DOWNLOAD FREALIGN

Set to T to refine astigmatism. Citations Publications citing this paper. Ewald sphere correction for single-particle electron microscopy. Factor to downweight density outside of mask normally 0. Number of CPUs to use for each reconstruction job. Stewart, A , Grigorieff N.

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Frrealign seed name for the alignment parameter files and 3D maps must also be entered, as well as the path to the particle stack excluding the extension.

Frealign: Getting Started

Discriminate particles with different scores during reconstruction. A list of active commands can be obtained by typing. The magnification MAG has to be set to the correct frdalign on the detector often different from the nominal magnification displayed by the microscope. NobleMichael S SpilmanM.

Matthias WolfDavid J. Alex StewartNikolaus Grigorieff. Number of bootstrap volumes to calculate real-space variance map. Beam tilt in mrad along X-axis.

FREALIGN: high-resolution refinement of single particle structures.

Width of cosine edge in reciprocal pixels to add to filter function. Not recommended in most cases. Set to T to output matching projections. Number of classes to use.

Create new account Request new password. The x,y shifts in the alignment parameter files do not have to be changed in any way when working with binning as they are given in units of Angstroms. Set to T to allow potential overfitting during refinement. Set to T to apply symmetry also in real space. Again, to start the brute-force search, type. Five flags of 0 or 1 e. frrealign

Frealign: Running Frealign

Use " MODE 3 " instead as described above. One line is required for each particle. Low-resolution limit frfalign particle alignment. Sherical aberration coefficient in millimeter. Outer radius of ftealign particle mask in Angstrom. Number of repetitions of grid search with random starting angles. Refinement mode, normally 1. Hongjin ZhengAdam S. Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

Set to T to restart job if it crashes.

For example, a dataset containing 10, particles requires a file with 10, lines of 1 Noise bias in the refinement of structures derived from single particles. Alternatively, a full Frealign parameter file can be supplied, containing the following columns: An example file with line can be found here. The particle images should have normalized densities for example, by setting the average density of each particle to 0 and the variance to 1.

To begin processing data, select a working directory where all the needed files are kept. Frealign can be run on a local Linux workstation or a cluster. Set to N if particles are dark on bright background, otherwise set to P.