Automated post data aquisition processing tool
Project description
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1343497.svg)](https://doi.org/10.5281/zenodo.1343497)
# Transphire
Cryo-EM on the fly processing pipeline.
If you have any questions contact: markus.stabrin@mpi-dortmund.mpg.de
## External programs
To enjoy the full functionaly of TranSPHIRE, install the following programs:
IMOD 4.9: http://bio3d.colorado.edu/imod MotionCor2 1.0.0/1.0.5/1.1.0: http://msg.ucsf.edu/em/software/motioncor2.html SumMovie 1.0.2: http://grigoriefflab.janelia.org/unblur CTER 1.0: http://sphire.mpg.de CTFFIND 4.1.8/4.1.10: http://grigoriefflab.janelia.org/ctf Gctf 1.06,1.18: https://www.mrc-lmb.cam.ac.uk/kzhang crYOLO 1.0.4: http://sphire.mpg.de
## Installation
TranSPHIRE needs an environment that includes Python version 3.6, QT version 5 and PyQt version 5.
### Installation using Anaconda
https://www.anaconda.com/download/#linux
Create a new virtual environment
> conda create -n transphire python=3.6 pyqt=5
Activate the environment
> source activate transphire
or
> conda activate transphire
Depending on your installation of anaconda.
Install transphire
> pip install transphire
### Installation inside your own environment that matches the requirements
Install transphire
> pip install transphire
## Run TranSPHIRE
Make sure, that you have your transphire environment active. If you start TranSPHIRE for the first time:
> transphire –edit_settings
In case the appearing window is too large for your screen, adjust the font size (default 20). For example:
> transphire –edit_settings –font 8
First got to the TranSPHIRE settings tab and after that the Font tab. Adjust the Font value. If necessary, the other options can be adjusted at a later point, after the GUI is opened.
Open the other tabs and adjust the settings according to your system.
Close the dialog and the GUI will open.
In the future, you only need to run:
> transphire
If you want to run TranSPHIRE, fill in the tabs from left to right (General to CTF) and press the Start button.
A more detailed tutorial will be available soon.
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