Xmipp

xmipp_angular_discrete_assign (v3.0)

Usage

Make a projection assignment using wavelets on a discrete library of projections This program assigns Euler angles to experimental projections by matching with ideal projections. This matching is done via a DWT correlation. For every experimental projection, different in-plane rotations and shifts are tried (by exhaustive search). For each possible combination of these two variables, the best correlating ideal projection is sought using a fast multirresolution algorithm. The method is fully described at http://www.ncbi.nlm.nih.gov/pubmed/15099579

Parameters

-i, --input <input_file>
List of images to align Alignment parameters can be provided Only the shifts are taken in consideration in global searches; in local searches, all parameters in the initial docfile are considered.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
-o, --output <output_file=>
Metadata with output alignment
--ref <selfile>
Metadata with the reference images and their angles Must be created with angular_project_library
--sym <symmetry_file=>
Symmetry file if any The definition of the symmetry is described at transform_symmetrize
--max_shift_change <r=0>
Maximum change allowed in shift
--psi_step <ang=5>
Step in psi in degrees
--shift_step <r=1>
Step in shift in pixels

Extra parameters

--search5D
Perform a 5D search instead of 3D+2D
--max_proj_change <ang=-1>
Maximum change allowed in rot-tilt
--max_psi_change <ang=-1>
Maximum change allowed in psi
--keep <th=50>
How many images are kept each round (%)
--smin <s=1>
Finest scale to consider (lowest value=0)
--smax <s=-1>
Coarsest scale to consider (highest value=log2(Xdim))
--pick <mth=1>
0 --> maximum of the first group 1 --> maximum of the most populated
--show_rot_tilt
Show the rot-tilt process
--show_psi_shift
Show the psi-shift process
--show_options
Show final options among which the angles are selected

Examples and notes

Typical use:
xmipp_angular_project_library -i referenceVolume.vol -o reference.stk --sampling_rate 5
xmipp_angular_discrete_assign -i projections.sel -o discrete_assignment.xmd --ref reference.doc

User's comments

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