frealign-2dx

Overview

Source code of the modified FREALIGN v9.11 used for processing 2D crystal data as described in:

Righetto, R. D., Biyani, N., Kowal, J., Chami, M. & Stahlberg, H. Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM. Nat. Commun. 10, 1722 (2019). http://doi.org/10.1038/s41467-019-09661-5

Main differences to the original FREALIGN v9.11 program are the implementation of:

• Alignment with local restraints in X,Y,PSI,THETA,PHI (calcfx.f)
• Auto-refinement algorithm (mult_refine_auto.com and mult_refine_auto_n.com)
• Focussed reconstruction (mask3dmerge.f) , i.e. the spherical mask applied in 3D reconstruction now can be anywhere within the box. That is, the FSC and map filtering are calculated with respect to the focussed region only. Not to be confused with, albeit related to, focussed classification.

New parameters are explained in the template mparameters file provided.

Installing from provided binaries

At the desired installation location, run

git clone https://github.com/C-CINA/frealign-2dx.git

The provided binaries (.exe files) located under the bin/ directory should be visible via your PATH environment variable (e.g. in your .bashrc profile):

export PATH=<path-to-frealign-2dx>/bin:$PATH

Compiling from source

For (statically) compiling the binaries using the PGI Fortran compiler (recommended):

cd src/
make -f Makefile_linux_amd64_pgi_static
make -f Makefile_linux_amd64_pgi_mp_static

For (statically) compiling the binaries using the GNU Fortran compiler:

cd src/
make -f Makefile_linux_amd64_gnu_static
make -f Makefile_linux_amd64_gnu_mp_static

Using the program

To start a normal FREALIGN refinement run, run the command frealign_run_refine. To use the auto-refiner, run frealign_run_refine_auto.

For more usage information, please check:

Getting started: http://grigoriefflab.janelia.org/frealign_getting_started

Running FREALIGN: http://grigoriefflab.janelia.org/frealign_running_frealign

Further reading

For detailed installation and usage instructions, please refer to the original FREALIGN documentation:

Comprehensive reference: Grigorieff, N. Frealign: An Exploratory Tool for Single-Particle Cryo-EM. in (ed. Enzymology, B. T.-M. in) (Academic Press, 2016). http://dx.doi.org/10.1016/bs.mie.2016.04.013

Official website: http://grigoriefflab.janelia.org/frealign

Contact

For bug reports and feature requests, please use GitHub's issue tracker. For other information, please contact us at http://c-cina.org.