PatternQuery:Service Organization - Revision history

Lukas at 09:12, 27 April 2015

2015-04-27T09:12:18Z

← Older revision		Revision as of 09:12, 27 April 2015
Line 1:		Line 1:
	'''~~Motive Query~~''' service is aimed for querying large datasets of structures from the [http://www.rcsb.org/pdb/home/home.do Protein Data Bank]. To perfect your query or query smaller datasets or even user-uploaded data, please use [[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]] instead.		'''PatternQuery''' service is aimed for querying large datasets of structures from the [http://www.rcsb.org/pdb/home/home.do Protein Data Bank]. To perfect your query or query smaller datasets or even user-uploaded data, please use [[PatternQuery:MotiveExplorer \| PatternQuery Explorer]] instead.

	If you would like to run '''~~MotiveQuery~~''' at your home institution, please download a [[~~MotiveQuery~~:Command_Line \| command-line]] version. The following visual will guide you through the process of submitting your calculation so as the interpreting results.		If you would like to run '''PatternQuery''' at your home institution, please download a [[PatternQuery:Command_Line \| command-line]] version. The following visual will guide you through the process of submitting your calculation so as the interpreting results.

	=Synopsis Page=		=Synopsis Page=
	[[File:~~MotiveQuery~~-Service0.png \| right \| thumb \| 650px\| '''~~MotiveQuery~~ Service''' UI]]		[[File:PatternQuery-Service0.png \| right \| thumb \| 650px\| '''PatternQuery Service''' UI]]
	The '''~~MotiveQuery~~''' synopsis page is divided into a number of tabs:		The '''PatternQuery''' synopsis page is divided into a number of tabs:
	* '''Quick Help''' and '''Samples''' tab provide information to help you orient yourself.		* '''Quick Help''' and '''Samples''' tab provide information to help you orient yourself.
	* '''Support''' provides a simple user interface for asking questions related to a '''~~MotiveQuery~~''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[~~MotiveQuery~~:MotiveExplorer \| ~~MotiveQuery~~ Explorer]] application where you can tune up your queries before doing the database-wide searches.		* '''Support''' provides a simple user interface for asking questions related to a '''PatternQuery''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[PatternQuery:MotiveExplorer \| PatternQuery Explorer]] application where you can tune up your queries before doing the database-wide searches.
	* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''~~MotiveQuery~~''' calculation.		* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''PatternQuery''' calculation.
	* '''Command Line Version''' enables you to download a ~~MotiveQuery~~ service and run it at your home institution over your in-house database in a supported format (.pdb, .cif, .pqr, .mol and *.sdf).		* '''Command Line Version''' enables you to download a PatternQuery service and run it at your home institution over your in-house database in a supported format (.pdb, .cif, .pqr, .mol and *.sdf).
	<br style="clear:both" />		<br style="clear:both" />

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	{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"		{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
	\|-		\|-
	\| [[File:~~MotiveQuery~~-Service1.png\| 650px]]		\| [[File:PatternQuery-Service1.png\| 650px]]
	\| [[File:~~MotiveQuery~~-Service2.png\| 650px]]		\| [[File:PatternQuery-Service2.png\| 650px]]
	\|-		\|-
	\| The UI of the '''~~MotiveQuery~~ Service''' job submission page allows user to submit a new query calculation. First time user can take a look at some of the example queries. If you have run any calculations with '''~~MotiveQuery~~''' already, you can browse the results.		\| The UI of the '''PatternQuery Service''' job submission page allows user to submit a new query calculation. First time user can take a look at some of the example queries. If you have run any calculations with '''PatternQuery''' already, you can browse the results.
	\| At first, ~~decide whether~~ you ~~would like~~ to query the ~~entire Protein Data Bank,~~ a ~~subset thereof based on a variety~~ of ~~different properties~~, or a ~~user provided list of PDB entries of interest~~.		\| At first, you can encode a pattern of you choice into a query. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[PatternQuery:How_to_build_a_query \| case studies]] or consult the [[PatternQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time. Do '''not forget''' to click '''Add+''' after you finish composing query. Multiple queries can be specified at time.
	\|-		\|-
	\| [[File:~~MotiveQuery~~-Service3.png\| 650px]]		\| [[File:PatternQuery-Service3.png\| 650px]]
	\| [[File:~~MotiveQuery~~-Service4.png\| 650px]]		\| [[File:PatternQuery-Service4.png\| 650px]]
	\|-		\|-
	\| ~~You can~~ to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please carefully read the hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a ~~sulfur~~ atom and ~~no nitrogen~~ atoms will be considered. Multiple filters can be applied at the same time.		\| Decide whether you would like to query the entire Protein Data Bank, a subset thereof based on a variety of different properties, or a user provided list of PDB entries of interest.
	\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time. Do '''not forget''' to click '''+ Add''' after you finish composing query.		\| You can query Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please carefully read the hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include logical expressions. For example: '''!S & N''' in ''Atom'' property means that just structures containing a nitrogen atom and none sulfur atoms will be considered. Multiple filters can be applied at the same time.
	\|-		\|-
	\| [[File:~~MotiveQuery~~-Service5.png\| 650px]]		\| [[File:PatternQuery-Service5.png\| 650px]]
	\|-		\|-
	\| As soon as you specify a query or queries and the data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here once the calculation finishes.		\| As soon as you specify a query or queries and the data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time, in most cases, can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here once the calculation finishes. Optionally you can provide an e-mail address and we will contact you directly once your calculation is done.
	\|}		\|}
	<br style="clear:both" />		<br style="clear:both" />

	'''Please continue reading to the [[~~MotiveQuery~~:Specifics Page \| Specifics page]], where you can find additional info on downloading and inspecting your results.		'''Please continue reading to the [[PatternQuery:Specifics Page \| Specifics page]], where you can find additional info on downloading and inspecting your results.

Lukas: Lukas moved page MotiveQuery:Service Organization to PatternQuery:Service Organization

2015-04-25T13:26:55Z

Lukas moved page MotiveQuery:Service Organization to PatternQuery:Service Organization

← Older revision	Revision as of 13:26, 25 April 2015
(No difference)

Lukas at 15:38, 20 April 2015

2015-04-20T15:38:42Z

Dave at 20:16, 28 December 2014

2014-12-28T20:16:55Z

← Older revision		Revision as of 20:16, 28 December 2014
Line 7:		Line 7:
	The '''MotiveQuery''' synopsis page is divided into a number of tabs:		The '''MotiveQuery''' synopsis page is divided into a number of tabs:
	* '''Quick Help''' and '''Samples''' tab provides information to help you orient better.		* '''Quick Help''' and '''Samples''' tab provides information to help you orient better.
	* '''Support''' provides a simple user interface for asking questions related to a '''MotiveQuery''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[MotiveQuery:~~Explorer~~ \| MotiveQuery Explorer]] application where you can tune up your queries before doing the database-wide searches.		* '''Support''' provides a simple user interface for asking questions related to a '''MotiveQuery''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application where you can tune up your queries before doing the database-wide searches.
	* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''MotiveQuery''' calculation.		* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''MotiveQuery''' calculation.
	* '''Command Line Version''' enables you to download a MotiveQuery service and run it at your home institution over your in-house database in a supported format (.pdb, .cif, .pqr, .mol and *.sdf).		* '''Command Line Version''' enables you to download a MotiveQuery service and run it at your home institution over your in-house database in a supported format (.pdb, .cif, .pqr, .mol and *.sdf).

Lukas at 13:05, 28 December 2014

2014-12-28T13:05:13Z

← Older revision		Revision as of 13:05, 28 December 2014
Line 33:		Line 33:
	\|}		\|}
	<br style="clear:both" />		<br style="clear:both" />

			'''Please continue reading to the [[MotiveQuery:Specifics Page \| Specifics page]], where you can find additional info on downloading and inspecting your results.

Lukas: /* Specifics Page */

2014-12-28T13:02:37Z

Specifics Page

← Older revision		Revision as of 13:02, 28 December 2014
Line 33:		Line 33:
	\|}		\|}
	<br style="clear:both" />		<br style="clear:both" />

	~~=Specifics Page=~~
	The '''MotiveQuery''' specifics page provides detailed information about detected fragments and their parent structures. All the results can be downloaded and further inspected by a different means. You can also come back later and check out the results with the web address provided.

	~~==Calculation Summary==~~

	~~{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"~~
	\|-
	~~\| [[File:MotiveQuery-Service-Results1.png\| 650px]]~~
	~~\| [[File:MotiveQuery-Service-Results2.png\| 650px]]~~
	\|-
	\| The Summary of the '''Specifics page''' is divided into the several panels. At first bookmark the web address, to come back later. Additionally, you can download all the provided results for their later inspection. The summary results of the calculation, so as the calculation setup are highlighted below. Click '''Query PDB Entry Details''' for inspecting further details of all of the input PDB structures.
	~~\| Filter the '''Structure table''' by a structure validation report so as the PDB id. Click the structure id for inspecting greater details.~~
	\|-
	~~\| [[File:MotiveQuery-Service-Results3.png\| 650px]]~~
	\|-
	~~\| Go to the '''Details''' tab in order to inspect individual fragments and their details.~~
	\|}

	~~==Fragment Details==~~
	'''Fragment details''' tab provide a valuable information about the composition and origin of the fragment. Structure validation report is provided for you convenience for all ligands and non-standard residues larger 6 atoms as well.

	~~{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"~~
	\|-
	~~\| [[File:MotiveQuery-Fragments1.png\| 650px]]~~
	~~\| [[File:MotiveQuery-Fragments2.png\| 650px]]~~
	\|-
	~~\| Select one of the queries for inspecting individual fragments. Browse the '''Fragment table''' and inspect details of particular fragment so as its visualization.~~
	\| Filter the '''Fragment table''' by a structure validation report result so as the fragment Id. Filtering by a variety of different properties such as the ''Year of publication'', ''Resolution'' or ''Enzymatic number'' also works. Click the structure id for inspecting greater details.
	\|-
	~~\| [[File:MotiveQuery-Fragments3.png\| 650px]]~~
	\|-
	~~\| After clicking fragment ID, all the additional informations are immediately visualized together with the fragment view.~~
	\|-
	\|}

	~~==Structure Details==~~
	'''Structure details''' tab provides a valuable information about fragment's parent structures. For example you can immediately access just fragments originating from a particular structure or structures. Filtering based on a variety of properties is available as well.

	~~{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"~~
	\|-
	~~\| [[File:MotiveQuery-Fragments4.png\| 650px]]~~
	~~\| [[File:MotiveQuery-Fragments5.png\| 650px]]~~
	\|-
	~~\| Click on the '''By PDB Entry''' tab for inspecting PDB entry-wide results.~~
	~~\| The page is divided into a fully customizable table (by structure properties) and details for an individual structure.~~
	\|-
	~~\| [[File:MotiveQuery-Fragments6.png\| 650px]]~~
	~~\| [[File:MotiveQuery-Fragments7.png\| 650px]]~~
	\|-
	~~\| Filter the '''Fragment table''' by a structure validation report so as the fragment Id id. Click the structure id for inspecting greater details.~~
	~~\| Inspect additional details of the PDB structures in different resources, such as PDB.org database or Validator<sup>DB</sup> storing their ligand validation information.~~
	\|-
	\|}

Lukas: /* Specifics Page */

2014-12-28T12:51:44Z

Specifics Page

← Older revision		Revision as of 12:51, 28 December 2014
Line 35:		Line 35:

	=Specifics Page=		=Specifics Page=
			The '''MotiveQuery''' specifics page provides detailed information about detected fragments and their parent structures. All the results can be downloaded and further inspected by a different means. You can also come back later and check out the results with the web address provided.

			==Calculation Summary==

			{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
			\|-
			\| [[File:MotiveQuery-Service-Results1.png\| 650px]]
			\| [[File:MotiveQuery-Service-Results2.png\| 650px]]
			\|-
			\| The Summary of the '''Specifics page''' is divided into the several panels. At first bookmark the web address, to come back later. Additionally, you can download all the provided results for their later inspection. The summary results of the calculation, so as the calculation setup are highlighted below. Click '''Query PDB Entry Details''' for inspecting further details of all of the input PDB structures.
			\| Filter the '''Structure table''' by a structure validation report so as the PDB id. Click the structure id for inspecting greater details.
			\|-
			\| [[File:MotiveQuery-Service-Results3.png\| 650px]]
			\|-
			\| Go to the '''Details''' tab in order to inspect individual fragments and their details.
			\|}

			==Fragment Details==
			'''Fragment details''' tab provide a valuable information about the composition and origin of the fragment. Structure validation report is provided for you convenience for all ligands and non-standard residues larger 6 atoms as well.

			{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
			\|-
			\| [[File:MotiveQuery-Fragments1.png\| 650px]]
			\| [[File:MotiveQuery-Fragments2.png\| 650px]]
			\|-
			\| Select one of the queries for inspecting individual fragments. Browse the '''Fragment table''' and inspect details of particular fragment so as its visualization.
			\| Filter the '''Fragment table''' by a structure validation report result so as the fragment Id. Filtering by a variety of different properties such as the ''Year of publication'', ''Resolution'' or ''Enzymatic number'' also works. Click the structure id for inspecting greater details.
			\|-
			\| [[File:MotiveQuery-Fragments3.png\| 650px]]
			\|-
			\| After clicking fragment ID, all the additional informations are immediately visualized together with the fragment view.
			\|-
			\|}

			==Structure Details==
			'''Structure details''' tab provides a valuable information about fragment's parent structures. For example you can immediately access just fragments originating from a particular structure or structures. Filtering based on a variety of properties is available as well.

			{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
			\|-
			\| [[File:MotiveQuery-Fragments4.png\| 650px]]
			\| [[File:MotiveQuery-Fragments5.png\| 650px]]
			\|-
			\| Click on the '''By PDB Entry''' tab for inspecting PDB entry-wide results.
			\| The page is divided into a fully customizable table (by structure properties) and details for an individual structure.
			\|-
			\| [[File:MotiveQuery-Fragments6.png\| 650px]]
			\| [[File:MotiveQuery-Fragments7.png\| 650px]]
			\|-
			\| Filter the '''Fragment table''' by a structure validation report so as the fragment Id id. Click the structure id for inspecting greater details.
			\| Inspect additional details of the PDB structures in different resources, such as PDB.org database or Validator<sup>DB</sup> storing their ligand validation information.
			\|-
			\|}

Lukas at 16:48, 27 December 2014

2014-12-27T16:48:30Z

← Older revision		Revision as of 16:48, 27 December 2014
Line 32:		Line 32:
	\| As soon as you specify a query or queries and so data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here upon the calculation finishes.		\| As soon as you specify a query or queries and so data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here upon the calculation finishes.
	\|}		\|}
			<br style="clear:both" />

			=Specifics Page=

Lukas: /* Job Submission */

2014-12-27T16:46:30Z

Job Submission

← Older revision		Revision as of 16:46, 27 December 2014
Line 26:		Line 26:
	\|-		\|-
	\| You can to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please read carefully hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include a logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a sulfur atom and none nitrogen atom will be considered. Multiple filters can be applied at the same time.		\| You can to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please read carefully hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include a logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a sulfur atom and none nitrogen atom will be considered. Multiple filters can be applied at the same time.
	\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time.		\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time. Do '''not forget''' to click '''+ Add''' after you finish composing query.
	\|-		\|-
	\| [[File:MotiveQuery-Service5.png\| 650px]]		\| [[File:MotiveQuery-Service5.png\| 650px]]

Lukas: /* Job submission */

2014-12-27T16:44:37Z

Job submission

← Older revision		Revision as of 16:44, 27 December 2014
Line 12:		Line 12:
	<br style="clear:both" />		<br style="clear:both" />

	=Job submission=		=Job Submission=

			{\| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
			\|-
			\| [[File:MotiveQuery-Service1.png\| 650px]]
			\| [[File:MotiveQuery-Service2.png\| 650px]]
			\|-
			\| The UI of the '''MotiveQuery Service''' job submission page allows user to submit a new query calculation. First time user can take a look at some of the example queries. If you have run any calculations with '''MotiveQuery''' already, you can browse the results.
			\| At first, decide whether you would like to query an entire Protein Data Bank, its subset based on a variety of different properties, or you have a list of PDB entries of your interest.
			\|-
			\| [[File:MotiveQuery-Service3.png\| 650px]]
			\| [[File:MotiveQuery-Service4.png\| 650px]]
			\|-
			\| You can to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please read carefully hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include a logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a sulfur atom and none nitrogen atom will be considered. Multiple filters can be applied at the same time.
			\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time.
			\|-
			\| [[File:MotiveQuery-Service5.png\| 650px]]
			\|-
			\| As soon as you specify a query or queries and so data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here upon the calculation finishes.
			\|}

← Older revision		Revision as of 15:38, 20 April 2015
Line 1:		Line 1:
	'''Motive Query''' service is aimed for querying large datasets of structures from the [http://www.rcsb.org/pdb/home/home.do Protein Data Bank]. ~~For the perfecting~~ your query or ~~querying~~ smaller datasets or even user-uploaded data, please use [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] instead.		'''Motive Query''' service is aimed for querying large datasets of structures from the [http://www.rcsb.org/pdb/home/home.do Protein Data Bank]. To perfect your query or query smaller datasets or even user-uploaded data, please use [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] instead.

	If you would like to run '''MotiveQuery''' at your home institution, please download a [[MotiveQuery:Command_Line \| command-line]] version. The following visual will guide you through the process of submitting ~~you~~ calculation so as the interpreting results.		If you would like to run '''MotiveQuery''' at your home institution, please download a [[MotiveQuery:Command_Line \| command-line]] version. The following visual will guide you through the process of submitting your calculation so as the interpreting results.

	=Synopsis Page=		=Synopsis Page=
	[[File:MotiveQuery-Service0.png \| right \| thumb \| 650px\| '''MotiveQuery Service''' UI]]		[[File:MotiveQuery-Service0.png \| right \| thumb \| 650px\| '''MotiveQuery Service''' UI]]
	The '''MotiveQuery''' synopsis page is divided into a number of tabs:		The '''MotiveQuery''' synopsis page is divided into a number of tabs:
	* '''Quick Help''' and '''Samples''' tab ~~provides~~ information to help you orient ~~better~~.		* '''Quick Help''' and '''Samples''' tab provide information to help you orient yourself.
	* '''Support''' provides a simple user interface for asking questions related to a '''MotiveQuery''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application where you can tune up your queries before doing the database-wide searches.		* '''Support''' provides a simple user interface for asking questions related to a '''MotiveQuery''' language or service. We do our best to come back to your questions as soon as possible. '''Query Playground''' represents an interface for the [[MotiveQuery:MotiveExplorer \| MotiveQuery Explorer]] application where you can tune up your queries before doing the database-wide searches.
	* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''MotiveQuery''' calculation.		* '''Query Protein Data Bank''' is a simple interface for creating a database wide '''MotiveQuery''' calculation.
Line 20:		Line 20:
	\|-		\|-
	\| The UI of the '''MotiveQuery Service''' job submission page allows user to submit a new query calculation. First time user can take a look at some of the example queries. If you have run any calculations with '''MotiveQuery''' already, you can browse the results.		\| The UI of the '''MotiveQuery Service''' job submission page allows user to submit a new query calculation. First time user can take a look at some of the example queries. If you have run any calculations with '''MotiveQuery''' already, you can browse the results.
	\| At first, decide whether you would like to query an entire Protein Data Bank, ~~its~~ subset based on a variety of different properties, or ~~you have~~ a list of PDB entries of ~~your~~ interest.		\| At first, decide whether you would like to query the entire Protein Data Bank, a subset thereof based on a variety of different properties, or a user provided list of PDB entries of interest.
	\|-		\|-
	\| [[File:MotiveQuery-Service3.png\| 650px]]		\| [[File:MotiveQuery-Service3.png\| 650px]]
	\| [[File:MotiveQuery-Service4.png\| 650px]]		\| [[File:MotiveQuery-Service4.png\| 650px]]
	\|-		\|-
	\| You can to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please read ~~carefully~~ hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include a logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a sulfur atom and ~~none~~ nitrogen ~~atom~~ will be considered. Multiple filters can be applied at the same time.		\| You can to query a subset of Protein Data Bank based on numerous metadata. At first select a property you would like to filter by, then select a comparison method and finally fill in the demanded value. Please carefully read the hints and examples below each selected property. Different properties can have different means of providing input values. Note that you can also include logical expressions. For example: '''S & !N''' in ''Atom'' property means that just structures containing a sulfur atom and no nitrogen atoms will be considered. Multiple filters can be applied at the same time.
	\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time. Do '''not forget''' to click '''+ Add''' after you finish composing query.		\| Once you select a data set, you can specify multiple queries which will be executed. If you are unsure on how to compose a query, try one of the provided examples. You can also take a look into our [[MotiveQuery:How_to_build_a_query \| case studies]] or consult the [[MotiveQuery:Language_Reference \| language reference]]. In case none of these help, ask us a question via '''Support''' tab. We will be happy to answer you in the shortest possible time. Do '''not forget''' to click '''+ Add''' after you finish composing query.
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	\| [[File:MotiveQuery-Service5.png\| 650px]]		\| [[File:MotiveQuery-Service5.png\| 650px]]
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	\| As soon as you specify a query or queries and so data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here ~~upon~~ the calculation finishes.		\| As soon as you specify a query or queries and the data set, you can tick an option to validate all the ligands and non-standard residues for their structure integrity using [[ValidatorDB:UserManual \| Validator<sup>DB</sup>]] and, finally, submit the calculation. Based on the number of processed structures, the execution time can be in the range of minutes (thousands of structures) to an hour (whole Protein Data Bank). Bookmark the newly generated web address as the results will be available here once the calculation finishes.
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	'''Please continue reading to the [[MotiveQuery:Specifics Page \| Specifics page]], where you can find additional info on downloading and inspecting your results.		'''Please continue reading to the [[MotiveQuery:Specifics Page \| Specifics page]], where you can find additional info on downloading and inspecting your results.