SecStrAnnotator:OneToOne - Revision history

Midlik at 13:59, 17 May 2022

2022-05-17T13:59:06Z

← Older revision		Revision as of 13:59, 17 May 2022
Line 1:		Line 1:
	This page is about '''SecStrAnnotator 2.1''' (the page for SecStrAnnotator 1.0 is [[SecStrAnnotator:OneToOne_v1.0 \| here]]).		This page is about '''SecStrAnnotator 2.3''' (the page for SecStrAnnotator 1.0 is [[SecStrAnnotator:OneToOne_v1.0 \| here]]).


Line 10:		Line 10:
	==Dependencies==		==Dependencies==

	===.NET ~~Core Runtime 3~~.0===		===.NET 6.0 runtime===

	Download and install from the official [https://dotnet.microsoft.com/ .NET ~~Core~~ website]. ~~Version~~ 3.1 ~~should work as well.~~		Download and install from the official [https://dotnet.microsoft.com/ .NET website]. (For SecStrAnnotator 2.0–2.2, use .NET Core 3.0 or .NET Core 3.1)

	===PyMOL===		===PyMOL===
Line 89:		Line 89:
	On Windows, you must find the location of PyMOL executable and insert it into the configuration file.		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>.		* 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.		* 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.		* We're looking for PyMOL.exe, not PyMOLWin.exe. PyMOLWin.exe will run asynchronously and it will probably not work.

Midlik: /* Auxiliary files and programs */

2020-04-09T15:08:55Z

Auxiliary files and programs

← Older revision		Revision as of 15:08, 9 April 2020
Line 85:		Line 85:
	</source>		</source>

	which assumes that <code>pymol</code> is installed and can be run directly (from <code>$PATH</code>) and that the other files are present in subdirectory as <code>scripts</code>.		which assumes that <code>pymol</code> is installed and can be run directly (from <code>$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.		On Windows, you must find the location of PyMOL executable and insert it into the configuration file.

Midlik: /* Dependencies */

2020-04-09T15:02:11Z

Dependencies

← Older revision		Revision as of 15:02, 9 April 2020
Line 20:		Line 20:
	===(DSSP)===		===(DSSP)===

	Only needed if using DSSP secondary structure assignment method (<code>--ssa dssp</code>)		Only needed if using DSSP secondary structure assignment method (<code>--ssa dssp</code>). In Ubuntu Linux it can be installed by running <code>sudo apt install dssp</code>.

	==Execution==		==Execution==

Midlik at 14:59, 9 April 2020

2020-04-09T14:59:51Z

← Older revision		Revision as of 14:59, 9 April 2020
Line 18:		Line 18:
	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>.		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>.

	===DSSP===		===(DSSP)===

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

	==Execution==		==Execution==

Midlik: /* Auxiliary files and programs */

2020-04-09T13:49:18Z

Auxiliary files and programs

← Older revision		Revision as of 13:49, 9 April 2020
Line 92:		Line 92:
	* To make it more fun, <code>ProgramData</code> is a hidden directory, which is by default invisible in File Explorer.		* 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.		* 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 used instead of~~ <code>\</code> ~~in the configuration file.~~ <code>\</code> ~~is a special escaping character in JSON~~.		* 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>		<source lang="json>

Midlik: /* Auxiliary files and programs */

2020-04-09T13:45:59Z

Auxiliary files and programs

← Older revision		Revision as of 13:45, 9 April 2020
Line 75:		Line 75:
	===Auxiliary files and programs===		===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:		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>		<source lang="json>
	{		{

Midlik: /* Execution */

2020-04-09T10:45:16Z

Execution

← Older revision		Revision as of 10:45, 9 April 2020
Line 31:		Line 31:

	<source lang="bash">		<source lang="bash">
	dotnet SecStrAnnotator.dll --help # Show help		dotnet SecStrAnnotator.dll --help # Show help

	dotnet SecStrAnnotator.dll --onlyssa my_data_directory 1tqn,A,7:478 # Only detect SSEs		dotnet SecStrAnnotator.dll --onlyssa my_data_directory 1tqn,A,7:478 # Only detect SSEs

	dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 # Detect and annotate SSEs		dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 # Detect and annotate SSEs

	dotnet SecStrAnnotator.dll --align cealign --matching mom --session ~~my_data_directory 2nnj,A 1tqn,A,7:478~~ # Detect and annotate SSEs		dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 --align cealign --matching mom --session # Detect and annotate SSEs
	</source>		</source>

Midlik: /* Annotation file format */

2020-04-09T10:41:01Z

Annotation file format

← Older revision		Revision as of 10:41, 9 April 2020
Line 108:		Line 108:
	<source lang="json>		<source lang="json>
	{		{
	"~~1og2~~": {		"1tqn": {
	"comment": "This is a demonstration of the annotation format.",		"comment": "This is a demonstration of the annotation format. It shows a few SSEs selected from the real annotation of 1tqn.",
	"secondary_structure_elements": [		"secondary_structure_elements": [
	{ "label": "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },		{ "label": "A", "chain_id": "A", "start": 36, "end": 47, "type": "H", "sequence": "FCMFDMECHKKY" },
	{ "label": "~~1-1~~", "chain_id": "A", "start": 65, "end": 69, "type": "E", "~~sheet_id~~": 1 },		{ "label": "B", "chain_id": "A", "start": 66, "end": 76, "type": "h", "sequence": "PDMIKTVLVKE" },
	{ "label": "1-2", "chain_id": "A", "start": 72, "end": 77, "type": "E", "sheet_id": 1 },		{ "label": "1-1", "chain_id": "A", "start": 50, "end": 55, "type": "E", "sheet_id": 1, "sequence": "VWGFYD" },
	{ "label": "B", "chain_id": "A", "start": 80, "end": 90, "type": "H" },		{ "label": "1-2", "chain_id": "A", "start": 58, "end": 63, "type": "E", "sheet_id": 1, "sequence": "QPVLAI" },
	{ "label": "1-3", "chain_id": "A", "start": ~~386~~, "end": ~~389~~, "type": "E", "sheet_id": 1 }		{ "label": "1-3", "chain_id": "A", "start": 372, "end": 375, "type": "E", "sheet_id": 1, "sequence": "VVMI" }
	],		],
	"beta_connectivity": [		"beta_connectivity": [
Line 125:		Line 125:
	</source>		</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~~.		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 1tqn.

Midlik: /* Annotation file format */

2020-04-09T10:33:12Z

Annotation file format

← Older revision		Revision as of 10:33, 9 April 2020
Line 112:		Line 112:
	"secondary_structure_elements": [		"secondary_structure_elements": [
	{ "label": "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },		{ "label": "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },
	{ "label": "1-1", "chain_id": "A", "start": 65, "end": 69, "type": "E" },		{ "label": "1-1", "chain_id": "A", "start": 65, "end": 69, "type": "E", "sheet_id": 1 },
	{ "label": "1-2", "chain_id": "A", "start": 72, "end": 77, "type": "E" },		{ "label": "1-2", "chain_id": "A", "start": 72, "end": 77, "type": "E", "sheet_id": 1 },
	{ "label": "B", "chain_id": "A", "start": 80, "end": 90, "type": "H" },		{ "label": "B", "chain_id": "A", "start": 80, "end": 90, "type": "H" },
	{ "label": "1-3", "chain_id": "A", "start": 386, "end": 389, "type": "E" }		{ "label": "1-3", "chain_id": "A", "start": 386, "end": 389, "type": "E", "sheet_id": 1 }
	],		],
	"beta_connectivity": [		"beta_connectivity": [

Midlik: /* Annotation file format */

2020-04-09T10:30:03Z

Annotation file format

← Older revision		Revision as of 10:30, 9 April 2020
Line 112:		Line 112:
	"secondary_structure_elements": [		"secondary_structure_elements": [
	{ "label": "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },		{ "label": "A", "chain_id": "A", "start": 50, "end": 61, "type": "H" },
	{ "label": "1.1", "chain_id": "A", "start": 65, "end": 69, "type": "E" },		{ "label": "1-1", "chain_id": "A", "start": 65, "end": 69, "type": "E" },
	{ "label": "1.2", "chain_id": "A", "start": 72, "end": 77, "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": "B", "chain_id": "A", "start": 80, "end": 90, "type": "H" },
	{ "label": "1.3", "chain_id": "A", "start": 386, "end": 389, "type": "E" }		{ "label": "1-3", "chain_id": "A", "start": 386, "end": 389, "type": "E" }
	],		],
	"beta_connectivity": [		"beta_connectivity": [
	[ "1.1", "1.2", -1 ],		[ "1-1", "1-2", -1 ],
	[ "1.2", "1.3", 1 ]		[ "1-2", "1-3", 1 ]
	]		]
	}		}
Line 125:		Line 125:
	</source>		</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.		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.