.. _`app:atomStructUtilsOperatorProtocol`:

Atomic Structure Chain Operator protocol
========================================

Protocol designed to perform two types of operations with chains from
atomic structures in *Scipion*: a) Chain extraction: An individual chain will be
extracted from a polymeric atomic structure. The extracted chain will be
saved as monomer in a new atomic structure and will not include HETATM
and water molecules. b) Chain addition: One or several chains will be
added to a reference atomic structure. The resulting addition will be
saved as a new polymeric atomic structure.

-  | Requirements to run this protocol and visualize results:

   -  | *Scipion* plugin: **scipion-em**

   -  | *Scipion* plugin: **scipion-em-atomstructutils**

   -  | *Scipion* plugin: **scipion-em-chimera**


-  | *Scipion* menu: *Model building -> Tools-Calculators* (:numref:`model_building_app_protocol_atomstructutils_operator_1` (A))

   .. figure:: Images_appendix/Fig154.svg
      :alt: Protocol **atomstructutils-operator**. A: Protocol location in *Scipion* menu. B: Protocol form to extract a chain from an atomic structure. C: Protocol form to add one or several chains to an atomic structure.
      :name: model_building_app_protocol_atomstructutils_operator_1
      :align: center
      :width: 90.0%

      Protocol **atomstructutils-operator**. A: Protocol location in *Scipion* menu. B: Protocol form to extract a chain from an atomic structure. C: Protocol form to add one or several chains to an atomic structure.

-  | Protocol form parameters (:numref:`model_building_app_protocol_atomstructutils_operator_1` (B and C)):

   -  | *Atomic structure 1*: PDBx/mmCIF atomic structure, previously downloaded or generated in *Scipion*.

   -  | *Operation*: Two types of operations can be performed with this protocol:

      -  | *addChain*: Addition of one or several chains to an initial atomic structure. By selecting this option, an additional param has to be completed (:numref:`model_building_app_protocol_atomstructutils_operator_1` (B)):

         -  | *Atomic structure 2*: One or several PDBx/mmCIF atomic structures, previously downloaded or generated in *Scipion*.


      -  | *extractChain*: Extraction of only one chain from a polymeric atomic structure. By selecting this option, three additional params have to be completed (:numref:`model_building_app_protocol_atomstructutils_operator_1` (C)):

         -  | *Chain*: Specific chain that has to be extracted. The wizard on the right helps the user to select that chain showing the number of the starting model structure, the name of the chain, and its number of residues.

         -  | *Start at residue #*: The default value (-1) allows to extract the whole chain. In case you would like to extract only a fraction of the chain, the number of the initial required residue should be indicated.

         -  | *End at residue #*: The default value (-1) allows to extract the whole chain. In case you would like to extract only a fraction of the chain, the number of the last required residue should be indicated.

-  | Protocol execution: Adding specific structure/chain label is
     recommended in *Run name* section, at the form top. To add the
     label, open the protocol form, press the pencil symbol at the right
     side of *Run name* box, complete the label in the new opened
     window, press OK and, finally, close the protocol. This label will
     be shown in the output summary content (see below). If you want to
     run again this protocol, do not forget to set to *Restart* the *Run
     mode*.

   | Press the *Execute* red button at the form bottom.

-  Visualization of protocol results:

   | After executing the protocol, press *Analyze Results* and *ChimeraX* graphics
     window will be opened by default. Atomic structures and volumes are
     referred to the origin of coordinates in *ChimeraX*. To show the relative
     position of atomic structure and electron density volume, the three
     coordinate axes are represented; X axis (red), Y axis (yellow), and
     Z axis (blue) (:numref:`model_building_app_protocol_volume_3`). Coordinate axes and the new atomic structure
     generated are model numbers *#1* and *#2*, respectively, in
     *Models* panel. Write in *ChimeraX* command line:

   ::

      split #2

   | to check the individual chains included in the new atomic structure
     generated.

-  | Summary content:
   | Since an atomic structure is generated:

   -  | Protocol output (below *Scipion* framework):
      | *atomstructutils - operator -> ouputPdb*;
      | *AtomStruct (pseudoatoms=True/ False, volume=True/ False)*.
      | Pseudoatoms is set to *True* when the structure is made of
        pseudoatoms instead of atoms. Volume is set to *True* when an
        electron density map is associated to the atomic structure.

   -  | *SUMMARY* box:
      | No summary information.