Focus 1.1

The current minor release version is 1.1.0.

Tutorial Movies

A number of movies is available that demonstrate installation, setup, and running FOCUS. The full playlist can be found on YouTube

Introductory and Tutorial Movies

Hardware recommendations

FOCUS requires C++, gfortran, Qt, tcsh and Python. It uses several third-party programs in the background. Several of these don't run under Microsoft Windows. For these reasons, FOCUS only works on LINUX or OS X machines. If you plan to use MotionCor2 or gCTF or other NVIDIA-GPU-enabled programs in the background, then you have to stay with LINUX, since Apple doesn't support NVIDIA GPUs unfortunately. However, if you plan to work with 2D crystals or only third-party programs that don't require NVIDIA GPUs, then OS X is also a suitable platform, provided you have at least 8 GB RAM.

Hardware recommendation for Linux

Hardware recommendation for Mac

Installation and setup

Focus depends on Qt5 for deploying a GUI. Other EM Suites are used wherever required. Find information on how to download, install and setup Focus software for the first time.

Download the software

Installation from source code

Setting up external software tools

Default installation directories

Movies

Getting started

Once Focus is installed it can be easily launched using the Command line or Desktop utilities provided with Focus. Following links give more information on launching Focus, adding a project, configuring global user settings and brief introduction of the GUI.

Launching Focus

Adding a new project

Introduction to GUI

Configuring user settings

Basic Usage

The links below would help you to start using Focus. The first things to do in any project is to import images and later once imported process them and manage them. Processing depends on the type of EM method used and is detailed in later sections.

Import images and movies

Managing Images using Project Library

Processing Images

Focus allows to process images via the precompiled scripts. Each script calls a few executables (external or internal) and fetches parameters associated with the project or the image from the configuration files as required. Processing can be either done manually for each image allowing to tune-in the parameters and later a bunch of images can be processed in parallel.

Manually processing an image

Parallel Processing

Movies

Remote Monitoring

Remote monitoring allows to see the status of the processing in Focus from a website that can be accessed remotely. This in turn helps to check the recording status of the microscope.

Setting up the server

Configuring Focus for remote monitoring

Collecting data in Focus

Setting up apps on Android and iOS

2D Crystal Processing

Focus includes scripts prebuilt to carry out complete 2D crystallographic image processing. Following pages describe how to start from images/movies, create final 2D maps, merge the data to produce 3D and finally refine the reconstruction to minimise the effects of missing cone.

Image Processing of 2D Crystal Images

2D Merging

3D Merging

Refining Merged Map

2D Crystal Test Images

Movies

Exporting the data

Once the images have been processed they can be exported. The export function in Focus organizes the image files and metadata in the arrangement required by the target package. For example, if the target package is RELION, the data will be reorganized so that all aligned average images and a single metadata STAR file are created in a single subfolder. On the other hand, if the target package is IMOD, the electron tomography data will be reorganized so that there is one MRC stack for each specimen location, containing the entire tilt series ordered by tilt angle, irrespective of the recording order (e.g., if they were acquired using the Hagen scheme).

Movies

FAQs

A list of FAQ is available in the following page:

Frequently Asked Questions

Workshops

From 2006 through 2016, we organised workshops aimed at teaching electron crystallography of membrane proteins

2016

The fifth edition of our hands-on workshop on “2D Electron Crystallography” (hosted at C-CINA)

Workshop 2016, C-CINA

2012

Workshops hosted at UC Davis and at C-CINA

Electron Crystallography Workshops Workshop 2012, UC Davis

2010

Workshop on Electron Crystallography, hosted at C-CINA.

Workshop 2010, C-CINA

2008

Workshops hosted at UC Davis and at C-CINA

Electron Crystallography Workshops Workshop 2008, UC Davis

2006

Workshop hosted at UC Davis on Electron Crystallography.

Workshop 2006, UC Davis

Documentation (for Electron Crystallography only)

2D Electron Crystallography with Focus

Data Flow

A pipeline of the programs, files and data involved in the processing of 2D crystal images is available here

Parameters

Find documentation of some of the important parameters involved in processing of 2D crystal images with Focus here

Frequently asked Questions

A list of frequently asked questions is complied and can be accessed here. Please use this list to find your question, and if you do not find any help, please contact us here.

Video Tutorials

Video tutorials are available here. Also refer to the workshops for more details.

Manual

The User Manual for 2dx

Explanation of the 2dx GUI

read more...

Beginning an Image Processing Project

read more...

Status Pane

read more...

Processing an individual image

read more...

The Full-Screen Image Navigator

read more...

Refining a lattice

read more...

Refining the CTF

read more...

Spot Selection

read more...

Tilt Geometry Definition

read more...

ML algorithm applied to 2d crystals

read more...

Data Flow

These pages describe the flow of data through the different programs. File names, formats and contents is listed. 2dx and the underlying MRC programs process and then evaluate images, and extract values for amplitudes and phases of Fourier spots. These are then handed over from one program to the next one, where each program does something to those values (e.g. correcting for the CTF, or merging several values together). Each program thereby unfortunately needs a different type of data that is therefore often in a different format, and the whole thing quickly gets very confusing. Most of these files are text files (ASCII), though, so that you can always open them with a text browser (vi, edit, SimpleText, or even Word (but don't save it back as “Word” file.doc file). We have here compiled a list of all the programs that are called in sequential order, and have listed the input and output files for these programs. For the output files we have then included a short description of the file format, followed by an example of how that should look like. This is only for reference purposes, in case somebody tries to follow the flow of data from one program to the next one. read more...

Screen Shots

FIXME

Movie Tutorials

FIXME

Known Bugs

A list of currently known bugs (sigh...)

There are currently no items in this folder.

Parameters

2dx Movies

FIXME

Version Change Log

2DX_GUI_UserGuide.pdf

2dx User Manual (.pdf)

Sample Prep Movies

FIXME

MRC Software

Download

Movies

Test Data

Utilities


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