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Input formats
The following data are required: (A) structures of individual molecules (sub-units); (B) labeling position data, (C) distance restraints.
A: Structures in pdb format are accepted. Multi-frame pdbs are not accepted. For screening, all structures must have the same atom numbering.
FPS reads the positions of the labels from TABS separated tables saved in text files. The columns refer to the LP name, the molecule name, a descriptor for the labeling position (donor, D; acceptor, A; undefined, U), a specifier for the type of the labeling position (XYZ or ATOM).
| Type of attachment | Molecule name | Label type | Record type | Label position |
|---|---|---|---|---|
| Labeling position name | rna4wj_armA-H5 | D | XYZ | -8.265 -5.266 3.39 |
| Molecule name | rna4wj_armA-H5 | U | XYZ | -0.067 9.54 47.4 |
An example for a labeling position file is shown below
Example
d7DA rna4wj_armA-H5 D AV3 20 4.5 5 4.5 1.5 205
c29DA rna4wj_armA-H5 D XYZ -8.265 -5.266 3.39
c8AB rna4wj_armB-H5 A AV1 22 3.5 236
b33AB rna4wj_armB-H5 A XYZ -3.568 -8.371 6.4
b5DC rna4wj_armC-H5 D AV3 20 4.5 5 4.5 1.5 144
An XYZ record can be followed by any number of lines with ATOM data from a pdb file. In this case these atoms will be aligned with corresponding atoms of structures to be filtered.
LP NAME [tab] Molecule name [tab] D/A/U [tab] AV1 [tab] Linker length [tab] width [tab] Dye radius [tab] Attachment point (atom ID)
Example
d7DA rna4wj_armA-H5 D AV1 20 4.5 3.5 205
LP NAME [tab] Molecule name [tab] D/A/U [tab] AV3 [tab] Linker length [tab] width [tab] Dye radius 1 [tab] Dye radius 2 [tab] Dye radius 3 [tab] Attachment point (atom ID)
Example
c8DB rna4wj_armB-H5 D AV3 20 4.5 5 4.5 1.5 236
c8AB rna4wj_armB-H5 A AV3 22 4.5 11 3 1.5 236
LP NAME [tab] Molecule name [tab] U [tab] ATOM [tab] Atom number
Example
BO5 rna4wj_armB-H5 U ATOM 451
Distance data files are [tab] separated text files. The first line specifies the type of the following entries. Valid values are: Rmp (mean position distances, default); RDAMean (simple average of RDA) and RDAMeanE (FRET-averaged RDA)
Example
RDAMeanE
The following lines are distance data records of the format: Labeling position 1 [tab] Labeling position 2 [tab] Distance (Angstrom) [tab] Error(+) [tab] Error(-)
Example
b5DC a12AD 53 2.7 2.7
b8DC c8AB 59.5 3.0 3.0
AO3 DO5 2.5 0.5 20.0