View source for SecStrAnnotator:OneToOne v1.0

This page is about '''SecStrAnnotator 1.0''', which is obsolete. Consider using a [[SecStrAnnotator:OneToOne | newer version]].


SecStrAnnotator finds annotation for a query protein ''Q'', based on the template protein ''T''. Thus, the input consists of the structure of ''T'', structure of ''Q'', and annotation of ''T''. 

Sometimes a single protein consists of several domains. In such cases, ''T'' and ''Q'' do not refer to the whole protein but only to one domain.

The annotation algorithm consists of three major steps. The first step is '''structural alignment and superimposition''' of the query protein with the template protein, so the corresponding parts of the two proteins are located close to each other. In the second step, '''secondary structure assignment (SSA)''' is performed – SSEs are detected in the query protein ''Q''. The third step is called '''matching''' – the algorithm will match the template SSEs to the query SSEs and for each annotated SSE in ''T'' it will select the corresponding SSE in ''Q''.

==Dependencies==

===PyMOL===

PyMOL is used by SecStrAnnotator for structural alignment and visualization. It can be downloaded from the [https://pymol.org/2/ PyMOL website]. In Ubuntu Linux it can also be installed by running <code>sudo apt install pymol</code>.

===Mono===

(Only needed for outside Windows)

On Windows, SecStrAnnotator.exe can be executed directly; however, on other operating systems it must be run using [https://www.mono-project.com/ Mono]. In Ubuntu Linux it can be installed by running <code>sudo apt install mono-devel</code>.

===DSSP===

(Only needed when using DSSP secondary structure assignment method (by <code>--ssa dssp</code>))

==Execution==

SecStrAnnotator is executed from command line. 

On Windows:
 SecStrAnnotator.exe <span style=color:gray>[</span><span style=color:green>OPTIONS</span><span style=color:gray>]</span> <span style=color:green>DIRECTORY</span> <span style=color:green>TEMPLATE</span> <span style=color:green>QUERY</span>

On Linux:
 mono SecStrAnnotator.exe <span style=color:gray>[</span><span style=color:green>OPTIONS</span><span style=color:gray>]</span> <span style=color:green>DIRECTORY</span> <span style=color:green>TEMPLATE</span> <span style=color:green>QUERY</span>

Example of a call:
 SecStrAnnotator.exe --align cealign --ssa geom-hbond --matching mom --session  my_data_directory 1og2,A,30:491 1tqn,A,28:499

===Arguments===

* <code><span style=color:green>DIRECTORY</span></code> is the directory containing all the input files. The output files will also be saved to this directory. 
* <code><span style=color:green>TEMPLATE</span></code> describes the template protein domain in one of the following formats: <code><span style=color:green>PDB</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span>,<span style=color:green>RANGES</span></code>. The whole argument must be written without spaces. Examples: 
** <code>1og2</code> (structure 1og2, chain A by default)
** <code>1og2,B</code> (chain B)
** <code>1og2,B,100:400</code> (residues 100–400 of the chain B)
** <code>1og2,B,:400</code> (residues up to 400 of the chain B)
** <code>1h9r,A,123:183,252:261</code> (residues 123–183 and 252–261 of the chain A)
* <code><span style=color:green>QUERY</span></code> describes the query protein domain and uses the same format as <code><span style=color:green>TEMPLATE</span></code>.

===Options===

There is a range of options which can be used to modify the behaviour of SecStrAnnotator.  The most important option is:
* <code>--help</code>  Prints the help message, which includes the description of all the other options.

===Input files===

* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>TEMPLATEPDB</span>.pdb</code>  – structure of the template protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>TEMPLATEPDB</span>-template.sses.json</code>  – annotation of the template domain
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>.pdb</code>  – structure of the query protein

===Output files===

* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-aligned.pdb</code> – structure of the query protein after superimposition on the template protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-detected.sses.json</code> – secondary structure assignment of the query protein, i.e. all detected SSEs
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-annotated.sses.json</code> – annotated SSEs in the query protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-annotated.pse</code> – PyMOL session with the visualization of the resulting annotation (only when executed with <code>--session</code> option)

===Auxiliary files and programs===

SecStrAnnotator has dependencies on other programs (PyMOL, optionally DSSP) and scripts. These auxiliary files need to be available in the system, and there location must be specified in the configuration file <code>SecStrAnnotator_config.json</code>. The configuration file itself must be in the same directory as <code>SecStrAnnotator.exe</code>. The default content of the configuration file is:
<source lang="json>
{
	"PymolExecutable":    "pymol",
	"DsspExecutable":     "./dssp",
	"PymolScriptAlign":   "./script_align.py",
	"PymolScriptSession": "./script_session.py"
}    
</source>

which assumes that <code>pymol</code> is installed and can be run directly (from <code>$PATH</code>) and that the other files are present in the same directory as <code>SecStrAnnotator.exe</code>. 

On Windows, the location of PyMOL executable must be manually inserted into the modification file (it is usually <code>C:\Program Files\PyMOL\PyMOL\PyMOL.exe</code>, but can be different; it should be PyMOL.exe, not PymolWin.exe):
<source lang="json>
{
	"PymolExecutable":    "C:\\Program Files\\PyMOL\\PyMOL\\PyMOL.exe",
	"DsspExecutable":     ".\\dssp",
	"PymolScriptAlign":   ".\\script_align.py",
	"PymolScriptSession": ".\\script_session.py"
}    
</source>
Note that <code>\\</code> must be used instead of <code>\</code> in the configuration file.

===Annotation file format===

All files with extension <code>.sses.json</code> are in SecStrAnnotator annotation format. A short example of this  format:
<source lang="json>
{
  "1og2": {
    "comment": "This is a demonstration of the annotation format.",
    "secondary_structure_elements": [
      { "label":   "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },
      { "label": "1.1", "chain_id": "A", "start": 65, "end": 69, "type": "E" },
      { "label": "1.2", "chain_id": "A", "start": 72, "end": 77, "type": "E" },
      { "label":   "B", "chain_id": "A", "start": 80, "end": 90, "type": "H" },
      { "label": "1.3", "chain_id": "A", "start": 386, "end": 389, "type": "E" }
    ],
    "beta_connectivity": [
      [ "1.1", "1.2", -1 ],
      [ "1.2", "1.3", 1 ]
    ]
  }
}  
</source>

The example describes two helices, named A and B, and a β-sheet consisting of three strands, named 1.1, 1.2, and 1.3. Strands 1.1 and 1.2 are connected by an anti-parallel β-ladder, strands 1.2 and 1.3 by a parallel β-ladder. All the SSEs are located on chain A of structure 1og2.


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