This folder contains the inputs needed for different stages of modeling. Some input files are shared across multiple stages of modeling.
These inputs are used to run the executables for sampling (executable: spb), rescoring with EM restraint (executable: spb_analysis), clustering (executable: spb_cluster), and density calculation (executable: spb_density and spb_density_perbead).
- 3OA7_A.pdb, 3OA7_B.pdb: PDB structure of Cnm67-C terminus.
- 4DS7_*_swapped.pdb: homology models of Spc110-Cmd1 dimer without the domain swap.
- CC_78_A.pdb, CC_78_B.pdb: coiled-coil domain of Spc42.
- CC_120_A.pdb,CC_120_B.pdb: coiled-coil domain of Spc110.
- fret_2014.dat: reshot FRET data between SPB protein termini.
- fret_new_exp.dat : internal FRET between Spc110-coiled coil and other SPB proteins.
The extra input for this step is the EM map (SPB_2d_padded.tiff) since we rescore with EM2D restraint in this step.
The extra input for this step is label.dat the file containing the bead labels on which clustering is performed.
We use the raw FRET data (rawdata_all_date.csv) to get the experimental FRET distributions and compare them to the model FRET distributions.
fret_exp.dat contains the experimental averages and standard deviations (data is identical to the FRET files used in sampling, with a minor change in format).