Organize data
=============

#. Create a new directory for your project

    .. note:: 
        Note that for Assembline your files can be located in arbitrary locations on your disk
        but it is more convenient to have them in a single directory
        and use relative paths in the JSON configuration file.

#. Collect sequences of your subunits

    Prepare a single FASTA-formatted file with all sequences of your subunits. A
    subunit is a protein of your complex.

    For example:

    ::

        >subunit1
        MVEHDKSGSKRQELRSNMRNLITLNKGKFKPTASTAEGDEDDLSFTLLDSVFDTLSDSI
        ISWRGDCDYFAVSSVEEVPDEDDETKSIKRRAFRVFSREGQLDSASEPVTGMEHQLSWK
        EMKKGKHPSIVCEFPKSEFTSEVDSLRQVAFINDSIVGVLLDTDNLSRIALLDIQDITQ
        RYKEAFIVCRTHRINLDILHDYAPELFIENLEVFINQIGRVDYLNLFISCLSEDDVTKT
        HGLALYRYDSEKQNVIYNIYAKHLSSNQMYTDAAVAYEMLGKLKEAMGAYQSAKRWREA
        RLIERLNQTKPDAVRVVEGLCRR
        >subunit2
        MVECITPEAIFIGANKQTQVSDIHKVKKIVAFGAGKTIALWDPIEPNNKGVYATLKGHE
        LLSNKQYKFQIDDELRVGINFEALIMGHDDWISSLQWHESRLQLLAATADTSLMVWEPD
        GEDDANEDDEEEEGGNKETPDITDPLSLLECPPMEDQLQRHLLWPEVEKLYGHGFEITC
        RLRWSHLKRNGKLFLGVGSSDLSTRIYSLAYE

#. Collect structures of your subunits

    Create a directory with structures of your subunits in PDB format.

    The subunit chains can be organized in the PDB files in any way:
    a PDB file can contain multiple subunits, extra proteins not used in modeling,
    domains of a subunit can be separate or together. The JSON configuration
    file will take care of reading only what is needed.

    .. warning:: 
        Make sure that the protein sequence and residue numbering in 
        the PDB files correspond to the sequences in the FASTA file.

#. [OPTIONALLY] To simplify definition of rigid
   bodies later: Prepare your PDB file such that each PDB file
   corresponds to an anticipated rigid body (i.e. there is 1-to-1 mapping between the
   PDB files and your anticipated rigid bodies).

   Read more about rigid bodies and alternative ways of preparing them here: :doc:`rigid_bodies`

#. Collect EM maps and put them into a subdirectory if you want to use EM
   restraints (read more :doc:`em_restraints`)

#. Collect CSV files with crosslinks in xQuest or `XlinkAnalyzer <https://www.embl-hamburg.de/XlinkAnalyzer/XlinkAnalyzer.html>`_ format,
   if you want to use crosslink restraints (read more :doc:`crosslink_restraints`)

#. You may have the following directory structure at this point:

    .. code-block:: bash

         complexX/
             X_sequences.fasta
             in_pdbs/
                 pdb1.pdb
                 pdb2.pdb
                 ...
             xlinks/
                 some_name.csv
                 ...
             EM/
                 map1.mrc
                 map2.mrc
                 ...