PatternQuery:Specifics Page: Difference between revisions

Latest revision as of 10:10, 27 April 2015

The PatternQuery specifics page provides detailed information about detected patterns 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


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, as well 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 result (no issues, missing atoms, chirality issues) as well as the PDB id. Click the structure id for inspecting greater details.

Go to the Details tab in order to inspect individual patterns and their details.

Pattern Details

Pattern details tab provides valuable information about the composition and origin of the pattern. The structure validation report is provided for your convenience for all ligands and non-standard residues larger 6 atoms as well.


Select one of the queries for inspecting individual patterns. Browse the Pattern table and inspect details of particular pattern as well as its visualization.	Filter the Pattern table by a structure validation result (no issues, missing atoms, chirality issues) as well as the pattern 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.

After clicking pattern ID, all the additional informations are immediately visualized together with the pattern view.

Structure Details

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


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.

Filter the Pattern table by a structure validation result (no issues, missing atoms, chirality issues) as well as the pattern 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^DB storing their ligand validation information.

@@ Line 1: / Line 1: @@
-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.
+The '''PatternQuery''' specifics page provides detailed information about detected patterns 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==
@@ Line 5: / Line 5: @@
 {| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
   |-
-  | [[File:MotiveQuery-Service-Results1.png| 650px]]
+  | [[File:PatternQuery-Service-Results1.png| 650px]]
-  | [[File:MotiveQuery-Service-Results2.png| 650px]]
+  | [[File:PatternQuery-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, as well as the calculation setup are highlighted below. Click '''Query PDB Entry Details''' for inspecting further details of all of the input PDB structures.
+  | 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, as well 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 result (no issues, missing atoms, chirality issues) as well as the PDB id. Click the structure id for inspecting greater details.
   |-
-  | [[File:MotiveQuery-Service-Results3.png| 650px]]
+  | [[File:PatternQuery-Service-Results3.png| 650px]]
   |-
-  | Go to the '''Details''' tab in order to inspect individual fragments and their details.
+  | Go to the '''Details''' tab in order to inspect individual patterns and their details.
   |}
-==Fragment Details==
+==Pattern Details==
-'''Fragment details''' tab provides valuable information about the composition and origin of the fragment. The structure validation report is provided for your convenience for all ligands and non-standard residues larger 6 atoms as well.
+'''Pattern details''' tab provides valuable information about the composition and origin of the pattern. The structure validation report is provided for your 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:PatternQuery-Patterns1.png| 650px]]
-  | [[File:MotiveQuery-Fragments2.png| 650px]]
+  | [[File:PatternQuery-Patterns2.png| 650px]]
   |-
-  | Select one of the queries for inspecting individual fragments.  Browse the '''Fragment table''' and inspect details of particular fragment as well as its visualization.
+  | Select one of the queries for inspecting individual patterns.  Browse the '''Pattern table''' and inspect details of particular pattern as well as its visualization.
-  | Filter the '''Fragment table''' by a structure validation result (no issues, missing atoms, chirality issues) as well 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.
+  | Filter the '''Pattern table''' by a structure validation result (no issues, missing atoms, chirality issues) as well as the pattern 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]]
+  | [[File:PatternQuery-Patterns3.png| 650px]]
   |-
-  | After clicking fragment ID, all the additional informations are immediately visualized together with the fragment view.
+  | After clicking pattern ID, all the additional informations are immediately visualized together with the pattern 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.
+'''Structure details''' tab provides a valuable information about pattern's parent structures. For example you can immediately access just patterns 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:PatternQuery-Patterns4.png| 650px]]
-  | [[File:MotiveQuery-Fragments5.png| 650px]]
+  | [[File:PatternQuery-Patterns5.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:PatternQuery-Patterns6a.png| 650px]]
-  | [[File:MotiveQuery-Fragments7.png| 650px]]
+  | [[File:PatternQuery-Patterns7.png| 650px]]
   |-
-  | Filter the '''Fragment table''' by a structure validation result (no issues, missing atoms, chirality issues) as well as the fragment id. Click the structure id for inspecting greater details.
+  | Filter the '''Pattern table''' by a structure validation result (no issues, missing atoms, chirality issues) as well as the pattern 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.
   |-
   |}