Volume 2 Chapter 10 Search Menu NUMERIC
Function
The PDB-SEARCH sub-menu is used to construct bibliographic and other simple searches of the Brookhaven Protein Data Bank (PDB) entries, all of which have been converted into the QUEST ASER search format.
When QUEST is used to search the PDB, the program will automatically start in this menu.
Only a subset of the available QUEST commands are applicable when searching the PDB. For example, there are no chemical or crystallographic structures stored in the PDB ASER file, so a connectivity search is guaranteed to produce no hits at all.
The PDB-SEARCH menu is customised to provide easy access to all the non-sequence data stored in the PDB ASER file.
Graphics QUEST3D Procedure
The PDB-SEARCH sub-menu is shown below.
This table summarises the buttons in the PDB-SEARCH sub-menu.
Function
Button
PDB-ID-CODE Prompts for a PDB ID code, for example, 1YCC, to be
located in the PDB ASER database. Each entry's PDB ID
code is stored in the form: ID-1YCC in the ASER *QUALIFIER
field.
*REFCODE Prompts for a CCDC reference code (refcode) to be located
in the PDB ASER database. Each entry's PDB ID code is
converted to a 6 character refcode by prefixing the PDB ID
code with a zero, suffixing it with a zero, and moving the
PDB numerical prefix to the end of the refcode. For
example, 1YCC becomes 0YCC01. This is done so that
related PDB entries (1YCC, 2YCC, etc.) will be grouped
together when the ASER file is sorted into alphanumeric
order by refcode.
SEQUENCE-SEARCH... Enters the PDB-SEQUENCE search menu, which is described in
the new manual pages 10-27aÉ
COMPND Prompts for some text to be located in the PDB COMPND
field.
For example, the PDB line:
COMPND CYTOCHROME C (ISOZYME 1) (REDUCED)
will be stored as follows in the database as:
Cytochrome c (isozyme 1) (reduced)
SOURCE Prompts for some text to be located in the PDB SOURCE
field.
For example, the PDB line:
SOURCE BAKER'S YEAST (SACCHAROMYCES $CEREVISIAE)
will be stored as follows in the database as:
Source: Baker's yeast (Saccharomyces cerevisiae)
CLASSIFICATION Prompts for some text to be located in the PDB functional
classification field.
For example, the PDB line:
HEADER ELECTRON TRANSPORT (CYTOCHROME)
will be stored as follows in the database as:
Class:Electron transport (cytochrome)
CONTRIBUTOR Prompts for some text to be located in the PDB data
contributors field.
For example, the PDB line:
AUTHOR G.V.LOUIE,G.D.BRAYER
will be stored as follows in the database as:
Data contributed by G.V.Louie,G.D.Brayer
DEPOSITION-DATE Prompts for some text to be located in the PDB deposition
date field. This is stored as text in the ISO format (2
digits for year, 2 digits for month, 2 digits for date),
and so searches on ranges of dates are not possible.
For example, the date in the PDB line:
HEADER ELECTRON TRANSPORT (CYTOCHROME)
09-MAY-90 1YCC 1YCC 2
will be stored as follows in the database as:
Deposition date 900509
*JRNL Each of these buttons prompts for information to be
*CODEN located from the PDB JRNL field.
*VOLUME
*YEAR For example, the PDB field:
*AUTHOR JRNL AUTH G.V.LOUIE,G.D.BRAYER
JRNL TITL HIGH-RESOLUTION REFINEMENT OF YEAST
JRNL TITL 2 ISO-1-*CYTOCHROME $C AND COMPARISONS WITH
OTHER
JRNL TITL 3 EUKARYOTIC CYTOCHROMES $C
JRNL REF J.MOL.BIOL. V. 214 527
1990
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836
070
will be stored as follows in the database as:
*JRNL = J.Mol.Biol.,
*CODEN = 70
*VOLUME = 214
*PAGE = 527
*YEAR = 1990
*AUTH = G.V.Louie,G.D.Brayer
*SURNAME Prompts for a complete surname to be located in the PDB
JRNL/AUTH field (as opposed to *AUTHOR which searches for
substrings of this PDB field). *SURNAME is particularly
useful when searching for very short names.
RESOLUTION Prompts for a resolution (in ngstroms) to be located.
Note that since the resolution is stored as text in the
database, it is not possible to search for ranges of
values.
For example, the PDB line:
REMARK 2 RESOLUTION. 1.23 ANGSTROMS.
will be stored as follows in the ASER *QUALIFER field:
Resolution 1.23A
NMR There is no prompt for this command. It immediately
creates a QUEST *QUALIFIER test, searching for the text
"Experimental:NMR".
For example, the PDB line:
EXPDTA NMR
will be stored as follows in the database as:
Experimental:NMR
THEORETICAL-MODEL There is no prompt for this command. It immediately
creates a QUEST *QUALIFIER test, searching for the text
"Experimental:theoretical model".
For example, the PDB line:
EXPDTA THEORETICAL MODEL
will be stored as follows in the database as:
Experimental:theoretical model
MAXIMUM-HITS Prompts for the maximum number of "hit" entries allowable
during this QUEST search.
BEGIN-AT-REFCODE Prompts for a refcode from which subsequent QUEST searches
will start. Note that the given refcode does not have to
exist in the database; the next entry in alphabetical
order after the given refcode will be used.
HITALL&START Declares that every entry in the PDB database should be a
"hit", and starts "browsing" immediately.
FASTQUEST For a description of this command, see Section 10, Page
13, Volume 2 of the Cambridge Structural Database System
documentation.
QUEST... For a description of this command, see Section 10, Page
46, Volume 2 of the Cambridge Structural Database System
documentation.
Volume 2 Chapter 10 Search Menu PDB-SEQUENCE.