pdbHelix

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pdbHelix is Eos's Command that creates helix symmetrical PDB of mrcImage file from a PDB file.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: PDB NULL
-o Optional Output: PDB NULL
-3 Optional Output: mrcImage(3D) NULL
-2 Optional Output: mrcImage(2D y-zProjection) NULL
-d Optional delta[A] 5
-p Essential deltaPhi 165
-dp Optional deltaDeltaPhi 5
-z Essential deltaz 5
-n Essential NumberOfMolecules 1
-nx Optional Pixel x 1
-ny Optional Pixel y 1
-nz Optional Pixel z 1
-Sx Optional Start x: [A] 0.0
-Sy Optional Start y: [A] 0.0
-Sz Optional Start z: [A] 0.0
-w Optional Weight 1.0
-dx Optional dx 2.5
-dy Optional dy 2.5
-dz Optional dz 2.5
-startn Optional start molecule's index 0
-startC Optional Start chain ID A
-deltaSeq Optional 1000
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　


-m details

Value Description
0


Execution example

Input file image

Input-121P-PDB.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
PDB data (a part)
...

ATOM      1  N   MET A   1      -7.176  32.630  -6.655  1.00 14.06           N  
ATOM      2  CA  MET A   1      -5.913  31.928  -6.676  1.00 17.27           C  
ATOM      3  C   MET A   1      -5.903  30.860  -5.600  1.00 16.41           C  
ATOM      4  O   MET A   1      -6.703  30.881  -4.654  1.00 16.12           O  
ATOM      5  CB  MET A   1      -4.712  32.869  -6.415  1.00 17.94           C  

...

HETATM 1547  O   HOH A 359      -4.312  38.871  -6.155  1.00 34.57           O  
HETATM 1548  O   HOH A 360       4.226  11.323  17.624  1.00 41.71           O  
HETATM 1549  O   HOH A 361      22.341  27.132  10.735  1.00 24.44           O  
HETATM 1550  O   HOH A 362      14.256  10.610  17.524  1.00 40.11           O  
HETATM 1551  O   HOH A 363      26.542  18.231  27.104  1.00 35.00           O  

...


Case: Options only essential

Case: p=165, z=5, n=10

PDB's image
Outdata-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.945663e-01 2.493555e+00 3.439075e+01

5.952335e+01

49.44 48.84 50.54
PDB data (a part)
...

ATOM      1  N   MET A   1      -7.176  32.630  -6.655  1.00 14.06   0       N  
ATOM      2  CA  MET A   1      -5.913  31.928  -6.676  1.00 17.27   0       C  
ATOM      3  C   MET A   1      -5.903  30.860  -5.600  1.00 16.41   0       C  
ATOM      4  O   MET A   1      -6.703  30.881  -4.654  1.00 16.12   0       O  
ATOM      5  CB  MET A   1      -4.712  32.869  -6.415  1.00 17.94   0       C  

...

HETATM 1547  O   HOH A 359      -4.312  38.871  -6.155  1.00 34.57   0       O  
HETATM 1548  O   HOH A 360       4.226  11.323  17.624  1.00 41.71   0       O  
HETATM 1549  O   HOH A 361      22.341  27.132  10.735  1.00 24.44   0       O  
HETATM 1550  O   HOH A 362      14.256  10.610  17.524  1.00 40.11   0       O  
HETATM 1551  O   HOH A 363      26.542  18.231  27.104  1.00 35.00   0       O  

...

ATOM      1  N   MET B   1      -1.514 -33.375  -1.655  1.00 14.06   0       N  
ATOM      2  CA  MET B   1      -2.552 -32.370  -1.676  1.00 17.27   0       C  
ATOM      3  C   MET B   1      -2.285 -31.336  -0.600  1.00 16.41   0       C  
ATOM      4  O   MET B   1      -1.518 -31.564   0.346  1.00 16.12   0       O  
ATOM      5  CB  MET B   1      -3.956 -32.969  -1.415  1.00 17.94   0       C  

...

HETATM 1547  O   HOH B 359      -5.895 -38.663  -1.155  1.00 34.57   0       O  
HETATM 1548  O   HOH B 360      -7.013  -9.843  22.624  1.00 41.71   0       O  
HETATM 1549  O   HOH B 361     -28.602 -20.425  15.735  1.00 24.44   0       O  
HETATM 1550  O   HOH B 362     -16.516  -6.559  22.524  1.00 40.11   0       O  
HETATM 1551  O   HOH B 363     -30.356 -10.740  32.104  1.00 35.00   0       O  

...

HETATM 1547  O   HOH J 359     -30.535  24.437  38.845  1.00 34.57   0       O  
HETATM 1548  O   HOH J 360      -5.018  10.995  62.624  1.00 41.71   0       O  
HETATM 1549  O   HOH J 361      -3.388  34.983  55.735  1.00 24.44   0       O  
HETATM 1550  O   HOH J 362       2.578  17.583  62.524  1.00 40.11   0       O  
HETATM 1551  O   HOH J 363       5.877  31.659  72.104  1.00 35.00   0       O  

...


mrcImage(3D)'s image

Outdata3-pdbHelix.png
xy-plane

Outdata4-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

7 (26, 47, 0)
0.144624
0.572148

0.00195444
mrcImage(2D y-zProjection)'s image
Outdata2-pdbHelix.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

63 (35, 6, 0)
9.93639
14.2042

0.403048


In the following, Setting at p=165, z=5, n=10

Option -w

Case: w=100

PDB's image
Outdata-w-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.945663e-01 2.493555e+00 3.439075e+01

5.952335e+01

49.44 48.84 50.54
mrcImage(3D)'s image

Outdata3-w-pdbHelix.png
xy-plane

Outdata4-w-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

700 (26, 47, 0)
14.4624
57.2148

0.195444


Option -dp

Case: dp=30

PDB's image
Outdata-dp-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-1.673933e+00 3.870905e+00 3.439075e+01

6.023098e+01

50.70 51.34 50.54
mrcImage(3D)'s image

Outdata3-dp-pdbHelix.png
xy-plane

Outdata4-dp-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

8 (31, 25, 4)
0.144624
0.584935

0.00199812


Option -nx, -ny, -nz

Case: nx=100, ny=100, nz=100

Case: No other settings
PDB's image
Outdata-nxnynz-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.945663e-01 2.493555e+00 3.439075e+01

5.952335e+01

49.44 48.84 50.54
mrcImage(3D)'s image

Outdata3-nxnynz-pdbHelix.png
xy-plane

Outdata4-nxnynz-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

63 (35, 6, 0)
1.4243
6.15131

0.0615131


Case: Sx=-50, Sy=-50, Sz=-10
PDB's image
Outdata-SxSySz-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.945663e-01 2.493555e+00 3.439075e+01

5.952335e+01

49.44 48.84 50.54
mrcImage(3D)'s image

Outdata3-SxSySz-pdbHelix.png
xy-plane

Outdata4-SxSySz-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

7 (30, 31, 12)
0.015491
0.189655

0.000189655


Case: dx=1, dy=1, dz=1, Sx=-50, Sy=-50, Sz=-10
PDB's image
Outdata-dxdydz-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-3.945663e-01 2.493555e+00 3.439075e+01

5.952335e+01

49.44 48.84 50.54
mrcImage(3D)'s image

Outdata3-dxdydz-pdbHelix.png
xy-plane

Outdata4-dxdydz-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

3 (70, 49, 38)
0.015491
0.125423

0.000125423


Option -startn

Case: startn=5

PDB's image
Outdata-startn-pdbHelix.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-2.306476e+00 -1.026480e+00 5.939075e+01

5.952301e+01

51.35 49.89 50.54
mrcImage(3D)'s image

Outdata3-startn-pdbHelix.png
xy-plane

Outdata4-startn-pdbHelix.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

7 (25, 24, 0)
0.140522
0.565188

0.00190309


Option -deltaSeq

Case: deltaSeq=1

PDB data (a part)
...

ATOM      1  N   MET A   1      -7.176  32.630  -6.655  1.00 14.06   0       N  
ATOM      2  CA  MET A   1      -5.913  31.928  -6.676  1.00 17.27   0       C  
ATOM      3  C   MET A   1      -5.903  30.860  -5.600  1.00 16.41   0       C  
ATOM      4  O   MET A   1      -6.703  30.881  -4.654  1.00 16.12   0       O  
ATOM      5  CB  MET A   1      -4.712  32.869  -6.415  1.00 17.94   0       C  

...

HETATM 1547  O   HOH A 359      -4.312  38.871  -6.155  1.00 34.57   0       O  
HETATM 1548  O   HOH A 360       4.226  11.323  17.624  1.00 41.71   0       O  
HETATM 1549  O   HOH A 361      22.341  27.132  10.735  1.00 24.44   0       O  
HETATM 1550  O   HOH A 362      14.256  10.610  17.524  1.00 40.11   0       O  
HETATM 1551  O   HOH A 363      26.542  18.231  27.104  1.00 35.00   0       O  


...

ATOM      1  N   MET B   2      -1.514 -33.375  -1.655  1.00 14.06   0       N  
ATOM      2  CA  MET B   2      -2.552 -32.370  -1.676  1.00 17.27   0       C  
ATOM      3  C   MET B   2      -2.285 -31.336  -0.600  1.00 16.41   0       C  
ATOM      4  O   MET B   2      -1.518 -31.564   0.346  1.00 16.12   0       O  
ATOM      5  CB  MET B   2      -3.956 -32.969  -1.415  1.00 17.94   0       C  

...

HETATM 1547  O   HOH B 360      -5.895 -38.663  -1.155  1.00 34.57   0       O  
HETATM 1548  O   HOH B 361      -7.013  -9.843  22.624  1.00 41.71   0       O  
HETATM 1549  O   HOH B 362     -28.602 -20.425  15.735  1.00 24.44   0       O  
HETATM 1550  O   HOH B 363     -16.516  -6.559  22.524  1.00 40.11   0       O  
HETATM 1551  O   HOH B 364     -30.356 -10.740  32.104  1.00 35.00   0       O  

...

HETATM 1547  O   HOH J 368     -30.535  24.437  38.845  1.00 34.57   0       O  
HETATM 1548  O   HOH J 369      -5.018  10.995  62.624  1.00 41.71   0       O  
HETATM 1549  O   HOH J 370      -3.388  34.983  55.735  1.00 24.44   0       O  
HETATM 1550  O   HOH J 371       2.578  17.583  62.524  1.00 40.11   0       O  
HETATM 1551  O   HOH J 372       5.877  31.659  72.104  1.00 35.00   0       O  

...


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