Help:Getting Started - Revision history

127.0.0.1: Added to the wiki via WikiImport-Script.

2024-11-22T11:05:25Z

Added to the wiki via WikiImport-Script.

← Older revision		Revision as of 13:05, 22 November 2024
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	;Tips		;Tips
	* If you have already an InchI-Key of the molecule you want to create, you can try to add it in the editor field of the chemical formula widget (other fields must be clear!). If it is known to PubChem, it will be drawn for you automatically.		* If you have already an InchI-Key of the molecule you want to create, you can try to add it in the editor field of the chemical formula widget (other fields must be clear!). If it is known to PubChem, it will be drawn for you automatically.
	* If you have already the SMILES string of a molecule, you can open the Ketcher editor, click on 'open' in the menu bar (second icon from the left), then "paste from clipboard". Now just copy&paste the SMILES string and let Ketcher draw the molecule for you.		* If you have already the SMILES string of a molecule, you can open the Ketcher editor, click on 'open' in the menu bar (second icon from the left), then "paste from clipboard". Now just copy&paste the SMILES string and let Ketcher draw the molecule for you.

84.178.68.3 at 14:38, 24 October 2024

2024-10-24T14:38:58Z

← Older revision		Revision as of 16:38, 24 October 2024
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	Every molecule gets assigned a number upon its first registration in the wiki. Should the same molecule be drawn again, it will automatically be recognized as the previously entered structure. Molecules with R-groups will generate "Collections" and the R-groups van be viewed by clicking on '''[Show R-groups]'''.		Every molecule gets assigned a number upon its first registration in the wiki. Should the same molecule be drawn again, it will automatically be recognized as the previously entered structure. Molecules with R-groups will generate "Collections" and the R-groups van be viewed by clicking on '''[Show R-groups]'''.

			;Tips
			* If you have already an InchI-Key of the molecule you want to create, you can try to add it in the editor field of the chemical formula widget (other fields must be clear!). If it is known to PubChem, it will be drawn for you automatically.
			* If you have already the SMILES string of a molecule, you can open the Ketcher editor, click on 'open' in the menu bar (second icon from the left), then "paste from clipboard". Now just copy&paste the SMILES string and let Ketcher draw the molecule for you.

	==== Molecule links ====		==== Molecule links ====

172.25.227.196 at 16:23, 23 May 2024

2024-05-23T16:23:20Z

← Older revision		Revision as of 18:23, 23 May 2024
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	Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.		Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.

	=== Adding tags to selected terms ===		== Selected functions ==

			==== Adding tags to selected terms ====
	Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"		Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"

172.25.227.196: /* Adding tags to selected terms */

2024-05-23T16:21:54Z

Adding tags to selected terms

← Older revision		Revision as of 18:21, 23 May 2024
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	Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.		Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.

	==== Adding tags to selected terms ====		=== Adding tags to selected terms ===
	Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"		Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"

172.25.227.196 at 16:21, 23 May 2024

2024-05-23T16:21:10Z

← Older revision		Revision as of 18:21, 23 May 2024
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	==== Investigation link ====		==== Investigation link ====
	Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.		Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search SMW query syntax] hold more information on how to write queries.

			==== Adding tags to selected terms ====
			Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"

ChN at 13:52, 11 July 2023

2023-07-11T13:52:40Z

Show changes

ChN at 09:55, 11 July 2023

2023-07-11T09:55:29Z

← Older revision		Revision as of 11:55, 11 July 2023
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	'''Publication pages (and topic pages) are the only ones that can be freely edited! Any changes to molecules or investigations must be made on the publication page. Only exception is adding an abbreviation to a molecule, this happens on the molecule page.'''		'''Publication pages (and topic pages) are the only ones that can be freely edited! Any changes to molecules or investigations must be made on the publication page. Only exception is adding an abbreviation to a molecule, this happens on the molecule page.'''

	Publication pages show the legally available data from published papers. These are		Publication pages show the legally available data from published papers. These are:

	~~I) The investigations~~: ~~Tables with data~~

			I) The investigations: Tables with data<br>
	II) Molecules used in the publication		II) Molecules used in the publication

	Currently, the pages are structured by the headlines		Currently, the pages are structured by the headlines:

	1) Catalyst		1) Catalyst<br>
	2) Photosensitizer		2) Photosensitizer<br>
	3) Investigation		3) Investigation<br>
	4) Sacrificial electron donor		4) Sacrificial electron donor<br>
	5) Additives (optional)		5) Additives (optional)<br>

	Each headline is formatted as sub-heading 2		Each headline is formatted as sub-heading 2
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	=== Molecule Drawings ===		=== Molecule Drawings ===
	To draw molecules in Ketcher 2:		To draw molecules in Ketcher 2:<br>
	Bonds between ligands and metal are '''hydrogen bonds''' by default, unless this adds surplus hydrogens to the structure and those hydrogens cannot be removed by an appropriate charge. In this case, use an '''any bond'''.		Bonds between ligands and metal are '''hydrogen bonds''' by default, unless this adds surplus hydrogens to the structure and those hydrogens cannot be removed by an appropriate charge. In this case, use an '''any bond'''.

	Remember to add charges on the molecule, especially on metal centers in complexes with counter ions.		Remember to add charges on the molecule, especially on metal centers in complexes with counter ions.<br>
	Position ligands with aromatic rings correctly around the center metal atom. Try to avoid using the clean-up function, as this distorts the aromatic rings.		Position ligands with aromatic rings correctly around the center metal atom. Try to avoid using the clean-up function, as this distorts the aromatic rings.

	Molecule collections with R-groups: Add R-groups when multiple rests are mentioned in literature. Use different (R1, R2, R3…) groups for different positions on the molecule, unless two positions are always substituted with the same rest. Specify the R-groups in the Ketcher “Define R-groups” menu.		Molecule collections with R-groups: Add R-groups when multiple rests are mentioned in literature. Use different (R1, R2, R3…) groups for different positions on the molecule, unless two positions are always substituted with the same rest. Specify the R-groups in the Ketcher “Define R-groups” menu.<br>
	R-groups can also be used for counter ions: add an unconnected R-group on the top right of the molecule drawing and specify one or multiple counter ions in the “Define R-groups” menu.		R-groups can also be used for counter ions: add an unconnected R-group on the top right of the molecule drawing and specify one or multiple counter ions in the “Define R-groups” menu.<br>
	Small organic molecule ligands: draw individually instead of abbreviation		Small organic molecule ligands: draw individually instead of abbreviation<br>
	CO: triple bond, negative charge on C, positive charge on O		CO: triple bond, negative charge on C, positive charge on O
	(example: https://pubchem.ncbi.nlm.nih.gov/compound/139130150)		(example: https://pubchem.ncbi.nlm.nih.gov/compound/139130150)

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	Columns with free text but guidelines:		Columns with free text but guidelines:

	Additives: free text; gases according to list (…)		Additives: free text; gases according to list (…)<br>
			Solvent ratio: e. g. 4:1<br>
	Solvent ratio: e. g. 4:1		Irradiation wavelength: number, “dark” (or empty), description of source<br>
			Columns with numbers: Leave empty when number is not given or zero
	Irradiation wavelength: number, “dark” (or empty), description of source

	Columns with numbers:

	Leave empty when number is not given or zero

	=== Comment banner ===		=== Comment banner ===

ChN at 09:53, 11 July 2023

2023-07-11T09:53:18Z

← Older revision		Revision as of 11:53, 11 July 2023
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	'''Auto generated pages according to templates (no edits possible):'''		'''Auto generated pages according to templates (no edits possible):'''

	- literature page (generated from DOI),		- literature page (generated from DOI),<br>
			- investigation (generated from investigation template input on publication page),<br>
	- investigation (generated from investigation template input on publication page),

	- molecule page (only add abbreviation)		- molecule page (only add abbreviation)

	=== Publication pages ===		=== Publication pages ===
	How to generate a new publication page: Authoring → Create a new Paper: enter title (default publication title, check formatting in the wiki), DOI, topic(s) it belongs to → Create paper		How to generate a new publication page: Authoring → Create a new Paper: enter title (default publication title, check formatting in the wiki), DOI, topic(s) it belongs to → Create paper<br>
	This leads to the new publication page with auto-generated infobox (About) from the DOI-generated literature page		This leads to the new publication page with auto-generated infobox (About) from the DOI-generated literature page

ChN at 09:36, 11 July 2023

2023-07-11T09:36:07Z

← Older revision		Revision as of 11:36, 11 July 2023
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	- literature page (generated from DOI),		- literature page (generated from DOI),

	- investigation (generated from investigation template input on publication page),		- investigation (generated from investigation template input on publication page),

	- molecule page (only add abbreviation)		- molecule page (only add abbreviation)

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	Publication pages show the legally available data from published papers. These are		Publication pages show the legally available data from published papers. These are

	I) The investigations: Tables with data		I) The investigations: Tables with data

	II) Molecules used in the publication		II) Molecules used in the publication

	Currently, the pages are structured by the headlines		Currently, the pages are structured by the headlines

	1) Catalyst		1) Catalyst
	2) Photosensitizer		2) Photosensitizer
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	The investigations are named: currently Table 1, Table 2		The investigations are named: currently Table 1, Table 2

	The appropriate molecules for 2) to 5) are drawn under their respective title. Solvents or gas atmosphere don’t need to be drawn, as do small (inorganic) additives.		The appropriate molecules for 1), 2), 4), 5) are drawn under their respective title. Solvents or gas atmosphere don’t need to be drawn, as do small (inorganic) additives.

	=== Molecule Drawings ===		=== Molecule Drawings ===
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	=== Investigations ===		=== Investigations ===

	Columns with free text but guidelines:		Columns with free text but guidelines:

	Additives: free text; gases according to list (…)		Additives: free text; gases according to list (…)

	Solvent ratio: e. g. 4:1		Solvent ratio: e. g. 4:1

	Irradiation wavelength: number, “dark” (or empty), description of source		Irradiation wavelength: number, “dark” (or empty), description of source

	Columns with numbers:		Columns with numbers:

	Leave empty when number is not given or zero		Leave empty when number is not given or zero

ChN at 09:33, 11 July 2023

2023-07-11T09:33:43Z

← Older revision		Revision as of 11:33, 11 July 2023
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	== Guidelines to style pages in this wiki ==		== Guidelines to style pages in this wiki ==

	'''Auto generated pages according to templates (no edits possible):		'''Auto generated pages according to templates (no edits possible):'''

	- literature page (generated from DOI),		- literature page (generated from DOI),
	- investigation (generated from investigation template input on publication page),		- investigation (generated from investigation template input on publication page),
	- molecule page (only add abbreviation)~~'''~~		- molecule page (only add abbreviation)

	=== Publication pages ===		=== Publication pages ===