Editing SecStrAnnotator:OneToOne (section)

===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.dll</code>. The default content of the configuration file is:
<source lang="json>
{
	"PymolExecutable":    "pymol",
	"PymolScriptAlign":   "./scripts/script_align.py",
	"PymolScriptSession": "./scripts/script_session.py",
	"DsspExecutable":     "mkdssp"
}    
</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 subdirectory <code>scripts</code>. 

On Windows, you must find the location of PyMOL executable and insert it into the configuration file.

* It will be probably some impossible-to-find file like <code>C:\Program Files\PyMOL\PyMOL\PyMOL.exe</code> or <code>C:\ProgramData\PyMOL\Scripts\pymol.exe</code> (or <code>C:/Users/Adam/miniconda3/Scripts/pymol.exe</code> if you installed PyMOL via <code>conda</code>). 
* To make it more fun, <code>ProgramData</code> is a hidden directory, which is by default invisible in File Explorer. 
* We're looking for PyMOL.exe, not PyMOLWin.exe. PyMOLWin.exe will run asynchronously and it will probably not work.
* Note that <code>\</code> is a special escaping character in JSON. Therefore use <code>/</code> or <code>\\</code> instead of <code>\</code>.

<source lang="json>
{
	"PymolExecutable":    "C:/ProgramData/PyMOL/Scripts/pymol.exe",
	"PymolScriptAlign":   "./scripts/script_align.py",
	"PymolScriptSession": "./scripts/script_session.py",
	"DsspExecutable":     "./dssp.exe"
}    
</source>