An alignment project puts together all the elements needed to complete the alignment of a set of particles: the data particles, some auxiliary files (as template, masks, inititial orientations),
Elements of an alignment project
A set of files representing the particles cropped out of the tomograms. The easiest format is the data folder|.
The initial density (or set of densities in a multiresolution project.)
Dynamo uses several masks. The most important is the alignment mask. The classification mask is only relevant for multireference analysis. The option for defininf a fourier mask on template is used in very few special cases. The smoothing mask is the one used for computing Fourier Shell Correlations.
They define the mathematical part of the project, in terms of sets of angles to scan, shifts to allow, used bandpass or binning options....
The environment parameters are used to define where the project will be run, both in terms of hardware (CPU,GPU,multiple GPU, cluster of CPUs, how many cores) and software (using Matlab or using a standalone version of Dynamo)
Creation of an alignment project
Alignment projects are most easily created with the dcp GUI, that guides the user step by step. However, they can also be created from the command line using the command dvpr or dcp.new. You can get information on their syntax through >> help dvpr >> help dcp.new Additionally, several utilities in Dynamo give you the option of creating
== Running an alignment project
Projects need to be checked and unfolder