.. _example_ccp4i2_dist_homologs:

=======================
Using multiple homologs
=======================
AMPLE can attempt molecular replacement with a number of homologous crystal structures to the target. This is something you might attempt when none of the individual structures proves sufficient alone to solve the target. AMPLE will find the structurally shared core between the homologs and use that superposition as a starting point for its clustering and truncation approach.

Running AMPLE
=============

AMPLE can be found in the CCP4i2 menu under the Molecular replacement tab (shown below)

.. figure:: ../images/ccp4i2_menu.png
   :align: center

This will take you to the submission page for AMPLE.

Submission options
------------------

On the submission page there are a number of input options:

.. figure:: ../images/ccp4i2_ample_submit.png
   :align: center

1. Input sequence – Path to the FASTA file
2. Input MTZ - Path to the MTZ file
3. Protein classification - Globular or Transmembrane
4. Model selection or building - select between a directory of existing models, a library of ideal helices or create *ab initio* models locally (shown below).

.. note::
    A Coiled-coil option will also be available soon


Advanced options
----------------

There is also an advanced options tab

.. figure:: ../images/ccp4i2_ample_advanced.png
   :align: center

This provides options relating to:

1. The rebuilding of the structure
2. Ensembling
3. And a box to add any other run flags not already available through the GUI.

For a full list possible options see :ref:`AMPLE options <cl_options>`.

Running AMPLE
=============
Input Files
-----------
AMPLE requires a FASTA file and an MTZ file in order to run. It also needs the homologous structures.

.. note::
   You can download all the data files `here <https://github.com/rigdenlab/ample-examples/archive/master.zip>`_.

AMPLE Setup
-----------

The FASTA and MTZ files can be submitted into the fields described above

When using multiple distant homologs the following options need to be input:

.. figure:: ../images/ccp4i2_input_homologs.png
   :align: center

Once these options have been selected the job can be set running.

AMPLE Output
============
Upon starting a results tab will appear within the CCP4i2 interface summarising the progress of the AMPLE run. This will contain the following sections:

Summary
-------
The summary tab contains information about the search from MrBUMP

MrBUMP Results
^^^^^^^^^^^^^^
This section displays a table with the results of running MrBUMP on each of the ensembles, for this example you will have information for the following headings.

.. figure:: ../images/ccp4i2_summary_homologs.png
   :align: center

* **ensemble_name:** this matches the name from the ensemble section.
* **MR_program:** the program used for Molecular Replacement.
* **Solution type:** the MrBUMP categorisation of the solution

  * *GOOD* - final Rfree <=0.35
  * *MARGINAL* - final Rfree <= 0.48 OR final Rfree <= 0.5 and the ratio between the initial and final Rfree is <= 0.8, OR final Rfree <= 0.55 and the ratio between the initial and final Rfree is <= 0.95
  * *POOR* - anything else
  * *no_job_directory* - a script has been prepared, but the job hasn’t been run yet
  * *unfinished* - the job is running or has stopped without generating any results

* **PHASER_LLG:** the PHASER log-likelihood gain for the Molecular Replacement solution.
* **PHASER_TFZ:** PHASER Translation Function Z-score for the Molecular Replacement solution.
* **REFMAC_Rfact:** Rfact score for REFMAC refinement of the Molecular Replacement solution.
* **REFMAC_Rfree:** Rfree score for REFMAC refinement of the Molecular Replacement solution.
* **SHELXE_CC:** SHELXE Correlation Coefficient score after C-alpha trace.
* **SHELXE_ACL:** Average Chain Length of the fragments of the SHELXE C-alpha trace.

Typically a result with a SHELXE CC score of 25 or higher **and** a SHELXE ACL of 10 or higher will indicate a correct solution.

Results
-------
The Results tab displays the final results of AMPLE after running MrBUMP on the ensembles.

.. figure:: ../images/ccp4i2_results_homologs.png
   :align: center

AMPLE output the atomic models, MTZ and map coefficients for the top 3 solutions in the AMPLE run.

.. note::
   The results you obtain may be slightly different to those presented above as you are generating a new slightly different set of *ab initio* models.

Citations
---------
This section lists the programs and algorithms that are using in the AMPLE job and gives a list of references to be cited should AMPLE find a solution.

.. figure:: ../images/ccp4i2_citation_homologs.png
   :align: center