Commit 6ae0a1c7 authored by Luka Stanisic's avatar Luka Stanisic

doc: minor fixes

parent a2585366
......@@ -679,7 +679,7 @@ The envelope function is
.. math:: \mathrm{Env}(s)=e^{-bs^2/2},
where parameter :math:`b` controls the Gaussian width and modulates the
.
CTF.
To calculate the BioEM posterior probability, we integrate numerically
the three parameters :math:`\Delta f`, :math:`b` and :math:`A`. To do
......@@ -989,7 +989,7 @@ Optional keywords:
Number of grid points used in the integration over
:math:`\cos(\beta) \in [-1,1]`.
- :inpar:`USE_QUATERNIONS`: (Integration of rientations) If using
- :inpar:`USE_QUATERNIONS`: (Integration of Orientations) If using
quaternions to the describe the orientations. *Recommended* for
uniformly sampling of :math:`SO3` with the quaternions lists
available in the **Quaternions** directory.
......@@ -999,7 +999,6 @@ Optional keywords:
quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
grid points per dimension.
- :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default
value of the electron wavelength ``(float)`` used to calculate the
CTF phase with the defocus. Default 0.019688 :math:`\AA`.
......@@ -1379,7 +1378,7 @@ We present the different parallelization options when using the
:envvar:`OMP_NUM_THREADS`. However,
:envvar:`BIOEM_PROJ_CONV_AT_ONCE` can also be modified as described
above. Importantly, for :envvar:`BIOEM_ALGO`\ ``=2`` the contribution of
:envvar:`BIOEM_PROJ_CONV_AT_ONCE` is signifcant. These
:envvar:`BIOEM_PROJ_CONV_AT_ONCE` is significant. These
OMP threads are used to work in parallel on the projections, the
convolutions, and if GPU is disabled on the center displacements
and comparisons.
......@@ -1545,11 +1544,12 @@ List of environment variables
.. envvar:: BIOEM_PROJ_CONV_AT_ONCE
(Default: 1 for :envvar:`BIOEM_ALGO`\ ``=1`` and :envvar:`=OMP_NUM_THREADS` for
:envvar:`BIOEM_ALGO`\ ``=2``) This defines the number of projections and
convolutions prepared at once. OpenMP threads (whose number is
defined by :envvar:`OMP_NUM_THREADS` environment variable) are used
to prepare these projections and convolutions in parallel. For
(Default: 1 for :envvar:`BIOEM_ALGO`\ ``=1`` and ``=``\
:envvar:`OMP_NUM_THREADS` for :envvar:`BIOEM_ALGO`\ ``=2``) This
defines the number of projections and convolutions prepared at
once. OpenMP threads (whose number is defined by
:envvar:`OMP_NUM_THREADS` environment variable) are used to prepare
these projections and convolutions in parallel. For
:envvar:`BIOEM_ALGO`\ ``=1`` :envvar:`BIOEM_PROJ_CONV_AT_ONCE`\
``=[x]`` is mostly relevant, if OpenMP is used, no GPU is used,
and/or the number of reference particle-image is very small. For
......
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