mrcImageSolventFlattening

mrcImageSolventFlattening is Eos's Command that performs smoothing about solvent.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage	NULL
-o	Essential	Output: mrcImage	NULL
-rmax	Optional	rmax [A]	190
-sd	Optional	Assign voxels below MeanOfSolvent+Range*SDofSolvent as Solvent	0
-density	Optional	embed mean lower than density value	0
-Floating	Optional	data minus mean of Solvent
-oparam	Optional	Output: Parameter	stdout
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode(-density is stronger)	0
-h	Optional	Help

-SD range : assign the voxels whose density is less than maen + range*SD as solvent range

-m details

Value	Description
0	mean of all density
1	mean of sphere surface density at rmax
2	mean of cylinder surface density at rmax
6	mean of 2D Edge X=0 or N.x-1

Execution example

Input file's image

Min Max Mean SD SE

0 (41, 10, 0) 255 (42, 36, 0) 111.211 32.7239 0.409049

Input file's image for m=1

xy-plane

yz-plane

Min Max Mean SD SE

-2255.49 (1, 42, 21) 4032.8 (49, 53, 30) 12.0338 475.034 0.48225

Input file's image for m=2

xy-plane

yz-plane

Min Max Mean SD SE

-0.307724 (52, 10, 79) 1.52145 (47, 41, 47) 0.00295664 0.0916201 0.000132783

Example of options only essential

-o 's image

Min Max Mean SD SE

111 (0, 0, 0) 255 (42, 36, 0) 123.826 21.2012 0.265015

-oparam 's data

Mean: 111.211
SD: 32.7239

Option -sd

Case: sd=1

-o 's image

Min Max Mean SD SE

143 (0, 0, 0) 255 (42, 36, 0) 146.528 11.5143 0.143928

-oparam 's data

Mean: 111.211
SD: 32.7239

Option -density

Case: density=64

-o 's image

Min Max Mean SD SE

64 (8, 0, 0) 255 (42, 36, 0) 111.86 31.5489 0.394361

-oparam 's data

Mean: 64
SD: 0

Option -Floating

-o 's image

Min Max Mean SD SE

0 (0, 0, 0) 143 (42, 36, 0) 12.3614 20.8806 0.261008

-oparam 's data

Mean: 111.211
SD: 32.7239

Option -m

Case: m=1

Case: No other settings

xy-plane

yz-plane

Min Max Mean SD SE

5.93088 (2, 0, 0) 4032.8 (49, 53, 30) 195.824 288.816 0.293204

-oparam 's data

rmax from caliculate:49.000000
meanOfSphereSurface 5.93088 at rmax 49[A]
Mean: 5.93088
SD: 391.086

Case: rmax=10

xy-plane

yz-plane

Min Max Mean SD SE

334.514 (0, 0, 0) 4032.8 (49, 53, 30) 404.478 184.129 0.186926

-oparam 's data

rmax from option:10.000000
meanOfSphereSurface 334.514 at rmax 10[A]
Mean: 334.514
SD: 673.352

Case: m=2

Case: No other settings

xy-plane

yz-plane

Min Max Mean SD SE

0.00126069 (0, 0, 0) 1.52145 (47, 41, 47) 0.0323659 0.0689534 9.99325e-05

-oparam 's data

rmax from caliculate:340.000000
meanOfCylinderSurface 0.00126069 at rmax 340[A]
Mean: 0.00126069
SD: 0.065755

Case: rmax=100

xy-plane

yz-plane

Min Max Mean SD SE

0.000652629 (0, 0, 0) 1.52145 (47, 41, 47) 0.0320589 0.0690925 0.000100134

-oparam 's data

rmax from option:100.000000
meanOfCylinderSurface 0.000652629 at rmax 100[A]
Mean: 0.000652629
SD: 0.0645217

Case: m=6

-o 's image

Min Max Mean SD SE

102 (0, 0, 0) 255 (42, 36, 0) 119.567 24.0291 0.300364

-oparam 's data

Mean: 102.875
SD: 24.7022