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

i <volume>
 Input volume

o <rootname=>
 Output rootname. If not given, the rootname of the input volume is taken. The output of the program is: [rootname].pdb (PDB file with the pseudo atoms). If verbose is set to 2, then also [rootname].vol (the approximation volume), [rootname].hist (histogram of the Gaussian intensities), [rootname]_rawDiff.vol (difference between the input volume and its approximation), [rootname]_relativeDiff.vol (the raw difference divided by the input volume at that location; this gives an idea of how much the error represents with respect to the input

sigma <s=1.5>
 Sigma of gaussians (in Angstroms) It should be comparable to the sampling rate

initialSeeds <N=300>
 Initial number of pseudoatoms

growSeeds <percentage=30>
 Percentage of growth At each iteration the smallest percentage/2 pseudoatoms will be removed, and percentage new pseudoatoms will be created.

stop <p=0.001>
 Stop criterion (0<p<1) for inner iterations At each iteration the current number of gaussians will be optimized until the average error does not decrease at least this amount relative to the previous iteration.

targetError <e=0.02>
 Finish when the average representation error is below this threshold (in percentage)

dontAllowMovement
 Don't allow pseudoatoms to move

dontAllowIntensity
 Don't allow pseudoatoms to change intensity

intensityFraction <f=0.01>
 In case of all pseudoatoms with the same intensity this parameter determines the fraction of intensity held by each pseudoatom

intensityColumn <s=occupancy>
 Where to write the intensity in the PDB file
where <s> can be:

Nclosest <N=3>
 N closest atoms, it is used only for the distance histogram

minDistance <d=0.001>
 Minimum distance between two pseudoatoms Set it to 1 to disable

penalty <p=10>
 Penalty for overshooting

sampling_rate <Ts=1>
 Sampling rate Angstroms/pixel

dontScale
 Don't scale atom weights in the PDB

binarize <threshold>
 Binarize the volume for a more uniform distribution

thr <n=1>
 Number of threads

mask <mask_type=circular>
 Statistics restricted to the mask area.
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 missingwedge mask for data collected between tilting angles th0 and thF (around the Yaxis)
 binary_file <binary_file> Read from file

center <x0=0> <y0=0> <z0=0>
 mask center
Examples and notes
xmipp_volume_to_pseudoatoms i volume.vol o pseudoatoms
User's comments
%COMMENT{type="tableappend"}%