pdbRhoFit

From EosPedia
Jump to: navigation, search

pdbRhoFit is Eos's Command.


List of option

Main option

Option Essential/Optional Description Default
-ipdb Essential Input: PDB (atom model) NULL
-imrc Essential Input: mrcImage NULL
-omrc Essential Output: mrcImage NULL
-otxt Optional Output: ASCII NULL
-opar Optional Output: ASCII(Parameter) stdout
-opdb Optional Output: PDB NULL
-xmin Optional xmin 0
-xmax Optional xmax 0
-xd Optional delta x 1
-ymin Optional ymin 0
-ymax Optional ymax 0
-yd Optional delta y 1
-zmin Optional zmin 0
-zmax Optional zmax 82
-zd Optional delta z 1
-EA Optional Euler Angle's Rotation Mode ZOYS
-phimin Optional phimin: [degree] 0
-phimax Optional phimax: [degree] 194
-phid Optional delta phi: [degree] 2
-psimin Optional psimin: [degree] 0
-psimax Optional psimax: [degree] 0
-psid Optional delta psi: [degree] 2
-thetamin Optional thetamin: [degree] 0
-thetamax Optional thetamax [degree] 0
-thetad Optional delta theta: [degree] 2
-nw Optional weight for normalize 100000000.0
-nC Optional Contour Level for Normalize 0.0
-I Optional Black is High Density.
-Zminus Optional Shift to -z
-Tlim Optional The atom will be neglected 60
-Centre Optional Filament-axis is x=0, y=0
-C Optional Variable: ContourLevel 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
    -opar   : 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
    -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 Count the atom number inside the contour.
1 Add the densities of atoms.


Execution example

Input file's image

pdb image

Input(pdb)-pdbRhoFit.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)-pdbRhoFit.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

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.548556e+02 1.552094e+02 9.389075e+01

3.286630e+01

26.73 23.32 28.04
mrcImage image
Outdata(mrc)-C-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1484 (94, 15, 0)
227.582
415.63

2.66069

Option -xmin, -xmax, xd

Case: xmin=0, xmax=10, xd=1, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

2.041704e+01 1.983455e+01 9.389075e+01

3.286621e+01

25.81 23.64 28.04
mrcImage image
Outdata(mrc)-xminxmaxxd-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (1, 0, 1)

1547 (1, 43, 0)
231.931
425.602

2.72453

Option -ymin, -ymax, -yd

Case: ymin=10, ymax=20, yd=2, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.475229e+02 2.818824e+01 9.389075e+01

3.286666e+01

23.76 25.30 28.04
mrcImage image
Outdata(mrc)-yminymaxyd-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (1, 0, 1)

1550 (44, 24, 0)
340.096
555.774

3.55783

Option -zmin, -zmax, -zd

Case: zmin=20, zmax=70, zd=2, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.548556e+02 1.552094e+02 8.189075e+01

3.286630e+01

26.73 23.32 28.04
mrcImage image
Outdata(mrc)-zminzmaxzd-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (1, 0, 1)

1484 (94, 0, 0)
231.435
423.41

4.84285

Option -EA

Case: EA=YOYS, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 2.519590e+01 9.389075e+01

3.286664e+01

24.77 23.85 28.04
mrcImage image
Outdata(mrc)-EA-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1188 (0, 48, 0)
41.5284
155.065

0.992658

Option -phimin, -phimax, -phid

Case: phimin=0, phimax=360, phid=3, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.727132e+01 1.572633e+02 9.389075e+01

3.286635e+01

23.50 26.28 28.04
mrcImage image
Outdata(mrc)-phiminphimaxphid-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1465 (62, 15, 0)
210
387.626

2.23316

Option -psimin, -psimax, psid

Case: psimin=30, psimax=60, psid=1, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.009141e+01 1.475229e+02 6.392447e+01

3.286696e+01

26.05 23.76 29.27
mrcImage image
Outdata(mrc)-psiminpsimaxpsid-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (66, 0, 0)

1550 (54, 41, 0)
269.644
502.548

3.2171

Option -thetamin, -thetamax, -thetad

Case: thetamin=90, thetamax=180, thetad=30, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.475229e+02 1.581092e+02 9.018824e+01

3.286666e+01

23.76 28.04 25.30
mrcImage image
Outdata(mrc)-thetaminthetamaxthetad-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (96, 36, 0)

1412 (6, 11, 0)
285.358
511.536

3.27464

Option -Centre

Case: Centre, C=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

8.522220e+01 5.908815e+01 1.488908e+02

3.286674e+01

27.86 22.87 28.04
mrcImage image
Outdata(mrc)-Centre-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (1, 0, 1)

1550 (0, 0, 0)
457.617
677.76

4.33874

Option -m

Case: m=1

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

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.471341e+02 1.621267e+02 9.389075e+01

3.286673e+01

27.86 22.87 28.04
mrcImage image
Outdata(mrc)-m1-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

0 (0, 0, 0)
0
0

0

Case: m=1, nC=2

pdb image
Outdata(pdb)-m1nC-pdbRhoFit.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
Outdata(mrc)-m1nC-pdbRhoFit.png

Min

Max
Mean
SD

SE

-0 (14, 0, 0)

194626 (0, 0, 0)
566.611
4738.59

30.3344

Case: m=1, nC=2, nw=1000

pdb image
Outdata(pdb)-m1nw-pdbRhoFit.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
Outdata(mrc)-m1nw-pdbRhoFit.png

Min

Max
Mean
SD

SE

-0 (14, 0, 0)

1.94626 (0, 0, 0)
0.00566611
0.0473859

0.000303344

Option -I

Case: I, m=1

pdb image
Outdata(pdb)-I-pdbRhoFit.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
Outdata(mrc)-I-pdbRhoFit.png

Min

Max
Mean
SD

SE

0 (14, 0, 0)

20.01 (0, 0, 0)
0.0582547
0.487186

0.00311876
Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=pdbRhoFit&oldid=3173"