pdbTwoProteinFit

pdbTwoProteinFit is Eos's Command for fitting position between two proteins.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-ires	Optional	Input: ASCII(ResidueInformation)	NULL
-isel	Optional	Output: Selected residue of in after fitting	NULL
-r	Essential	Reference: PDB	NULL
-rres	Optional	Reference: ASCII(ResidueInformation)	NULL
-rsel	Optional	Output: Selected residue of in after fitting	NULL
-o	Essential	Output: PDB	NULL
-oMatrix	Optional	Output: Matrix: ASCII	stdout
-oParam	Optional	Output: Param: ASCII	stdout
-oDis	Optional	Output: PDB Distance as Temp: PDB	stdout
-oDis2	Optional	Output: Distance List for Ca: ASCII	stdout
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0

Input fileとReference file format

ResidueNumberToBeFitted
...
If |, all residules are sellected till the residue in the next line

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

Reference 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 -ires, -rres

-ires, -rrse: use the following data

-ires 's data

1
2
3
4
5
6

-rres 's data

1
2
3
4
5
6

-o 's data(White: Input file)

same angle to Reference file

another angle

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

5.097651e-01 1.932045e+01 1.188975e+01 3.286711e+01 23.93 24.14 28.04

-oMatrix 's data

       0.058145       -0.998308        0.000001 
      -0.998308       -0.058145       -0.000001 
       0.000001       -0.000001       -1.000000 
      25.311117       26.828215       -0.000868 

-oParam 's data

RMSBefore: 26.607964
RMSSelectedBefore: 9.794701
RMSSelectedAfter: 1.277625
RMSAfter: 17.793636

-oDis 's data

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

-oDis2 's data

00001        1.447996
00002        1.329491
00003        0.065775
00004        0.242391
00005        1.683475
00006        1.741168
00007        1.578526
00008        6.625490
00009        3.641384

...

00157       12.396196
00158        8.092867
00159        3.598508
00160        3.239969
00161        1.259487
00162        4.196125
00163        7.037861
00164        6.740162
00165       11.073485
00166       16.325453