Commit e89360c7 authored by Luka Stanisic's avatar Luka Stanisic

doc: improvements

parent 65055f01
......@@ -16,9 +16,9 @@
# 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.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
import os
import sys
sys.path.insert(0, os.path.abspath('exts/'))
# -- General configuration ------------------------------------------------
......@@ -34,6 +34,7 @@ extensions = ['sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.imgmath',
'sphinx.ext.ifconfig',
'inpar',
'sphinxcontrib.bibtex']
# 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
~~~~~~~~~~~~
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>
......@@ -550,15 +554,17 @@ Micrograph parameters
Mandatory inputs for the description of the experimental particle-image
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
pixels in each dimension, *e.g.*, for a particle-image of 220 x 220
pixels, then ``(int)= 220``.
We assume a square particle-image. Here, ``(int)`` is the number
of pixels in each dimension, *e.g.*, for a particle-image of 220
x 220 pixels, then ``(int)= 220``.
In the BioEM calculation, the integration over the model orientations,
PSF parameters, and center displacement are performed numerically. To do
......@@ -600,12 +606,12 @@ Uniform sampling of SO3
To uniformly sample *SO3*, we recommend using a list of quaternions
generated with the successive orthonormal images method from
ref. :cite:`Yershova2010`. In the directory **Quaternions**,
we provide lists of quaternions that have been generated using this
method. Here, it is necessary to follow section :ref:`ortfile` because a list
of quaternions is read from a separate file. To use quaternions the
keyword ``USE_QUATERNIONS`` in the input-parameter file is also
required.
ref. :cite:`Yershova2010`. In the directory **Quaternions**, we
provide lists of quaternions that have been generated using this
method. Here, it is necessary to follow section :ref:`ortfile` because
a list of quaternions is read from a separate file. To use quaternions
the keyword :inpar:`USE_QUATERNIONS` in the input-parameter file is
also required.
Non-uniform sampling
^^^^^^^^^^^^^^^^^^^^
......@@ -622,9 +628,11 @@ quaternions:
:math:`\gamma` will be the same as that of :math:`\alpha`. The
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.
......@@ -636,9 +644,11 @@ quaternions:
- *Grid-sampling of quaternions:* With BioEM it is also possible to
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]`.
......@@ -678,11 +688,14 @@ parameter, its integration limits, and number of grid points:
*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,
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
wavelength is 0.019688\ :math:`\AA`, which corresponds to a :math:`300
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`.
......@@ -706,7 +720,8 @@ The keyword in parameter file is:
*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
:math:`x` within :math:`[x_c-10,x_c+10]` (where :math:`x_c` is the
......@@ -722,75 +737,100 @@ ref. :cite:`CossioHummerJSB_2013`.
Priors
~~~~~~
- | *Uniform model prior probability:* To include a uniform model prior
use the following keyword in the input-parameter file
| ``PRIOR_MODEL (float)``
| where ``(float)`` is the value of the model’s prior.
- | *Prior for orientations:* It is possible to assign prior
probabilities for each orientation. The keyword
| ``PRIOR_ANGLES``
| allows to read the prior of each orientation from the input file of
orientations (see section :ref:`ortfile`). An extra column of format
“%12.6f” should be added in the orientations-file, which indicates
the value of the prior probability for each orientation.
- | *Prior for* :math:`b` *envelope parameter:* To avoid full loss of the
high-frequency components in Fourier space, the code utilizes a
Gaussian prior on the :math:`b` envelope parameter
.. math:: p(b)=\frac{1}{\sqrt{2\pi}\sigma_b}e^{-b^2/2\sigma_b^2},
| where :math:`\sigma_b` is the Gaussian width. By default the
Gaussian prior is centered at zero, and :math:`\sigma_b=100\AA`, to
modify the width include in the input-parameter file the keyword
| ``SIGMA_PRIOR_B_CTF (float)``
| where ``(float)`` is the desired :math:`\sigma_b`. See also the
supporting information of ref. :cite:`BioEM_server`.
- | *Prior for* :math:`\Delta f` *defocus parameter:* BioEM implements a
Gaussian prior on the :math:`\Delta f` defocus parameter
.. math:: p(\Delta f)=\frac{1}{\sqrt{2\pi}\sigma_{\Delta f}}e^{-(\Delta f - \Delta f_c)^2/2\sigma_{\Delta f}^2},
| where :math:`\sigma_{\Delta f}` is the Gaussian width and
:math:`\Delta f_c` is the Gaussian center. By default
:math:`\sigma_{\Delta f}=1.0\mu`\ m, and
:math:`\Delta f_c=3.0\mu`\ m. To modify these values include in the
input-parameter file the keyword
| ``SIGMA_PRIOR_DEFOCUS (float)``
| where ``(float)`` is the desired :math:`\sigma_{\Delta f}`, and
| ``PRIOR_DEFOCUS_CENTER (float)``
| 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
| ``SIGMA_PRIOR_AMP_CTF (float)``
| where ``(float)`` is the desired :math:`\sigma_{A}`, and
| ``PRIOR_AMP_CTF_CENTER (float)``
| to change the Gaussian center :math:`A_c`.
- *Uniform model prior probability:* To include a uniform model prior
use the following keyword in the input-parameter file
.. inpar:: PRIOR_MODEL
.. object:: PRIOR_MODEL (float)
where ``(float)`` is the value of the model’s prior.
- *Prior for orientations:* It is possible to assign prior
probabilities for each orientation. The keyword
.. inpar:: PRIOR_ANGLES
.. object:: PRIOR_ANGLES
allows to read the prior of each orientation from the input file of
orientations (see section :ref:`ortfile`). An extra column of format
“%12.6f” should be added in the orientations-file, which indicates
the value of the prior probability for each orientation.
- *Prior for* :math:`b` *envelope parameter:* To avoid full loss of
the high-frequency components in Fourier space, the code utilizes a
Gaussian prior on the :math:`b` envelope parameter
.. math:: p(b)=\frac{1}{\sqrt{2\pi}\sigma_b}e^{-b^2/2\sigma_b^2},
where :math:`\sigma_b` is the Gaussian width. By default the
Gaussian prior is centered at zero, and :math:`\sigma_b=100\AA`, to
modify the width include in the input-parameter file the keyword
.. inpar:: SIGMA_PRIOR_B_CTF
.. object:: SIGMA_PRIOR_B_CTF (float)
where ``(float)`` is the desired :math:`\sigma_b`. See also the
supporting information of ref. :cite:`BioEM_server`.
- *Prior for* :math:`\Delta f` *defocus parameter:* BioEM implements a
Gaussian prior on the :math:`\Delta f` defocus parameter
.. math:: p(\Delta f)=\frac{1}{\sqrt{2\pi}\sigma_{\Delta f}}e^{-(\Delta f - \Delta f_c)^2/2\sigma_{\Delta f}^2},
where :math:`\sigma_{\Delta f}` is the Gaussian width and
:math:`\Delta f_c` is the Gaussian center. By default
:math:`\sigma_{\Delta f}=1.0\mu`\ m, and :math:`\Delta
f_c=3.0\mu`\ m. To modify these values include in the
input-parameter file the keyword
.. inpar:: SIGMA_PRIOR_DEFOCUS
.. object:: SIGMA_PRIOR_DEFOCUS (float)
where ``(float)`` is the desired :math:`\sigma_{\Delta f}`, and
.. inpar:: PRIOR_DEFOCUS_CENTER
.. object:: PRIOR_DEFOCUS_CENTER (float)
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:
Posterior probability as a function of orientations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| One can write out the log-posterior as a function of each orientation.
In this case, the integration is performed over the CTF parameters,
particle-center, normalization, offset and noise, but not over the
orientations. The keyword in parameter file is
| ``WRITE_PROB_ANGLES (int)``
| With this feature there is an additional output file ``ANG_PROB``
where ``(int)`` orientations with highest posterior are written. The
orientations in this file are sorted in decreasing order.
One can write out the log-posterior as a function of each orientation.
In this case, the integration is performed over the CTF parameters,
particle-center, normalization, offset and noise, but not over the
orientations. The keyword in parameter file is
.. inpar:: WRITE_PROB_ANGLES
.. object:: WRITE_PROB_ANGLES (int)
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
------------
......@@ -829,11 +869,13 @@ Formats for the particle-images
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
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
separator ``PARTICLE``. Pixel indexes should start at 0, and all
pixels should be included.
.. inpar:: PARTICLE
- *Text file:* Data are formatted as “%8d%8d%16.8f” where the first
two 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 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.
To do so, the additional commandline keyword is needed:
......@@ -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
multiple *mrc* files.
.. inpar:: NO_MAP_NORM
.. note::
When *mrc* particles are read, by default the intensities are
......@@ -884,11 +927,12 @@ orientations file is described in the following:
- *Quaternions*. A set of quaternions is a four-dimensional vector
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
containing the quaternions should be “%12.6f%12.6f%12.6f%12.6f”,
ordered as :math:`q_1`, :math:`q_2`, :math:`q_3`, and :math:`q_4`,
respectively. To use quaternions the keyword ``USE_QUATERNIONS``
should be placed in the input-parameter file.
:math:`q_4`) each within :math:`[-1,1]`. The format for this
file containing the quaternions should be
“%12.6f%12.6f%12.6f%12.6f”, ordered as :math:`q_1`, :math:`q_2`,
:math:`q_3`, and :math:`q_4`, respectively. To use quaternions
the keyword :inpar:`USE_QUATERNIONS` should be placed in the
input-parameter file.
- **Prior for orientations.** Its possible to assign prior
probabilities to each orientation. To do so, one should add at the
......@@ -904,95 +948,97 @@ the input-parameter.
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
number of pixels along an axis. This should coincide with the number
of pixels read from the micrograph.
- :inpar:`NUMBER_PIXELS` ``(int)``: Assuming a square particle-image,
it is the number of pixels along an axis. This should coincide with
the number of pixels read from the micrograph.
- ``GRIDPOINTS_ALPHA (int)``: (Integration of Orientations) Number of
grid points used in the integration over Euler angle
:math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle space
is performed. The integral over Euler angle :math:`\gamma` is
- :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of Orientations)
Number of grid points used in the integration over Euler angle
:math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle
space is performed. The integral over Euler angle :math:`\gamma` is
identical to that of :math:`\alpha`.
- ``GRIDPOINTS_BETA (int)``: (Integration of Orientations) Number of
grid points used in the integration over
- :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of Orientations)
Number of grid points used in the integration over
: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
uniformly sampling of :math:`SO3` with the quaternions lists
available in the **Quaternions** directory.
- ``GRIDPOINTS_QUATERNION (int)``: (Integration of Orientations) For a
hypercubic grid quaternion sampling. Each quaternion is within
:math:`[-1,1]`. ``(int)`` is the number of grid points per dimension.
- :inpar:`GRIDPOINTS_QUATERNION` ``(int)``: (Integration of
Orientations) For a hypercubic grid quaternion sampling. Each
quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
grid points per dimension.
- ``CTF_DEFOCUS (float) (float) (int)``: (CTF Integration) Grid
sampling of CTF defocus, :math:`\Delta f`. Units of micro-meters.
``(float) (float)`` are the starting and ending limits, respectively,
and ``(int)`` is the number of grid points.
- :inpar:`CTF_DEFOCUS` ``(float) (float) (int)``: (CTF Integration)
Grid sampling of CTF defocus, :math:`\Delta f`. Units of
micro-meters. ``(float) (float)`` are the starting and ending
limits, respectively, and ``(int)`` is the number of grid points.
- ``CTF_B_ENV (float) (float) (int)``: (CTF Integration) Grid sampling
of envelope parameter :math:`b`. Units of Å\ :math:`^2`.
``(float) (float)`` are the starting and ending limits, respectively,
and ``(int)`` is the number of grid points.
- :inpar:`CTF_B_ENV` ``(float) (float) (int)``: (CTF Integration)
Grid sampling of envelope parameter :math:`b`. Units of Å\
:math:`^2`. ``(float) (float)`` are the starting and ending
limits, respectively, and ``(int)`` is the number of grid points.
- ``CTF_AMPLITUDE (float) (float) (int)``: (CTF Integration) Grid
sampling of the CTF amplitude, :math:`A` (adimensional
- :inpar:`CTF_AMPLITUDE` ``(float) (float) (int)``: (CTF Integration)
Grid sampling of the CTF amplitude, :math:`A` (adimensional
:math:`\in [0,1]`). ``(float) (float)`` are the starting and ending
limits, respectively, and ``(int)`` is the number of grid points.
- ``DISPLACE_CENTER (int) (int)``: (Integration of particle center
displacement) Sampling within a square grid. Units of pixels.
``(int) (int)`` are the maximum displacement from the center in both
directions, and the grid spacing, respectively.
- :inpar:`DISPLACE_CENTER` ``(int) (int)``: (Integration of particle
center displacement) Sampling within a square grid. Units of
pixels. ``(int) (int)`` are the maximum displacement from the
center in both directions, and the grid spacing, respectively.
Optional keywords:
^^^^^^^^^^^^^^^^^^
- ``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`.
- :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`.
- ``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.
- ``SIGMA_PRIOR_B_CTF (float)``: To change the Gaussian width of the
prior probability of the CTF envelope parameter :math:`b` (section
:ref:`priorsec`). **Default** 100 Å.
- :inpar:`SIGMA_PRIOR_B_CTF` ``(float)``: To change the Gaussian width
of the prior probability of the CTF envelope parameter :math:`b`
(section :ref:`priorsec`). **Default** 100 Å.
- ``SIGMA_PRIOR_DEFOCUS (float)``: To change the Gaussian width of the
prior of the defocus :math:`\sigma_{\Delta f}` (section :ref:`priorsec`).
**Default** 1 :math:`\mu`\ m.
- :inpar:`SIGMA_PRIOR_DEFOCUS` ``(float)``: To change the Gaussian
width of the prior of the defocus :math:`\sigma_{\Delta f}`
(section :ref:`priorsec`). **Default** 1 :math:`\mu` m.
- ``PRIOR_DEFOCUS_CENTER (float)``: To change the Gaussian center of
the prior of the defocus :math:`\Delta f_c` (section :ref:`priorsec`).
**Default** 3 :math:`\mu`\ m.
- :inpar:`PRIOR_DEFOCUS_CENTER` ``(float)``: To change the Gaussian
center of the prior of the defocus :math:`\Delta f_c` (section
:ref:`priorsec`). **Default** 3 :math:`\mu` m.
- ``SIGMA_PRIOR_AMP_CTF (float)``: To change the Gaussian width of the
prior of the amplitude :math:`\sigma_{A}` (section :ref:`priorsec`).
**Default** 0.3.
- :inpar:`SIGMA_PRIOR_AMP_CTF` ``(float)``: To change the Gaussian
width of the prior of the amplitude :math:`\sigma_{A}` (section
:ref:`priorsec`). **Default** 0.3.
- ``PRIOR_AMP_CTF_CENTER (float)``: To change the Gaussian center of
the prior of the amplitude :math:`A_c` (section :ref:`priorsec`).
**Default** 0.
- :inpar:`PRIOR_AMP_CTF_CENTER` ``(float)``: To change the Gaussian
center of the prior of the amplitude :math:`A_c` (section
: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.
- ``WRITE_PROB_ANGLES (int)``: To write out the posterior as a function
of the best ``(int)`` orientation.
- :inpar:`WRITE_PROB_ANGLES` ``(int)``: To write out the posterior as
a function of the best ``(int)`` orientation.
.. _anaout:
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
:option:`--OutputFile` as described in section :ref:`biout`. This file
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
maximum of the posterior are in a reasonable range (*e.g.*, not at the
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.
Optional outputs
......@@ -1027,10 +1078,13 @@ Optional outputs
The optional output files for BioEM are:
- ``ANG_PROB``: Related to section :ref:`angprob`. This file has the
posterior probabilities for each orientation, which was specified
with the keyword ``WRITE_PROB_ANGLES`` in the parameter inputfile.
For the Euler angles, the format of the output file is
.. outpar:: ANG_PROB
.. object:: ANG_PROB
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
......@@ -1768,11 +1822,11 @@ Commandline input and execution
.. note::
1. Check coordinates in the output ``COORDREAD`` file to verify
that the model is correct.
1. Check coordinates in the output :outpar:`COORDREAD` file to
verify that the model is correct.
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`).
3. The *Param\_Input* file is an example for a debug run. It has
......@@ -1896,7 +1950,7 @@ Commandline input and execution
**Important!:** in the input-parameter file one has to add the
keyword:
``USE_QUATERNIONS``
:inpar:`USE_QUATERNIONS`
**Files:**
......@@ -2066,11 +2120,11 @@ BioEM:
Eq. :eq:`pmom` are performed apart from that over the
orientations. The keyword in the parameter file is
``WRITE_PROB_ANGLES X``
:inpar:`WRITE_PROB_ANGLES` ``x``
an additional outputfile ``ANG_PROB`` is generated with the best
``X`` orientations. An example of the parameter input is provide in
the *Param\_Input\_WritePAng* file.
an additional outputfile :outpar:`ANG_PROB` is generated with the
best ``x`` orientations. An example of the parameter input is
provide in the *Param\_Input\_WritePAng* file.
.. _modcom:
......
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