Xmipp

xmipp_volume_align (v3.0)

Usage

Align two volumes varying orientation, position and scale

Parameters

--i1 <volume1>
the first volume to align
--i2 <volume2>
the second one
--rot <rot0=0> <rotF=0> <step_rot=1>
in degrees
--tilt <tilt0=0> <tiltF=0> <step_tilt=1>
in degrees
--psi <psi0=0> <psiF=0> <step_psi=1>
in degrees
--scale <sc0=1> <scF=1> <step_sc=1>
size scale margin
--grey_scale <sc0=1> <scF=1> <step_sc=1> ( requires --least_squares )
grey scale margin
--grey_shift <sh0=0> <shF=0> <step_sh=1> ( requires --least_squares )
grey shift margin
-z <z0=0> <zF=0> <step_z=1>
Z position in pixels
-y <y0=0> <yF=0> <step_y=1>
Y position in pixels
-x <x0=0> <xF=0> <step_x=1>
X position in pixels
--show_fit
Show fitness values
--apply <file=>
Apply best movement to --i2 and store results in this file
--mean_in_mask
Use the means within the mask
--covariance
Covariance fitness criterion
--least_squares
LS fitness criterion
--local
Use local optimizer instead of exhaustive search
--onlyShift
Only shift

Mask Options

--mask <mask_type=circular>


where <mask_type> can be:
    • circular <R> circle/sphere mask if R>0 => outside R if R<0 => inside R
    • DWT_circular <R> <smin> <smax> circle/sphere mask smin and smax define the scales to be kept
    • rectangular <Xrect> <Yrect> <Zrect=-1> 2D or 3D rectangle if X,Y,Z > 0 => outside rectangle if X,Y,Z < 0 => inside rectangle
    • crown <R1> <R2> 2D or 3D crown if R1,R2 > 0 => outside crown if R1,R2 < 0 => inside crown
    • cylinder <R> <H> 2D circle or 3D cylinder if R,H > 0 => outside cylinder if R,H < 0 => inside cylinder
    • cone <theta> 3D cone (parallel to Z) if theta > 0 => outside cone if theta < 0 => inside cone
    • wedge <th0> <thF> 3D missing-wedge mask for data collected between tilting angles th0 and thF (around the Y-axis)
    • binary_file <binary_file> Read from file
    • gaussian <sigma> 2D or 3D gaussian if sigma > 0 => outside gaussian if sigma < 0 => inside gaussian
    • raised_cosine <R1> <R2> 2D or 3D raised_cosine if R1,R2 > 0 => outside sphere if R1,R2 < 0 => inside sphere
    • raised_crown <R1> <R2> <pixwidth> 2D or 3D raised_crown if R1,R2 > 0 => outside sphere if R1,R2 < 0 => inside sphere
    • blob_circular <R1> <blob_radius> 2D or 3D blob circular if blob_radius > 0 => outside sphere if blob_radius < 0 => inside sphere
    • blob_crown <R1> <R2> <blob_radius> 2D or 3D blob_crown if blob_radius > 0 => outside sphere if blob_radius < 0 => inside sphere
    • blackman 2D or 3D Blackman mask always inside blackman
    • sinc <w> 2D or 3D sincs if w > 0 => outside sinc if w < 0 => inside sinc
-m <blob_order=2>
Order of blob
-a <blob_alpha=10.4>
Alpha of blob
--center <x0=0> <y0=0> <z0=0>
mask center

Examples and notes

Typically you first look for a rough approximation of the alignment using exhaustive search. For instance, for a global rotational alignment use
xmipp_volume_align --i1 volume1.vol --i2 volume2.vol --rot 0 360 15 --tilt 0 180 15 --psi 0 360 15
Then, assume the best alignment is obtained for rot=45, tilt=60, psi=90 Now you perform a local search to refine the estimation and apply
xmipp_volume_align --i1 volume1.vol --i2 volume2.vol --rot 45 --tilt 60 --psi 90 --local --apply volume2aligned.vol

User's comments

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