relion_tomo_reconstruct_particle

This program constructs high-resolution 3D reference maps from a given optimisation set. It is similar to relion_reconstruct, except that it does not require pre-extracted particle images. Instead, it extracts square windows of arbitrary size (--b argument) directly from the tilt series and it uses those for the reconstruction (using Fourier inversion). It considers the defoci of the individual particles, as well as particle motion and higher-order aberrations.

The output consists of a pair of maps (one for each half set) as well as a merged map. In addition, the numerator (data term) and denominator (weight term) (see Eq. 3 in the Relion paper) of all 3 maps are also written out to facilitate further processing.

Relevant program arguments:

• --i and/or --p, --t and --mot: input optimisation-set and/or its components (see optimisation set).
• --b: box size of the reconstruction. Note that this is independent of the box size that has been used to refine the particle. This allows the user to construct a 3D map of arbitrary size to gain an overview of the structure surrounding the particle. A sufficiently large box size also allows more of the high-frequency signal to be captured that has been delocalised by the CTF.
• --crop: cropped box size. If set, the program will output an additional set of maps that have been cropped to this size. This is useful if a map is desired that is smaller than the box size required to retrieve the CTF-delocalised signal.
• --bin: downsampling (binning) factor. Note that this does not alter the box size. The reconstructed region instead becomes larger.
• --SNR: apply a Wiener filter with this signal-to-noise ratio. If omitted, the reconstruction will use a heuristic to prevent divisions by excessively small numbers. Please note that using a low (even though realistic) SNR might wash out the higher frequencies, which could make the map unsuitable to be used for further refinement.
• --sym: name of the symmetry class (e.g. C6 for six-fold point symmetry).
• --mem: (approximate) maximum amount of memory to be used for the reconstruction (see below).
• --j: number of threads used for the non-reconstruction parts of the program (e.g. symmetry application or gridding correction). This should be set to the number of CPU cores available.
• --j_out: number of threads that compute partial reconstructions in parallel. This is faster, but it requires additional memory for each thread. When used together with the --mem argument, this number will be reduced to (approximately) maintain the imposed memory limitation.
• --j_in: number of threads to be used for each partial reconstruction. This is a slower way to parallelise the procedure, but it does not require additional memory. Unless memory is limited, the --j_out option should be preferred. The product of --j_out and --j_in should not exceed the number of CPU cores available.
• --o: name of the output directory (that will be created).

Program output:

After running the program, the output directory (--o argument) will contain the following items:

• <half1/half2/merged>.mrc: the reconstructed cropped maps.
• <half1/half2/merged>_full.mrc: the reconstructed full-size maps, in case the full size (--b argument) differs from the cropped size (--crop argument).
• data_<half1/half2/merged>.mrc: the reconstructed data term at full size.
• weight_<half1/half2/merged>.mrc: the reconstructed weight term at full size.
• note.txt: a text file containing the command issued to run the program.