.. _swamp_mr_commandline: Performing molecular replacement with SWAMP ------------------------------------------- In this tutorial you will use SWAMP to perform molecular replacement on a bacteriorhodopsin structure `1UCQ `_. The required files for this have been provided `here `_. 1. Obtain predictions about your target structure ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Before running SWAMP, it is necessary to first obtain `transmembrane topology `_ and `residue contact `_ predictions for your structure of interest. For the purpose of this example, the data has been already provided as ``1ucq.topcons`` and ``1ucq.psicov`` respectively. It is important to note that SWAMP will assume the provided contact prediction file is in ``psicov`` format, which is the default format of the server provided at the link. However, if you decide to use a different contact prediction tool, you can use `ConKit `_ to convert across file formats. 2. Running swamp-mr ^^^^^^^^^^^^^^^^^^^ Once all the required input files are gathered, SWAMP-MR can be executed on the terminal as follows: .. code-block:: shell swamp-mr 1ucq.mtz 1ucq.fasta 1ucq.psicov 1ucq.topcons Additional options are available, check them out :ref:`here `. After running the above command, SWAMP will create the directory ``SWAMP_0``. Within this directory, all the metadata that SWAMP uses to solve the structure of interest is stored. First, SWAMP will run a CMO scan of the target predicted contacts against the library of helical pairs. Metadata obtained with this scan can be found at ``SWAMP_0/swamp_scan``. After identifying the valid search models, SWAMP will a try to solve the structure with a subroutine consisting of ``phaser`` for molecular replacement, ``refmac5`` for refinement and ``shelxe`` for model building and density modification. Results for this subroutine are found at ``SWAMP_0/swamp_mr``. Additionally, a full swamp-mr run can result quite time consuming, so if you wish to check out the results swamp has obtained at any given point you can use :ref:`swamp-results `. 2. Table of results ^^^^^^^^^^^^^^^^^^^ Once SWAMP has finished execution of all MR jobs, a table summarising the obtained results will be printed: +-------------+-------------+---------+-----+-------------+-------------+------------+------------+-------------+-------------+---------+----------+-------------+----------+ | SEARCH_ID | RUN_ID | LLG | TFZ | PHSR_CC_LOC | PHSR_CC_ALL | RFMC_RFREE | RFMC_RFACT | RFMC_CC_LOC | RFMC_CC_ALL | SHXE_CC | SHXE_ACL | IS_EXTENDED | SOLUTION | +=============+=============+=========+=====+=============+=============+============+============+=============+=============+=========+==========+=============+==========+ | 951 | 1 | 82.286 | 6.0 | 0.529 | 0.21 | 0.6018 | 0.5927 | 0.608 | 0.248 | 35.33 | 25.0 | YES | YES | +-------------+-------------+---------+-----+-------------+-------------+------------+------------+-------------+-------------+---------+----------+-------------+----------+ | 277 | 1 | 41.006 | 8.5 | 0.619 | 0.41 | 0.5745 | 0.5355 | 0.65 | 0.434 | 32.63 | 21.0 | YES | YES | +-------------+-------------+---------+-----+-------------+-------------+------------+------------+-------------+-------------+---------+----------+-------------+----------+ | 169 | 1 | 71.073 | 5.0 | 0.125 | 0.02 | 0.6215 | 0.5897 | 0.112 | 0.026 | 23.08 | 9.0 | YES | NO | +-------------+-------------+---------+-----+-------------+-------------+------------+------------+-------------+-------------+---------+----------+-------------+----------+ | 1008 | 1 | 90.720 | 6.4 | 0.218 | 0.12 | 0.5793 | 0.5922 | 0.22 | 0.125 | 23.03 | 21.0 | NO | NO | +-------------+-------------+---------+-----+-------------+-------------+------------+------------+-------------+-------------+---------+----------+-------------+----------+ This table and the information it contains can be interpreted in the same way as the output generated by ``swamp-results``, if you wish to read about it click :ref:`here `.