.. _program_tomo_reconstruct_particle: relion_tomo_reconstruct_particle ================================ This program constructs high-resolution 3D reference maps from a given :ref:`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 :ref:`optimisation set `). - ``--b``: box size of the reconstruction. Note that this is independent of the box size 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: - **.mrc**: the reconstructed cropped maps. - **_full.mrc**: the reconstructed full-size maps, in case the full size (``--b`` argument) differs from the cropped size (``--crop`` argument). - **data_.mrc**: the reconstructed data term at full size. - **weight_.mrc**: the reconstructed weight term at full size. - **note.txt**: a text file containing the command issued to run the program.