Volume_to_pseudoatoms_v3

!xmipp_volume_to_pseudoatoms (v3.0)

Usage

Creates a set of pseudoatoms representing the density of an EM volume. This is useful for the vector quantization process needed in problems like docking, approximation of structures by Alpha Shapes, Normal Mode Analysis, etc.

The volume is approximated by Gaussians of a desired size. The user can specify whether the Gaussians can have different intensities or not, as well as the level of precision with which she desires to approximate the input EM volume.

Parameters

$: Input volume $`-o <rootname`> $`--sigma <s`1.5> $`--initialSeeds <N`300> $`--growSeeds <percentage`30> $`--stop <p`0.001> $`--targetError <e`0.02> $: Don't allow pseudoatoms to move $``: Don't allow pseudoatoms to change intensity $--intensityFraction <f0.01> $`--intensityColumn <s`occupancy> where <s> can be:

• • $--Nclosest <N3> $--minDistance <d0.001> $--penalty <p10> $--sampling_rate <Ts1> $: Don't scale atom weights in the PDB $: Binarize the volume for a more uniform distribution $--thr <n1> $--mask <mask_typecircular> where <mask_type> can be:
  • $--center <x00> <y0=0> <z0=0>

Examples and notes

xmipp_volume_to_pseudoatoms -i volume.vol -o pseudoatoms

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