Volume_align_v3

!xmipp_volume_align (v3.0)

Usage

Align two volumes varying orientation, position and scale

Parameters

$: the first volume to align $: the second one $--rot <rot00> <rotF=0> <step_rot=1> $--tilt <tilt00> <tiltF=0> <step_tilt=1> $--psi <psi00> <psiF=0> <step_psi=1> $--scale <sc01> <scF=1> <step_sc=1> $--grey_scale <sc01> <scF=1> <step_sc=1> $--grey_shift <sh00> <shF=0> <step_sh=1> $-z <z00> <zF=0> <step_z=1> $-y <y00> <yF=0> <step_y=1> $-x <x00> <xF=0> <step_x=1> $: Show fitness values $`--apply <file`> $: Use the means within the mask $: Covariance fitness criterion $: LS fitness criterion $: Use local optimizer instead of exhaustive search $: Only shift

Mask Options $--mask <mask_typecircular> where <mask_type> can be:

• • 2D or 3D sincs if w > 0> outside sinc if w < 0 => inside sinc -m &lt;blob_order2> $-a <blob_alpha10.4> $--center <x00> <y0=0> <z0=0>

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

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