pdbShapeFit

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pdbShapeFit 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(3D) NULL
-C Essential Contour 0.0
-CM Optional ContourMode: refer to mrcImageContourSurfaceCreate 0
-omrc Optional Output: mrcImage NULL
-otxt Optional Output: ASCII stdout
-opdb Optional Output: PDB NULL
-xmin Optional x min 0
-xmax Optional x max 0
-xd Optional delta x 1
-ymin Optional y min 0
-ymax Optional y max 0
-yd Optional delta y 1
-zmin Optional z min 0
-zmax Optional z max 82
-zd Optional delta z 1
-EA Optional Euler Angle: Rotation Mode ZOYS
-phimin Optional phi min: [degree] 0
-phimax Optional phi max: [degree] 194
-phid Optional delta phi: [degree] 2
-psimin Optional psi min: [degree] 0
-psimax Optional psi max: [degree] 0
-psid Optional delta psi: [degree] 2
-thetamin Optional theta min: [degree] 0
-thetamax Optional theta max: [degree] 0
-thetad Optional delta theta: [degree] 2
-PSM Optional PDB SurfaceMode: refer to pdbSurface 0
-order Optional order: refer to pdbSurface 1.7
-refine Optional refine: refer to pdbSurface 2
-size Optional size: refer to pdbSurface 3
-weight Optional weight: refer to pdbSurface 100
-mergin Optional mergin: refer to pdbSurface 3.0
-thres Optional threshold: refer to pdbSurface 0.0
-I Optional Black is High Density.
-Centre Optional Filament-axis is x=0, y=0
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　 


    -ipdb   : Filename : An atomic model to be fitted (PDB) 
    -imrc   : Filename : 3-D density map (mrc-formated) 
    -omrc   : Filename : fitting score map (MRC) 
                         z=0: a max-score map of an phi-z plane which includes a max score point.
                              The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
                         z=1: a max-score map of an psi-theta plane which includes a max score point.
                              The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
                         z=2: a score map of an x-y plane which includes a max score point.
    -otxt   : Filename : fitting results (Text)
    -opdb   : Filename : An atomic model with a maximum score after fitting 
    -x|y|zmin   : Initial value of z (should <= zmax)
    -x|y|zmax   : Final   value of z
    -x|y|zd     : Delta z for fitting (should !=0)
    -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
    -phi|psi|thetamax : Final value of phi  (should !=0)
    -phi|psi|thetad   : Delta phi for fitting (should >0)
    -C      : Contour level of map file
    -Inverse: Protein has high density on the image
    -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
    -EA     : Euler Angle Set : ZOYS: z -> y -> x


-CM, -PSM details

cf. pdbSurface(-m)


-m details

Value Description
0 Count the atom number inside the contour.


Execution example

Input file's image

-ipdbのfile's image
Input-121P-PDB1.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 9.408175e+00 2.622422e+01

3.286665e+01

24.77 22.88 23.78


-imrcのfile's image

Input-121P.png
xy-plane

Input1-121P.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

3500.79 (49, 53, 30)
11.0585
118.123

0.118123


Case: Options only essential

Case: C=1000

-omrc 's image
Outdata1-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

17460.5 (57, 81, 0)
1189.56
2672.72

29.6348


-opdb 's image

Outdata-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.037972e+02 2.611602e+01 1.072242e+02

3.286633e+01

20.84 31.41 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     104.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     108.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     120.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3
 START       4.00     4

...

 START      71.00    71
 START      72.00    72
 START      73.00    73
   MAX     106.00      73.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      74.00    74
 START      75.00    75
 START      76.00    76
   MAX     106.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      77.00    77
   MAX     110.00      77.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      78.00    78
   MAX     110.00      78.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      79.00    79
   MAX     112.00      79.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      80.00    80
 START      81.00    81
   MAX     114.00      81.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      82.00    82


In the following, Setting at C=1000

Option -xmin, -xmax, -xd

Case: xmin=-45, xmax=-40, xd=1

-omrc 's image

Outdata-x-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1871.6 (19, 82, 0)
18.8875
125.884

0.805859


-opdb 's image

Outdata1-x-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-2.053717e+00 -8.841410e+00 1.082242e+02

3.286615e+01

32.81 21.54 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX      24.00       0.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      52.00       0.00       0.00       0.00     -41.00       0.00 (phi,z,psi,theta,x,y)
   MAX      52.00       0.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3
 START       4.00     4
 START       5.00     5

...

 START      66.00    66
 START      67.00    67
   MAX      40.00      67.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      52.00      67.00       0.00       0.00     -45.00       0.00 (phi,z,psi,theta,x,y)
 START      68.00    68
   MAX      50.00      68.00       0.00       0.00     -44.00       0.00 (phi,z,psi,theta,x,y)
 START      69.00    69
   MAX      42.00      69.00       0.00       0.00     -41.00       0.00 (phi,z,psi,theta,x,y)
 START      70.00    70
 START      71.00    71
 START      72.00    72
 START      73.00    73
   MAX      26.00      73.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      28.00      73.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      44.00      73.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
 START      74.00    74
   MAX      38.00      74.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      42.00      74.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      44.00      74.00       0.00       0.00     -41.00       0.00 (phi,z,psi,theta,x,y)
   MAX      50.00      74.00       0.00       0.00     -44.00       0.00 (phi,z,psi,theta,x,y)
 START      75.00    75
   MAX      36.00      75.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      38.00      75.00       0.00       0.00     -41.00       0.00 (phi,z,psi,theta,x,y)
 START      76.00    76
   MAX      36.00      76.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
   MAX      38.00      76.00       0.00       0.00     -41.00       0.00 (phi,z,psi,theta,x,y)
   MAX      62.00      76.00       0.00       0.00     -44.00       0.00 (phi,z,psi,theta,x,y)
 START      77.00    77
 START      78.00    78
   MAX      26.00      78.00       0.00       0.00     -40.00       0.00 (phi,z,psi,theta,x,y)
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82
   MAX      38.00      82.00       0.00       0.00     -42.00       0.00 (phi,z,psi,theta,x,y)


Option -ymin, -ymax, yd

Case: ymin=10, ymax=20, -yd=2

-omrc 's image

Outdata-y-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (25, 0, 0)

19993 (0, 82, 0)
585.102
1957.56

12.5315


-opdb 's image

Outdata1-y-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 2.740817e+01 1.082242e+02

3.286665e+01

24.77 22.88 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00      10.00 (phi,z,psi,theta,x,y)
   MAX       0.00       0.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
   MAX       2.00       0.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
   MAX       4.00       0.00       0.00       0.00       0.00      16.00 (phi,z,psi,theta,x,y)
   MAX       6.00       0.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3

...

 START      67.00    67
 START      68.00    68
 START      69.00    69
 START      70.00    70
 START      71.00    71
   MAX       4.00      71.00       0.00       0.00       0.00      16.00 (phi,z,psi,theta,x,y)
 START      72.00    72
   MAX       0.00      72.00       0.00       0.00       0.00      10.00 (phi,z,psi,theta,x,y)
   MAX       0.00      72.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
 START      73.00    73
   MAX       0.00      73.00       0.00       0.00       0.00      10.00 (phi,z,psi,theta,x,y)
   MAX       0.00      73.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
   MAX       2.00      73.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      74.00    74
   MAX       0.00      74.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
 START      75.00    75
   MAX       0.00      75.00       0.00       0.00       0.00      16.00 (phi,z,psi,theta,x,y)
   MAX       2.00      75.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      76.00    76
   MAX       2.00      76.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      77.00    77
   MAX       0.00      77.00       0.00       0.00       0.00      10.00 (phi,z,psi,theta,x,y)
   MAX       0.00      77.00       0.00       0.00       0.00      12.00 (phi,z,psi,theta,x,y)
   MAX       2.00      77.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      78.00    78
 START      79.00    79
   MAX       0.00      79.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      80.00    80
   MAX       0.00      80.00       0.00       0.00       0.00      16.00 (phi,z,psi,theta,x,y)
   MAX       2.00      80.00       0.00       0.00       0.00      14.00 (phi,z,psi,theta,x,y)
 START      81.00    81
   MAX       0.00      81.00       0.00       0.00       0.00      16.00 (phi,z,psi,theta,x,y)
 START      82.00    82
   MAX       0.00      82.00       0.00       0.00       0.00      18.00 (phi,z,psi,theta,x,y)


Option -zmin, -zmax, -zd

Case: zmin=-50, zmax=0, zd=10

-omrc 's image
Outdata-z-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (2, 0, 0)

16454.1 (57, 3, 0)
2533.37
3898.09

160.755


-opdb 's image

Outdata1-z-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.037972e+02 2.611602e+01 6.224217e+00

3.286633e+01

20.84 31.41 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START     -50.00     0
   MAX       0.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      98.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     100.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     102.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     104.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     106.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     108.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -40.00     1
   MAX       0.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      98.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     100.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -30.00     2
   MAX       0.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      98.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     100.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     102.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     106.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -20.00     3
   MAX       2.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     104.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     106.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     108.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -10.00     4
 START       0.00     5


Case: xmin=-45, xmax=-40, xd=1, ymin=10, ymax=20, -yd=2, zmin=-50, zmax=0, zd=10

-omrc 's image

Outdata-xyz-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (0, 0, 0)

11998.3 (22, 2, 0)
888.403
2512.16

59.8134


-opdb 's image

Outdata1-xyz-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.096946e+00 1.047954e+01 6.224217e+00

3.286679e+01

32.81 21.48 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START     -40.00     0
   MAX      10.00     -40.00       0.00       0.00     -42.00      18.00 (phi,z,psi,theta,x,y)
   MAX      12.00     -40.00       0.00       0.00     -41.00      18.00 (phi,z,psi,theta,x,y)
   MAX      12.00     -40.00       0.00       0.00     -40.00      20.00 (phi,z,psi,theta,x,y)
   MAX      14.00     -40.00       0.00       0.00     -40.00      18.00 (phi,z,psi,theta,x,y)
   MAX      14.00     -40.00       0.00       0.00     -40.00      20.00 (phi,z,psi,theta,x,y)

...

   MAX      36.00     -20.00       0.00       0.00     -40.00      20.00 (phi,z,psi,theta,x,y)
   MAX      38.00     -20.00       0.00       0.00     -42.00      18.00 (phi,z,psi,theta,x,y)
   MAX      38.00     -20.00       0.00       0.00     -41.00      20.00 (phi,z,psi,theta,x,y)
   MAX      38.00     -20.00       0.00       0.00     -40.00      20.00 (phi,z,psi,theta,x,y)
   MAX      44.00     -20.00       0.00       0.00     -40.00      20.00 (phi,z,psi,theta,x,y)
 START     -10.00     3
 START       0.00     4


Option -EA

Case: EA=ZOYR

-omrc 's image

Outdata-EA-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (33, 0, 0)

19653 (48, 52, 0)
3049.75
4177.12

46.3153


-opdb 's image

Outdata1-EA-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 2.761016e+01 9.386633e+00

3.286632e+01

24.77 24.25 24.51


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX       2.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2

...

 START      49.00    49
 START      50.00    50
   MAX      90.00      50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      51.00    51
 START      52.00    52
   MAX      96.00      52.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      53.00    53
 START      54.00    54
 START      55.00    55

...

 START      78.00    78
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82


Option -phimin, -phimax, -phid

Case: phimin=110, phimax=120, phid=0.5, zmin=-50, zmax=0, zd=10

-omrc 's image
Outdata-phi-pdbShapeFit.png

Min

Max
Mean
SD

SE

1612.66 (18, 0, 0)

17187.2 (10, 3, 0)
9376.62
4795.62

427.228


-opdb 's image

Outdata1-phi-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.041970e+02 2.706718e+01 6.224217e+00

3.286664e+01

20.85 31.57 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START     -50.00     0
   MAX     110.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -40.00     1
   MAX     110.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     115.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     115.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -30.00     2
   MAX     110.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.50     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -20.00     3
   MAX     110.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.50     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     115.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -10.00     4
 START       0.00     5


Option -psimin, -psimax, -psid

Case: psimin=0, psimax=30, psid=1, phimin=110, phimax=120, phid=0.5, zmin=-50, zmax=0, zd=10

-omrc 's image

Outdata-psi-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (21, 0, 0)

19827.3 (2, 5, 0)
3478.04
6409.94

271.354


-opdb 's image

Outdata1-psi-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.070398e+02 2.330635e+01 1.362995e+01

3.286660e+01

23.58 30.86 25.25


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START     -50.00     0
   MAX     110.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -50.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -40.00     1
   MAX     110.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -40.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -40.00       2.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -40.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     115.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -30.00     2
   MAX     110.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -30.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.50     -30.00       2.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.50     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -20.00     3
   MAX     110.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -20.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -20.00       2.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.00     -20.00       1.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -20.00       3.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -10.00     4
   MAX     110.00     -10.00       5.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -10.00       7.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -10.00       8.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -10.00       9.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -10.00      10.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       0.00     5
   MAX     111.00       0.00      13.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)


Option -thetamin, -thetamax, -thetad

Case: thetamin=0, thetamax=30, thetad=1, phimin=110, phimax=120, phid=0.5, zmin=-50, zmax=0, zd=10

-omrc 's image

Outdata-theta-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (21, 0, 0)

19973 (20, 4, 0)
2716.39
5643.66

238.915


-opdb 's image

Outdata1-theta-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.059440e+02 2.368945e+01 8.182193e+00

3.286613e+01

21.25 30.38 24.79


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START     -50.00     0
   MAX     110.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -50.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.50     -50.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.00     -50.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -50.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -50.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -40.00     1
   MAX     110.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -40.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -40.00       0.00       4.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.00     -40.00       0.00       2.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -40.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     112.50     -40.00       0.00       3.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     113.00     -40.00       0.00       3.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -40.00       0.00       4.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     115.50     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00     -40.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.50     -40.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -30.00     2
   MAX     110.00     -30.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -30.00       0.00       1.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -30.00       0.00       2.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.00     -30.00       0.00       7.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -20.00     3
   MAX     110.00     -20.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -20.00       0.00       3.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00     -20.00       0.00       4.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     111.00     -20.00       0.00       6.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START     -10.00     4
   MAX     113.50     -10.00       0.00       3.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     114.00     -10.00       0.00       3.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00     -10.00       0.00      11.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.50     -10.00       0.00       9.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     117.50     -10.00       0.00      18.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     118.00     -10.00       0.00      18.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     118.50     -10.00       0.00      19.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     119.00     -10.00       0.00      11.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     119.00     -10.00       0.00      21.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     120.00     -10.00       0.00      21.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       0.00     5


Option -order

Case: order=5

-omrc 's image
Outdata-order-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

4935.67 (0, 78, 0)
328.982
719.83

7.98138


-opdb 's image

Outdata1-order-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 9.408175e+00 1.042242e+02

3.286665e+01

24.77 22.88 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3

...

 START      75.00    75
   MAX       0.00      75.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      76.00    76
   MAX       0.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      77.00    77
   MAX       0.00      77.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      78.00    78
   MAX       0.00      78.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82


Option -refine

Case: refine=6

-omrc 's image
Outdata-refine-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

2694.47 (53, 74, 0)
228.952
462.304

5.12596


-opdb 's image

Outdata1-refine-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.000143e+02 1.878688e+01 1.002242e+02

3.286725e+01

21.61 29.76 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3

...

 START      72.00    72
 START      73.00    73
 START      74.00    74
   MAX     106.00      74.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      75.00    75
 START      76.00    76
 START      77.00    77
 START      78.00    78
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82



Option -size

Case: size=6

-omrc 's image
Outdata-size-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

19706.7 (57, 81, 0)
1310
2977.78

33.0172


-opdb 's image

Outdata1-size-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.037972e+02 2.611602e+01 1.072242e+02

3.286633e+01

20.84 31.41 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     102.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     104.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     108.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     120.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
 START       3.00     3

...

 START      73.00    73
   MAX     106.00      73.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      74.00    74
 START      75.00    75
   MAX     110.00      75.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      76.00    76
   MAX     106.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      77.00    77
   MAX     110.00      77.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      78.00    78
   MAX     110.00      78.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      79.00    79
   MAX     112.00      79.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      80.00    80
 START      81.00    81
   MAX     114.00      81.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      82.00    82


Option -mergin

Case: mergin=1

-omrc 's image

Outdata-mergin-pdbShapeFit.png
z=1

Min

Max
Mean
SD

SE

0 (18, 0, 0)

9266.14 (55, 81, 0)
510.565
1333.56

14.7863


-opdb 's image

Outdata1-mergin-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.020337e+02 2.238539e+01 1.072242e+02

3.286628e+01

21.27 30.66 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      88.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      90.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     100.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     102.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     104.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     108.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     116.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
   MAX     116.00       1.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       2.00     2
 START       3.00     3

...

 START      75.00    75
   MAX     110.00      75.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      76.00    76
   MAX     112.00      76.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      77.00    77
   MAX     108.00      77.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      78.00    78
   MAX     108.00      78.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      79.00    79
 START      80.00    80
 START      81.00    81
   MAX     110.00      81.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      82.00    82


Option -ther

Case: ther=4

-omrc 's image
Outdata-ther-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (18, 0, 0)

377.267 (48, 70, 0)
19.106
43.4095

0.481319


-opdb 's image

Outdata1-ther-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

9.391364e+01 1.048177e+01 9.622422e+01

3.286686e+01

22.45 26.89 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX       0.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX       6.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX       8.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      10.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      80.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      82.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX      86.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
 START       2.00     2
   MAX      86.00       2.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       3.00     3
 START       4.00     4
 START       5.00     5

...

 START      70.00    70
   MAX      96.00      70.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START      71.00    71
 START      72.00    72
 START      73.00    73
 START      74.00    74
 START      75.00    75
 START      76.00    76
 START      77.00    77
 START      78.00    78
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82


Option -Centre

-omrc 's image
Outdata-Centre-pdbShapeFit.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1100 (61, 1, 0)
16.2356
74.3868

0.82479


-opdb 's image

Outdata1-Centre-pdbShapeFit.png
White:Input Blue:Output

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

3.831380e+01 4.964767e+01 2.722422e+01

3.286710e+01

21.36 32.45 23.78


-otxt 's data
REMARK Create Contour Surface of mrcImage
REMARK Create Surface of pdbFile 
 START       0.00     0
   MAX      94.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     102.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     110.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     118.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     120.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
   MAX     122.00       0.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       1.00     1
   MAX     122.00       1.00       0.00       0.00       0.00       0.00 (phi,z,psi,theta,x,y)
 START       2.00     2
 START       3.00     3
 START       4.00     4

...

 START      78.00    78
 START      79.00    79
 START      80.00    80
 START      81.00    81
 START      82.00    82


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