Commit e89360c7 authored by Luka Stanisic's avatar Luka Stanisic
Browse files

doc: improvements

parent 65055f01
...@@ -16,9 +16,9 @@ ...@@ -16,9 +16,9 @@
# add these directories to sys.path here. If the directory is relative to the # add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here. # documentation root, use os.path.abspath to make it absolute, like shown here.
# #
# import os import os
# import sys import sys
# sys.path.insert(0, os.path.abspath('.')) sys.path.insert(0, os.path.abspath('exts/'))
# -- General configuration ------------------------------------------------ # -- General configuration ------------------------------------------------
...@@ -34,6 +34,7 @@ extensions = ['sphinx.ext.intersphinx', ...@@ -34,6 +34,7 @@ extensions = ['sphinx.ext.intersphinx',
'sphinx.ext.todo', 'sphinx.ext.todo',
'sphinx.ext.imgmath', 'sphinx.ext.imgmath',
'sphinx.ext.ifconfig', 'sphinx.ext.ifconfig',
'inpar',
'sphinxcontrib.bibtex'] 'sphinxcontrib.bibtex']
# Setting up flags # Setting up flags
......
def setup(app):
app.add_crossref_type('inpar', 'inpar', 'single: %s')
app.add_crossref_type('outpar', 'outpar', 'single: %s')
return {'version': '0.1'} # identifies the version of our extension
...@@ -521,8 +521,12 @@ BioEM output ...@@ -521,8 +521,12 @@ BioEM output
~~~~~~~~~~~~ ~~~~~~~~~~~~
By default, the main BioEM output file is called By default, the main BioEM output file is called
``Output_Probabilities``. To change the name of the output file use the
following commandline keyword .. outpar:: Output_Probabilities
.. object:: Output_Probabilities
To change the name of the output file use the following commandline
keyword
.. option:: --OutputFile <arg> .. option:: --OutputFile <arg>
...@@ -550,15 +554,17 @@ Micrograph parameters ...@@ -550,15 +554,17 @@ Micrograph parameters
Mandatory inputs for the description of the experimental particle-image Mandatory inputs for the description of the experimental particle-image
are are
- ``PIXEL_SIZE (float)`` .. inpar:: PIXEL_SIZE
.. object:: PIXEL_SIZE (float)
Pixel size in :math:`\AA` of the experimental micrograph. Pixel size in :math:`\AA` of the experimental micrograph.
- ``NUMBER_PIXELS (int)`` .. inpar:: NUMBER_PIXELS
.. object:: NUMBER_PIXELS (int)
We assume a square particle-image. Here, ``(int)`` is the number of We assume a square particle-image. Here, ``(int)`` is the number
pixels in each dimension, *e.g.*, for a particle-image of 220 x 220 of pixels in each dimension, *e.g.*, for a particle-image of 220
pixels, then ``(int)= 220``. x 220 pixels, then ``(int)= 220``.
In the BioEM calculation, the integration over the model orientations, In the BioEM calculation, the integration over the model orientations,
PSF parameters, and center displacement are performed numerically. To do PSF parameters, and center displacement are performed numerically. To do
...@@ -600,12 +606,12 @@ Uniform sampling of SO3 ...@@ -600,12 +606,12 @@ Uniform sampling of SO3
To uniformly sample *SO3*, we recommend using a list of quaternions To uniformly sample *SO3*, we recommend using a list of quaternions
generated with the successive orthonormal images method from generated with the successive orthonormal images method from
ref. :cite:`Yershova2010`. In the directory **Quaternions**, ref. :cite:`Yershova2010`. In the directory **Quaternions**, we
we provide lists of quaternions that have been generated using this provide lists of quaternions that have been generated using this
method. Here, it is necessary to follow section :ref:`ortfile` because a list method. Here, it is necessary to follow section :ref:`ortfile` because
of quaternions is read from a separate file. To use quaternions the a list of quaternions is read from a separate file. To use quaternions
keyword ``USE_QUATERNIONS`` in the input-parameter file is also the keyword :inpar:`USE_QUATERNIONS` in the input-parameter file is
required. also required.
Non-uniform sampling Non-uniform sampling
^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^
...@@ -622,9 +628,11 @@ quaternions: ...@@ -622,9 +628,11 @@ quaternions:
:math:`\gamma` will be the same as that of :math:`\alpha`. The :math:`\gamma` will be the same as that of :math:`\alpha`. The
keywords in the parameter file are keywords in the parameter file are
``GRIDPOINTS_ALPHA (int)`` .. inpar:: GRIDPOINTS_ALPHA
.. object:: GRIDPOINTS_ALPHA (int)
``GRIDPOINTS_BETA (int)`` .. inpar:: GRIDPOINTS_BETA
.. object:: GRIDPOINTS_BETA (int)
where ``(int)`` is the number of grid points. where ``(int)`` is the number of grid points.
...@@ -636,9 +644,11 @@ quaternions: ...@@ -636,9 +644,11 @@ quaternions:
- *Grid-sampling of quaternions:* With BioEM it is also possible to - *Grid-sampling of quaternions:* With BioEM it is also possible to
generate a grid in quaternion space. One should provide the keywords generate a grid in quaternion space. One should provide the keywords
``USE_QUATERNIONS`` .. inpar:: USE_QUATERNIONS
.. object:: USE_QUATERNIONS
``GRIDPOINTS_QUATERNION (int)`` .. inpar:: GRIDPOINTS_QUATERNION
.. object:: GRIDPOINTS_QUATERNION (int)
where ``(int)`` is the grid spacing in each dimension :math:`[-1,1]`. where ``(int)`` is the grid spacing in each dimension :math:`[-1,1]`.
...@@ -678,11 +688,14 @@ parameter, its integration limits, and number of grid points: ...@@ -678,11 +688,14 @@ parameter, its integration limits, and number of grid points:
*Parameter – (start) – (end) – (gridpoints)* *Parameter – (start) – (end) – (gridpoints)*
``CTF_DEFOCUS (float) (float) (int)`` .. inpar:: CTF_DEFOCUS
.. object:: CTF_DEFOCUS (float) (float) (int)
``CTF_B_ENV (float) (float) (int)`` .. inpar:: CTF_B_ENV
.. object:: CTF_B_ENV (float) (float) (int)
``CTF_AMPLITUDE (float) (float) (int)`` .. inpar:: CTF_AMPLITUDE
.. object:: CTF_AMPLITUDE (float) (float) (int)
The defocus, :math:`\Delta f`, should be in units of :math:`\mu`\ m, The defocus, :math:`\Delta f`, should be in units of :math:`\mu`\ m,
and :math:`b` in Å\ :math:`^2`. The amplitude parameter :math:`A` is and :math:`b` in Å\ :math:`^2`. The amplitude parameter :math:`A` is
...@@ -690,7 +703,8 @@ adimensional within :math:`[0,1]`. The default value of the electron ...@@ -690,7 +703,8 @@ adimensional within :math:`[0,1]`. The default value of the electron
wavelength is 0.019688\ :math:`\AA`, which corresponds to a :math:`300 wavelength is 0.019688\ :math:`\AA`, which corresponds to a :math:`300
kV` microscope. To change this value use the keyword kV` microscope. To change this value use the keyword
``ELECTRON_WAVELENGTH (float)`` .. inpar:: ELECTRON_WAVELENGTH
.. object:: ELECTRON_WAVELENGTH (float)
where ``(float)`` should be in :math:`\AA`. where ``(float)`` should be in :math:`\AA`.
...@@ -706,7 +720,8 @@ The keyword in parameter file is: ...@@ -706,7 +720,8 @@ The keyword in parameter file is:
*Parameter - (max displ.) - (grid-space)* *Parameter - (max displ.) - (grid-space)*
``DISPLACE_CENTER (int) (int)`` .. inpar:: DISPLACE_CENTER
.. object:: DISPLACE_CENTER (int) (int)
If ``[DISPLACE_CENTER 10 2]``, the integration will be done along If ``[DISPLACE_CENTER 10 2]``, the integration will be done along
:math:`x` within :math:`[x_c-10,x_c+10]` (where :math:`x_c` is the :math:`x` within :math:`[x_c-10,x_c+10]` (where :math:`x_c` is the
...@@ -722,75 +737,100 @@ ref. :cite:`CossioHummerJSB_2013`. ...@@ -722,75 +737,100 @@ ref. :cite:`CossioHummerJSB_2013`.
Priors Priors
~~~~~~ ~~~~~~
- | *Uniform model prior probability:* To include a uniform model prior - *Uniform model prior probability:* To include a uniform model prior
use the following keyword in the input-parameter file use the following keyword in the input-parameter file
| ``PRIOR_MODEL (float)``
| where ``(float)`` is the value of the model’s prior. .. inpar:: PRIOR_MODEL
.. object:: PRIOR_MODEL (float)
- | *Prior for orientations:* It is possible to assign prior
probabilities for each orientation. The keyword where ``(float)`` is the value of the model’s prior.
| ``PRIOR_ANGLES``
| allows to read the prior of each orientation from the input file of - *Prior for orientations:* It is possible to assign prior
orientations (see section :ref:`ortfile`). An extra column of format probabilities for each orientation. The keyword
“%12.6f” should be added in the orientations-file, which indicates
the value of the prior probability for each orientation. .. inpar:: PRIOR_ANGLES
.. object:: PRIOR_ANGLES
- | *Prior for* :math:`b` *envelope parameter:* To avoid full loss of the
high-frequency components in Fourier space, the code utilizes a allows to read the prior of each orientation from the input file of
Gaussian prior on the :math:`b` envelope parameter orientations (see section :ref:`ortfile`). An extra column of format
“%12.6f” should be added in the orientations-file, which indicates
.. math:: p(b)=\frac{1}{\sqrt{2\pi}\sigma_b}e^{-b^2/2\sigma_b^2}, the value of the prior probability for each orientation.
| where :math:`\sigma_b` is the Gaussian width. By default the - *Prior for* :math:`b` *envelope parameter:* To avoid full loss of
Gaussian prior is centered at zero, and :math:`\sigma_b=100\AA`, to the high-frequency components in Fourier space, the code utilizes a
modify the width include in the input-parameter file the keyword Gaussian prior on the :math:`b` envelope parameter
| ``SIGMA_PRIOR_B_CTF (float)``
| where ``(float)`` is the desired :math:`\sigma_b`. See also the .. math:: p(b)=\frac{1}{\sqrt{2\pi}\sigma_b}e^{-b^2/2\sigma_b^2},
supporting information of ref. :cite:`BioEM_server`.
where :math:`\sigma_b` is the Gaussian width. By default the
- | *Prior for* :math:`\Delta f` *defocus parameter:* BioEM implements a Gaussian prior is centered at zero, and :math:`\sigma_b=100\AA`, to
Gaussian prior on the :math:`\Delta f` defocus parameter modify the width include in the input-parameter file the keyword
.. math:: p(\Delta f)=\frac{1}{\sqrt{2\pi}\sigma_{\Delta f}}e^{-(\Delta f - \Delta f_c)^2/2\sigma_{\Delta f}^2}, .. inpar:: SIGMA_PRIOR_B_CTF
.. object:: SIGMA_PRIOR_B_CTF (float)
| where :math:`\sigma_{\Delta f}` is the Gaussian width and
:math:`\Delta f_c` is the Gaussian center. By default where ``(float)`` is the desired :math:`\sigma_b`. See also the
:math:`\sigma_{\Delta f}=1.0\mu`\ m, and supporting information of ref. :cite:`BioEM_server`.
:math:`\Delta f_c=3.0\mu`\ m. To modify these values include in the
input-parameter file the keyword - *Prior for* :math:`\Delta f` *defocus parameter:* BioEM implements a
| ``SIGMA_PRIOR_DEFOCUS (float)`` Gaussian prior on the :math:`\Delta f` defocus parameter
| where ``(float)`` is the desired :math:`\sigma_{\Delta f}`, and
| ``PRIOR_DEFOCUS_CENTER (float)`` .. math:: p(\Delta f)=\frac{1}{\sqrt{2\pi}\sigma_{\Delta f}}e^{-(\Delta f - \Delta f_c)^2/2\sigma_{\Delta f}^2},
| to change the Gaussian center :math:`\Delta f_c`. See also the
supporting information of ref. :cite:`BioEM_server`. where :math:`\sigma_{\Delta f}` is the Gaussian width and
:math:`\Delta f_c` is the Gaussian center. By default
- | *Prior for* :math:`A` *amplitude parameter:* BioEM implements a :math:`\sigma_{\Delta f}=1.0\mu`\ m, and :math:`\Delta
Gaussian prior on the :math:`A` amplitude parameter f_c=3.0\mu`\ m. To modify these values include in the
input-parameter file the keyword
.. math:: p(A)=\frac{1}{\sqrt{2\pi}\sigma_{A}}e^{-(A - A_c)^2/2\sigma_{A}^2},
.. inpar:: SIGMA_PRIOR_DEFOCUS
| where :math:`\sigma_{A}` is the Gaussian width and :math:`A_c` is .. object:: SIGMA_PRIOR_DEFOCUS (float)
the Gaussian center. By default :math:`\sigma_{A}=0.3`, and
:math:`A_c=0`. To modify these values include in the where ``(float)`` is the desired :math:`\sigma_{\Delta f}`, and
input-parameter file the keyword
| ``SIGMA_PRIOR_AMP_CTF (float)`` .. inpar:: PRIOR_DEFOCUS_CENTER
| where ``(float)`` is the desired :math:`\sigma_{A}`, and .. object:: PRIOR_DEFOCUS_CENTER (float)
| ``PRIOR_AMP_CTF_CENTER (float)``
| to change the Gaussian center :math:`A_c`. to change the Gaussian center :math:`\Delta f_c`. See also the
supporting information of ref. :cite:`BioEM_server`.
- *Prior for* :math:`A` *amplitude parameter:* BioEM implements a
Gaussian prior on the :math:`A` amplitude parameter
.. math:: p(A)=\frac{1}{\sqrt{2\pi}\sigma_{A}}e^{-(A - A_c)^2/2\sigma_{A}^2},
where :math:`\sigma_{A}` is the Gaussian width and :math:`A_c` is
the Gaussian center. By default :math:`\sigma_{A}=0.3`, and
:math:`A_c=0`. To modify these values include in the input-parameter
file the keyword
.. inpar:: SIGMA_PRIOR_AMP_CTF
.. object:: SIGMA_PRIOR_AMP_CTF (float)
where ``(float)`` is the desired :math:`\sigma_{A}`, and
.. inpar:: PRIOR_AMP_CTF_CENTER
.. object:: PRIOR_AMP_CTF_CENTER (float)
to change the Gaussian center :math:`A_c`.
.. _angprob: .. _angprob:
Posterior probability as a function of orientations Posterior probability as a function of orientations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| One can write out the log-posterior as a function of each orientation. One can write out the log-posterior as a function of each orientation.
In this case, the integration is performed over the CTF parameters, In this case, the integration is performed over the CTF parameters,
particle-center, normalization, offset and noise, but not over the particle-center, normalization, offset and noise, but not over the
orientations. The keyword in parameter file is orientations. The keyword in parameter file is
| ``WRITE_PROB_ANGLES (int)``
| With this feature there is an additional output file ``ANG_PROB`` .. inpar:: WRITE_PROB_ANGLES
where ``(int)`` orientations with highest posterior are written. The .. object:: WRITE_PROB_ANGLES (int)
orientations in this file are sorted in decreasing order.
With this feature there is an additional output file
:outpar:`ANG_PROB` where ``(int)`` orientations with highest posterior
are written. The orientations in this file are sorted in decreasing
order.
File Formats File Formats
------------ ------------
...@@ -829,11 +869,13 @@ Formats for the particle-images ...@@ -829,11 +869,13 @@ Formats for the particle-images
Two format options are allowed for the the particle-image file: Two format options are allowed for the the particle-image file:
- *Text file:* Data are formatted as “%8d%8d%16.8f” where the first two .. inpar:: PARTICLE
columns are the pixel indexes, and the third column is the intensity
at that pixel. Multiple particles are read in the same file with the - *Text file:* Data are formatted as “%8d%8d%16.8f” where the first
separator ``PARTICLE``. Pixel indexes should start at 0, and all two columns are the pixel indexes, and the third column is the
pixels should be included. intensity at that pixel. Multiple particles are read in the same
file with the separator :inpar:`PARTICLE`. Pixel indexes should
start at 0, and all pixels should be included.
- *.mrc file:* BioEM also reads standard *.mrc* particle-image files. - *.mrc file:* BioEM also reads standard *.mrc* particle-image files.
To do so, the additional commandline keyword is needed: To do so, the additional commandline keyword is needed:
...@@ -855,6 +897,7 @@ Two format options are allowed for the the particle-image file: ...@@ -855,6 +897,7 @@ Two format options are allowed for the the particle-image file:
``LIST`` is the name of the file containing the list of names of the ``LIST`` is the name of the file containing the list of names of the
multiple *mrc* files. multiple *mrc* files.
.. inpar:: NO_MAP_NORM
.. note:: .. note::
When *mrc* particles are read, by default the intensities are When *mrc* particles are read, by default the intensities are
...@@ -884,11 +927,12 @@ orientations file is described in the following: ...@@ -884,11 +927,12 @@ orientations file is described in the following:
- *Quaternions*. A set of quaternions is a four-dimensional vector - *Quaternions*. A set of quaternions is a four-dimensional vector
over the real numbers (:math:`q_1`, :math:`q_2`, :math:`q_3`, over the real numbers (:math:`q_1`, :math:`q_2`, :math:`q_3`,
:math:`q_4`) each within :math:`[-1,1]`. The format for this file :math:`q_4`) each within :math:`[-1,1]`. The format for this
containing the quaternions should be “%12.6f%12.6f%12.6f%12.6f”, file containing the quaternions should be
ordered as :math:`q_1`, :math:`q_2`, :math:`q_3`, and :math:`q_4`, “%12.6f%12.6f%12.6f%12.6f”, ordered as :math:`q_1`, :math:`q_2`,
respectively. To use quaternions the keyword ``USE_QUATERNIONS`` :math:`q_3`, and :math:`q_4`, respectively. To use quaternions
should be placed in the input-parameter file. the keyword :inpar:`USE_QUATERNIONS` should be placed in the
input-parameter file.
- **Prior for orientations.** Its possible to assign prior - **Prior for orientations.** Its possible to assign prior
probabilities to each orientation. To do so, one should add at the probabilities to each orientation. To do so, one should add at the
...@@ -904,95 +948,97 @@ the input-parameter. ...@@ -904,95 +948,97 @@ the input-parameter.
BioEM posterior probability computation: BioEM posterior probability computation:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- ``PIXEL_SIZE (float)``: Micrograph pixel size in Å. - :inpar:`PIXEL_SIZE` ``(float)``: Micrograph pixel size in Å.
- ``NUMBER_PIXELS (int)``: Assuming a square particle-image, it is the - :inpar:`NUMBER_PIXELS` ``(int)``: Assuming a square particle-image,
number of pixels along an axis. This should coincide with the number it is the number of pixels along an axis. This should coincide with
of pixels read from the micrograph. the number of pixels read from the micrograph.
- ``GRIDPOINTS_ALPHA (int)``: (Integration of Orientations) Number of - :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of Orientations)
grid points used in the integration over Euler angle Number of grid points used in the integration over Euler angle
:math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle space :math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle
is performed. The integral over Euler angle :math:`\gamma` is space is performed. The integral over Euler angle :math:`\gamma` is
identical to that of :math:`\alpha`. identical to that of :math:`\alpha`.
- ``GRIDPOINTS_BETA (int)``: (Integration of Orientations) Number of - :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of Orientations)
grid points used in the integration over Number of grid points used in the integration over
:math:`\cos(\beta) \in [-1,1]`. :math:`\cos(\beta) \in [-1,1]`.
- ``USE_QUATERNIONS``: (Integration of Orientations) If using - :inpar:`USE_QUATERNIONS`: (Integration of Orientations) If using
quaternions to the describe the orientations. *Recommended* for quaternions to the describe the orientations. *Recommended* for
uniformly sampling of :math:`SO3` with the quaternions lists uniformly sampling of :math:`SO3` with the quaternions lists
available in the **Quaternions** directory. available in the **Quaternions** directory.
- ``GRIDPOINTS_QUATERNION (int)``: (Integration of Orientations) For a - :inpar:`GRIDPOINTS_QUATERNION` ``(int)``: (Integration of
hypercubic grid quaternion sampling. Each quaternion is within Orientations) For a hypercubic grid quaternion sampling. Each
:math:`[-1,1]`. ``(int)`` is the number of grid points per dimension. quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
grid points per dimension.
- ``CTF_DEFOCUS (float) (float) (int)``: (CTF Integration) Grid - :inpar:`CTF_DEFOCUS` ``(float) (float) (int)``: (CTF Integration)
sampling of CTF defocus, :math:`\Delta f`. Units of micro-meters. Grid sampling of CTF defocus, :math:`\Delta f`. Units of
``(float) (float)`` are the starting and ending limits, respectively, micro-meters. ``(float) (float)`` are the starting and ending
and ``(int)`` is the number of grid points. limits, respectively, and ``(int)`` is the number of grid points.
- ``CTF_B_ENV (float) (float) (int)``: (CTF Integration) Grid sampling - :inpar:`CTF_B_ENV` ``(float) (float) (int)``: (CTF Integration)
of envelope parameter :math:`b`. Units of Å\ :math:`^2`. Grid sampling of envelope parameter :math:`b`. Units of Å\
``(float) (float)`` are the starting and ending limits, respectively, :math:`^2`. ``(float) (float)`` are the starting and ending
and ``(int)`` is the number of grid points. limits, respectively, and ``(int)`` is the number of grid points.
- ``CTF_AMPLITUDE (float) (float) (int)``: (CTF Integration) Grid - :inpar:`CTF_AMPLITUDE` ``(float) (float) (int)``: (CTF Integration)
sampling of the CTF amplitude, :math:`A` (adimensional Grid sampling of the CTF amplitude, :math:`A` (adimensional
:math:`\in [0,1]`). ``(float) (float)`` are the starting and ending :math:`\in [0,1]`). ``(float) (float)`` are the starting and ending
limits, respectively, and ``(int)`` is the number of grid points. limits, respectively, and ``(int)`` is the number of grid points.
- ``DISPLACE_CENTER (int) (int)``: (Integration of particle center - :inpar:`DISPLACE_CENTER` ``(int) (int)``: (Integration of particle
displacement) Sampling within a square grid. Units of pixels. center displacement) Sampling within a square grid. Units of
``(int) (int)`` are the maximum displacement from the center in both pixels. ``(int) (int)`` are the maximum displacement from the
directions, and the grid spacing, respectively. center in both directions, and the grid spacing, respectively.
Optional keywords: Optional keywords:
^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^
- ``ELECTRON_WAVELENGTH (float)``: To change the default value of the - :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default
electron wavelength ``(float)`` used to calculate the CTF phase with value of the electron wavelength ``(float)`` used to calculate the
the defocus. Default 0.019688 :math:`\AA`. CTF phase with the defocus. Default 0.019688 :math:`\AA`.
- ``PRIOR_MODEL (float)``: Prior probability of model. **Default** 1. - :inpar:`PRIOR_MODEL` ``(float)``: Prior probability of
model. **Default** 1.
- ``PRIOR_ANGLES``: To read the prior of each orientation in the input - :inpar:`PRIOR_ANGLES`: To read the prior of each orientation in the input
file of orientations. file of orientations.
- ``SIGMA_PRIOR_B_CTF (float)``: To change the Gaussian width of the - :inpar:`SIGMA_PRIOR_B_CTF` ``(float)``: To change the Gaussian width
prior probability of the CTF envelope parameter :math:`b` (section of the prior probability of the CTF envelope parameter :math:`b`
:ref:`priorsec`). **Default** 100 Å. (section :ref:`priorsec`). **Default** 100 Å.
- ``SIGMA_PRIOR_DEFOCUS (float)``: To change the Gaussian width of the - :inpar:`SIGMA_PRIOR_DEFOCUS` ``(float)``: To change the Gaussian
prior of the defocus :math:`\sigma_{\Delta f}` (section :ref:`priorsec`). width of the prior of the defocus :math:`\sigma_{\Delta f}`
**Default** 1 :math:`\mu`\ m. (section :ref:`priorsec`). **Default** 1 :math:`\mu` m.
- ``PRIOR_DEFOCUS_CENTER (float)``: To change the Gaussian center of - :inpar:`PRIOR_DEFOCUS_CENTER` ``(float)``: To change the Gaussian
the prior of the defocus :math:`\Delta f_c` (section :ref:`priorsec`). center of the prior of the defocus :math:`\Delta f_c` (section
**Default** 3 :math:`\mu`\ m. :ref:`priorsec`). **Default** 3 :math:`\mu` m.
- ``SIGMA_PRIOR_AMP_CTF (float)``: To change the Gaussian width of the - :inpar:`SIGMA_PRIOR_AMP_CTF` ``(float)``: To change the Gaussian
prior of the amplitude :math:`\sigma_{A}` (section :ref:`priorsec`). width of the prior of the amplitude :math:`\sigma_{A}` (section
**Default** 0.3. :ref:`priorsec`). **Default** 0.3.
- ``PRIOR_AMP_CTF_CENTER (float)``: To change the Gaussian center of - :inpar:`PRIOR_AMP_CTF_CENTER` ``(float)``: To change the Gaussian
the prior of the amplitude :math:`A_c` (section :ref:`priorsec`). center of the prior of the amplitude :math:`A_c` (section
**Default** 0. :ref:`priorsec`). **Default** 0.
- ``NO_MAP_NORM``: Condition to not normalize to zero mean and unit - :inpar:`NO_MAP_NORM`: Condition to not normalize to zero mean and unit
variance the input maps. variance the input maps.
- ``WRITE_PROB_ANGLES (int)``: To write out the posterior as a function - :inpar:`WRITE_PROB_ANGLES` ``(int)``: To write out the posterior as
of the best ``(int)`` orientation. a function of the best ``(int)`` orientation.
.. _anaout: .. _anaout:
Output format Output format
~~~~~~~~~~~~~ ~~~~~~~~~~~~~
The main BioEM output file is called ``Output_Probabilities`` by The main BioEM output file is called :outpar:`Output_Probabilities` by
default. Its name can be changed using the commandline default. Its name can be changed using the commandline
:option:`--OutputFile` as described in section :ref:`biout`. This file :option:`--OutputFile` as described in section :ref:`biout`. This file
contains the logarithm of the posterior probability of the model to contains the logarithm of the posterior probability of the model to
...@@ -1019,7 +1065,12 @@ values of the log-posterior are finite, and the parameters that give a ...@@ -1019,7 +1065,12 @@ values of the log-posterior are finite, and the parameters that give a
maximum of the posterior are in a reasonable range (*e.g.*, not at the maximum of the posterior are in a reasonable range (*e.g.*, not at the
borders of the integration limits). borders of the integration limits).
The output file ``COORDREAD`` is always generated. It is good to check The output file
.. outpar:: COORDREAD
.. object:: COORDREAD
is always generated. It is good to check
that the model coordinates, radius and density are read correctly. that the model coordinates, radius and density are read correctly.
Optional outputs Optional outputs
...@@ -1027,10 +1078,13 @@ Optional outputs ...@@ -1027,10 +1078,13 @@ Optional outputs
The optional output files for BioEM are: The optional output files for BioEM are:
- ``ANG_PROB``: Related to section :ref:`angprob`. This file has the .. outpar:: ANG_PROB
posterior probabilities for each orientation, which was specified .. object:: ANG_PROB
with the keyword ``WRITE_PROB_ANGLES`` in the parameter inputfile.
For the Euler angles, the format of the output file is Related to section :ref:`angprob`. This file has the posterior
probabilities for each orientation, which was specified with the
keyword :inpar:`WRITE_PROB_ANGLES` in the parameter inputfile.
For the Euler angles, the format of the output file is
.. code-block:: bash .. code-block:: bash
...@@ -1768,11 +1822,11 @@ Commandline input and execution ...@@ -1768,11 +1822,11 @@ Commandline input and execution
.. note:: .. note::
1. Check coordinates in the output ``COORDREAD`` file to verify 1. Check coordinates in the output :outpar:`COORDREAD` file to
that the model is correct. verify that the model is correct.
2. The *txt* particle-image file can contain multiple particles 2. The *txt* particle-image file can contain multiple particles
that are distinguished by the separator ``PARTICLE`` (see that are distinguished by the separator :inpar:`PARTICLE` (see
section :ref:`partimag`). section :ref:`partimag`).
3. The *Param\_Input* file is an example for a debug run. It has 3. The *Param\_Input* file is an example for a debug run. It has
...@@ -1896,7 +1950,7 @@ Commandline input and execution ...@@ -1896,7 +1950,7 @@ Commandline input and execution
**Important!:** in the input-parameter file one has to add the **Important!:** in the input-parameter file one has to add the
keyword: