Editing SecStrAnnotator:OneToMany (section)

=Procedure=

==Preparing structural data==

A list of PDB structures corresponding to a protein family can be obtained from [http://www.ebi.ac.uk/pdbe/pdbe-rest-api PDBe REST API] using <code>domains_from_pdbeapi.py</code>. The protein family can be identified by a CATH code, such as 1.10.630.10 ([http://cathdb.info/ CATH]), or by a Pfam accession, such as PF00067 ([https://pfam.xfam.org/ Pfam]):

 python3 domains_from_pdbeapi.py 1.10.630.10 > family_from_cath.json
 
 python3 domains_from_pdbeapi.py PF00067 > family_from_pfam.json

The structures are then downloaded from [https://www.ebi.ac.uk/pdbe/ PDBe] by <code>download_from_pdbe.py</code>:

 python3 download_from_pdbe.py family_from_cath.json my_structure_directory

In this moment, all necessary structures should be in the directory <code>my_structure_directory</code>.

==Selection of a template domain and obtaining its annotation==

In this step, one of the domains from the protein family should be selected as a template domain. Suppose that we have selected the domain which is located on the chain A of PDB entry 2nnj.

If an SSE annotation of the template domain is available in the literature, it can be converted into the [[SecStrAnnotator:OneToOne#Annotation file format | SecStrAnnotator format]] and used as the template annotation.

If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:

 dotnet SecStrAnnotator.dll --onlyssa my_structure_directory 2nnj,A

This will create file <code>my_structure_directory/2nnj-detected.sses.json</code>. Rename this file to <code>2nnj-template.sses.json</code> and optionally refine the annotation in the file:

* Remove unnecessary SSEs which you don't want to annotate.
* Add SSEs which were not detected but should be annotated.
* Rename the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of default H0, H1, H4, H6...).
* If you add/remove β-strands, don't forget to update also the <code>beta_connectivity</code> section.

==Running the annotation algorithm on each member of the family==

 python3 SecStrAnnotator_batch.py my_structure_directory 2nnj,A family_from_cath.json

<br style="clear:both" />
----

[[SecStrAnnotator:UserManual | Back to the main page]]