pdbCrystalCreate

pdbCrystalCreate is Eos's Command that creates the crystal structure by PDB file.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-I	Essential	Input: ASCII(Crystal Information)	NULL
-o	Essential	Output: PDB	NULL
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0

-I format

aAxis       %15.6g %15.6g %15.6g
bAxis       %15.6g %15.6g %15.6g
cAxis       %15.6g %15.6g %15.6g
CellLength  %15.6g %15.6g %15.6g
Origin      %15.6g %15.6g %15.6g
N           %15d %15d %15d
StartN      %15d %15d %15d
SpaceGroup  %15d
HelixInfo   %10d %10d %10d

Parameter Order is important

Dependent between CellLength and a|b|cAxis.
Because each of aAxis, bAxis, cAxis must be a unit vector.
SpaceGroup: 0: P1Symmmetry(, 1: HelicalSymmmetry(Not implemented)

HelixInfo: turn unit n-strand

Execution example

Input file image

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

Option -I

Case: input data1

execute with the following.

aAxis         1 0 0
bAxis         1 0 0
cAxis         1 0 0
CellLength 1 1 1
N               2 2 2
StartN       1 1 1

Output

aAxis                     1               0               0
bAxis                     1               0               0
cAxis                     1               0               0
CellLength                1               1               1
Origin                    0               0               0
N                         2               2               2
StartN                    1               1               1
SpaceGroup                0
Program Start
1 1 1
3 0 0
pdbFileGoToEndPDB: 14
1 1 2
4 0 0
pdbFileGoToEndPDB: 14
1 2 1
4 0 0
pdbFileGoToEndPDB: 14

...

2 1 2
5 0 0
pdbFileGoToEndPDB: 14
2 2 1
5 0 0
pdbFileGoToEndPDB: 14
2 2 2
6 0 0
pdbFileGoToEndPDB: 14

Output file's image

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

1.055301e+01 2.519590e+01 1.189075e+01 3.401123e+01 26.27 23.85 28.04

Case: input data2

execute with the following.

aAxis         1 0 0
bAxis         1 0 0
cAxis         1 0 0
CellLength 1 1 1
Origin        5 5 5
N               2 2 2
StartN       1 1 1

Output file's image

White is Output file by input data1.

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

1.555301e+01 3.019590e+01 1.689075e+01 3.401123e+01 26.27 23.85 28.04

Case: input data3

execute with the following.

aAxis         1 0 0
bAxis         1 0 0
cAxis         0 5 0
CellLength 1 1 1
N               2 2 2
StartN       1 1 1

Output file's image

White is Output file by input data1.

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

9.053012e+00 2.669590e+01 1.189075e+01 3.386472e+01 25.77 24.35 28.04

Case: input data4

execute with the following.

aAxis           1   0   0
bAxis           1   0   0
cAxis           1   0   0
CellLength 10 10 10
N                 2   2   2
StartN         1   1   1

Output file's image

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

5.105301e+01 2.519590e+01 1.189075e+01 4.525700e+01 39.77 23.85 28.04