dat with data formated as
printf"%8d%8d%12.4f\n" where the first two columns are
the pixel indexes and the third column is the intensity.
Multiple particles are read in the same file with the
separator "PARTICLE" & Number.
-- For this case it is recommended all particles
to be normalized to zero average and unit standard deviation.
* Standard MRC particle file. If reading multiple MRCs
provide in command line
--Particlesfile FILE --ReadMRC --ReadMultipleMRC
where FILE contains the names of each mrc file to be read.
If only one MRC on command line
--Particlesfile FILEMRC --ReadMRC
where FILEMRC is the name of the single mrc file.
#### MODEL FORMAT:
A directory with example EM particles, models, and input files are provided in the Tutorial_BioEM directory.
A tutorial is provided in chapter 4 of the BioEM_Manual.pdf
* Standard PDB file: Reading only CA atoms and corresponding
residues with proper density.
* *.txt *.dat file: With format printf"%f %f %f %f %f\n",
the first three columns as the coordinates of atoms or
voxels, fourth column is the radius (\AA) and the
last column is the corresponding density.
(Useful for all atom representation or 3D EM density maps).
[1] Cossio, P and Hummer, G. J Struct Biol. 2013 Dec;184(3):427-37. doi: 10.1016/j.jsb.2013.10.006.
## Installation
### Installation
To build and install bioEM a cmake procedure is used, for example:
......@@ -123,3 +102,9 @@ Dependencies and software requirements:
* CUDA (required to build and run the GPU version)
for free software see: https://developer.nvidia.com/cuda-downloads
For details on the installation chapter 1 of the BioEM_Manual.pdf.
In chapter 3 of the BioEM_Manual.pdf a
detailed description of the BioEM performance variables
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment