pdbRhoFitTm

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pdbRhoFitTm is Eos's Command.


Contents

List of option

Main option

Option Essential/Optional Description Default
-ipdb Essential Input: [pdb] (原子モデル) NULL
-imrc Essential Input: mrcImage NULL
-Sx Essential xの回転軸 55
-Sy Essential yの回転軸 110
-Sz Essential zの回転軸 110
-omrc Essential Output: mrcImage NULL
-otxt Optional Output: [テキスト] NULL
-opdb Optional Output: [pdb] NULL
-xmin Optional xの最小 0
-xmax Optional xの最大 0
-xd Optional xの間隔 1
-ymin Optional yの最小 0
-ymax Optional yの最大 0
-yd Optional yの間隔 1
-zmin Optional zの最小 0
-zmax Optional zの最大 82
-zd Optional zの間隔 1
-EA Optional Euler Angleの回転Mode ZOYS
-phimin Optional phiの最小: [degree] 0
-phimax Optional phiの最大: [degree] 194
-phid Optional phiの間隔: [degree] 2
-psimin Optional psiの最小: [degree] 0
-psimax Optional psiの最大: [degree] 0
-psid Optional psiの間隔: [degree] 2
-thetamin Optional thetaの最小: [degree] 0
-thetamax Optional thetaの最大: [degree] 0
-thetad Optional thetaの間隔: [degree] 2
-nw Optional weight for normalize 100000000.0
-nC Optional Contour Level for Normalize 0.0
-I Optional 黒を高密度とする
-Zminus Optional Shift to -z
-Tfactor Optional Consider T factor
-Tlim Optional The atom will be neglected 60
-Centre Optional Filament-axis is x=0, y=0
-C Optional 可変Input: コンターレベル 0.0 ...
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　 
    -ipdb   : Filename of pdb file of atomic model
    -imrc   : Filename of mrc file of contour map
    -omrc   : Filename of mrc file of fitting results
    -otxt   : Filename of text file of fitting results
    -opdb   : Filename of pdb file with a max score after fitting results
    -zmin   : Initial value of z (should <= zmax)
    -zmax   : Final value of z
    -zd     : Delta z for fitting (should >0)
    -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
    -phimax : Final value of phi (should >0)
    -phid   : Delta phi for fitting (should >0)
    -C      : Contour level (variable and MUST be last option)
    -Inverse: Protein has high density on the image
    -Sx	    : x of rotation axis
    -Sy     : y of rotation axis
    -Sz     : z of rotation axis
    -Zminus : Atomic model shift to -z while fitting
    -Tfactor: Consider temperature factor
    -Tlim   : The atoms whose T factor is above Tlim will be neglected
    -Centre : Filament-axis is x=0, y=0

-m details

Value Description
0 輪郭内の原子数をカウントする
1 原子の密度を加える


Execution example

Input file's image

pdb image

Input(pdb)-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 2.519590e+01 1.189075e+01

3.286664e+01

24.77 23.85 28.04

mrcImage image

Input(mrc)-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

5 (34, 41, 36)
0.00471829
0.0933498

0.000162869

Option -C

Case: C=1, Sx=55, Sy=110, Sz=110

pdb image
Outdata(pdb)-C-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-4.127895e+01 1.871655e+02 2.597458e+00

3.823911e+01

21.51 36.99 20.84
mrcImage image
Outdata(mrc)-C-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (10, 0, 0)

15519 (32, 8, 0)
125.844
1103.92

7.06681

Option -Sx

Case: Sx=0, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-Sx-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-4.086051e+01 2.123659e+02 2.597458e+00

3.823867e+01

32.66 29.04 20.84
mrcImage image
Outdata(mrc)-Sx-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (15, 0, 0)

12888 (4, 8, 0)
95.5124
842.466

5.39311

Option -Sy

Case: Sy=0, Sx=55, Sz=110, C=1

pdb image
Outdata(pdb)-Sy-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

2.957797e+00 -1.917446e+01 2.597458e+00

3.823857e+01

33.06 28.34 20.84
mrcImage image
Outdata(mrc)-Sy-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

14125 (93, 8, 0)
119.109
992.326

6.35246

Option -Sz

Case: Sz=0, Sx=55, Sy=110, C=1

pdb image
Outdata(pdb)-Sz-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-4.127895e+01 1.871655e+02 2.597458e+00

3.823911e+01

21.51 36.99 20.84
mrcImage image
Outdata(mrc)-Sz-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (10, 0, 0)

15519 (32, 8, 0)
125.844
1103.92

7.06681

Option -xmin, -xmax, xd

Case: xmin=0, xmax=2, xd=1, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-xminxmaxxd-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.366163e+01 1.936936e+02 -1.402542e+00

3.823834e+01

21.46 37.49 20.84
mrcImage image
Outdata(mrc)-xminxmaxxd-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (10, 0, 0)

16153 (30, 4, 0)
133.759
1154.61

7.3913

Option -ymin, -ymax, yd

Case: ymin=10, ymax=30, yd=5, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-yminymaxyd-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-2.960260e+01 2.098140e+02 3.597458e+00

3.823860e+01

22.15 37.81 20.84
mrcImage image
Outdata(mrc)-yminymaxyd-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (15, 0, 0)

16212 (28, 9, 0)
145.389
1144.65

7.32756

Option -zmin, -zmax, -zd

Case: zmin=20, zmax=70, zd=2, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-zminzmaxzd-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-2.960260e+01 1.998140e+02 1.459746e+01

3.823860e+01

22.15 37.81 20.84
mrcImage image
Outdata(mrc)-zminzmaxzd-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (10, 0, 0)

7065 (28, 0, 0)
12.826
216.816

2.47988

Option -EA

Case: EA=YOYS, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-EA-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.367327e+02 -2.186292e-01 2.095572e+02

3.823908e+01

34.54 22.99 22.20
mrcImage image
Outdata(mrc)-EA-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (9, 0, 0)

11951 (0, 1, 0)
19.1756
362.85

2.32281

Option -phimin, -phimax, -phid

Case: phimin=0, phimax=360, phid=3, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-phiminphimaxphid-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.280264e+02 1.054504e+01 2.597458e+00

3.823844e+01

23.11 37.92 20.84
mrcImage image
Outdata(mrc)-phiminphimaxphid-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (7, 0, 0)

15675 (21, 8, 0)
82.6776
875.943

5.04642

Option -psimin, -psimax, psid

Case: psimin=30, psimax=60, psid=6, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-psiminpsimaxpsid-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-9.654431e+01 8.513753e+01 2.044136e+02

3.823914e+01

34.74 27.68 23.43
mrcImage image
Outdata(mrc)-psiminpsimaxpsid-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

13241 (32, 24, 0)
217.879
1196.44

7.65912

Option -thetamin, -thetamax, -thetad

Case: thetamin=30, thetamax=60, thetad=10, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-thetaminthetamaxthetad-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

7.654526e+01 1.778230e+02 3.222245e+02

3.823855e+01

33.84 20.73 30.97
mrcImage image
Outdata(mrc)-thetaminthetamaxthetad-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

17440 (1, 59, 0)
150.133
1133.08

7.25353

Option -Centre

Case: Centre, Sx=55, Sy=110, Sz=110, C=1

pdb image
Outdata(pdb)-Centre-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

5.449082e+01 1.100415e+02 1.245975e+02

3.823843e+01

37.79 23.42 20.84
mrcImage image
Outdata(mrc)-Centre-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

28 (68, 20, 0)
0.166913
1.31871

0.00844185

Option -m

Case: m=1, Sx=55, Sy=110, Sz=110

pdb image
Outdata(pdb)-m1-pdbRhoFitTm.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-4.127895e+01 1.871655e+02 2.597458e+00

3.823911e+01

21.51 36.99 20.84
mrcImage image
Outdata(mrc)-m1-pdbRhoFitTm.png

Min

Max
Mean
SD

SE

0 (10, 0, 0)

15519 (32, 8, 0)
125.844
1103.92

7.06681
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