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 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.