About fit libraries

Fit libraries are lists of possible positions of your input structures in the EM map (non-redundant rigid body fits). The positions are used in the global optimization step of Assembline to generate a large number of combinations of the pre-calculated fits through a Monte Carlo integrative modelling procedure. Each position (fit) has its associated score and p-value, which are used as FitRestraints during the modelling (see figure below).

Efitter pipeline for fit libraries

Note

Read more in the Assembline manual about fit libriaries section.

The fit libraries are typically generated by fitting every input structure into the EM map separately, a procedure handled by the Efitter pipeline of Assembline.

Note

This part of the Assembline pipeline (efitter) will generate all requested libraries per input structure in a single run (automated) according to user’s predefined parameters.

For this tutorial, the fit libraries are already provided in the systematic_fits/ directory in the folders CR_Y_complex/ & NR_Y_complex/ (for the rest of the modelled subcomplexes and Nup116 k.o. models the global optimization from Assembline was not used) from our git repository.

The systematic_fits/ directory is organized as the following in terms of input data:

systematic_fits/

    # Electron microscopy maps
    em_maps/

    #input structures for modelling
    PDB/

Follow the next steps if you want to generate them yourself using the Efitter pipeline (which is a wrapper around UCSF Chimera FitMapTool).

To skip and jump to setting up the integrative modelling sections, move to Setting up the JSON project file