Query Refinements Help

You may understand and further refine your query results by using the "drill-downs" by category, the "Refine Query" form or "Remove Similar" drop down menu.

Drill-down

The "drill-down" charts and links aim to give an insight of the main characteristics of the PDB entries in the query results and enable to easily focus on the subset of interest.

Clicking on the small summary charts which are available for some of the most important characteristics of PDB entries, will reveal more detailed summary information and links that can be used to refine results with a single mouse click. (see image)

Moving the mouse cursor over the drill down links and the small chart icon, will pop-up more detailed charts, while by clicking again on the chart icons, will focus in a large chart image of the data distribution for this category. (see image)

The "drill-downs" aim to be simple rather than complete and provide a small number of drill-down options. Drill-down groups of small size, are not even displayed in the charts.

Drilling down by clicking on a link will either present more granular drill-down options, or a "inactive" label that indicates that further drill down is not possible since all results belong in a single group. (see image)

Note: For categories of numbers or dates like resolution or release date, the drill down links include the lower bound value but do not include the upper bound value. So for example the drill-down of 1.5-2.0 Armstrong, will include the entries with exactly 1.5 resolution but not the ones with exactly 2.0 resolution (these will be included in the next 2.0-2.5 group)

If the available drill-down options are not satisfactory, clicking on the alternative "more choices ..." link will display the "Refine Query" form for the corresponding category, where it is possible to refine the query more precisely.

 

Drill-down Categories

  • Resolution
    Initial groups are: less than 1.5, 1.5-2.0, 2.0-2.5, 2.5-3.0 and more than 3. If the user drills down inside a group (or all the results belong to a single group), then there will be at most 6 groups of almost equal size (1 decimal digit). The groups are lower bound inclusive and upper bound exclusive, so the entries will resolution 2.0 are in the 2.0-2.5 group (and not in the 1.5-2.0 group)
  • Release Date
    Groups are: before 2000, 2000-2005, 2005-2010, 2010 and later. Drilling down on one of them presents yearly groups (decade groups for before 2000) and drilling down further presents monthly groups. The groups are lower bound inclusive and upper bound exclusive, so the entries of 2005 are in the 2005-2010 group (and not in the 2000-2005 group)
  • Experimental Method
  • Polymer type
    Complexes with polymers of different types are presented separately. So the "drill-down" link "Protein" will result in pure protein entries.
  • Organism
    The exact organisms/strains assigned to a PDB entry are presented. Drilling down on the "Escherichia coli" link for example will not result in entries of E. Coli strains (otherwise these entries would be counted twice in the charts). The "Other" drill-down link can be used to exclude the presented groups from the results, and allows to navigate over organisms.
    On the root level, organism groups include cases of hybrid entries (cases where an entry has a polymer chain of this organism and a polymer chain from another organism).
    But when the user drills-down on a single organism (all results include that organism) the hybrid entries are listed explicitly.
    For instance the initial grouping may display "Homo Sapiens (10)" but when the user drills down, he may get "Homo Sapiens (8)", "Homo Sapiens / E. Coli (2)". In the second drill down, the "Homo Sapiens" link will include the entries that are pure human (see image)
  • Taxonomy
    Gives the taxonomic group of an entry: one of, Eukaryota, Bacteria, Viruses, Archaea, Other. Again for hybrid entries, the root drill-down will not display hybrid cases explicitely but drilling down in a group will show these up. (see image)
  • Sequence length
    This is only used for sequence/polymer results (for example when someone does a sequence search)

 

Refine Query

This link will present the advanced search interface, which will list all the search criteria of the current query.

Using this form you may change parameters of these criteria, remove any that you wish or add new criteria from the available "Query types".

For more information for Advanced Search look at the Advanced Search Overview

 

Remove Similar

Filter search results based on sequence similarity and keep only "unique" structures.

Selecting a percent value from the pull down menu will filter the search results in such a way that multiple structures whose sequences have at least the specified level of sequence identity will be represented by a single structure.

For further information on the methodology used for clustering and ranking sequence similar structures in the PDB, see Redundancy in the Protein Data Bank.

 

 

Drill-down chart examples


Mouse over the chart icons and drill-down links to reveal more detailed chart images

 

 


Click on the drill-down links to restrict the query results

 

 


Drilling down on a group may reveal more granular options