Volume 2 Chapter 10 Search Menu PDB-SEARCH
Function
The PDB-SEQUENCE sub-menu is used to construct sequence based searches of the Brookhaven Protein Data Bank (PDB) entries, all of which have been converted into the QUEST ASER search format.
Basic QUEST Procedure
The equivalent test construction in Basic QUEST is discussed under *PDBSEQ.
It should be read carefully before using the Graphics QUEST3D interface.
Graphics QUEST3D Procedure
The PDB-SEQUENCE sub-menu is shown below.
This table summarises the buttons in the PEPTIDE-SEQ sub-menu.
Function
Button
PDEF Begins the specification of a user-defined amino acid group
("Peptide Definition").
If a red box is displayed around this button, you are
currently in the middle of building a "definition" of a new
amino acid type, and the prompt in the dialog area will show
the allowed amino-acids; otherwise, you are a building a
"sequence" of amino acids which will constitute your test,
and the prompt in the dialog area will show the sequence thus
far.
+ Specifies that subsequently selected amino-acids are to be
added to the definition.
- Specifies that subsequently selected amino-acids are to be
subtracted from the definition.
= Declares that the current PDEF is now complete. The
newly-defined group is shown in the "USER-DEFINED" section of
the menu, and may now be included in the sequence.
NON-STANDARD-CODE Prompts for an amino-acid or heterogen 3-character code, to
be added to the current sequence. The list of all known PDB
codes is searched, to ensure that a valid code was entered.
LEFT-END Sets the allowable bonding pattern at the left hand end of
Terminal[%] the sequence.
Non-terminal[-] Turning off both options is equivalent to selecting just
Terminal[%].
On first entering this sub-menu, both these options will be
turned on.
RIGHT-END Sets the allowable bonding pattern at the right hand end of
Terminal[%] the sequence.
Non-terminal[-] Turning off both options is equivalent to selecting just
Terminal[%].
On first entering this sub-menu, both these options will be
turned on.
EXHAUSTIVE_SEARCH By default, QUEST will only locate the first occurrence of
the given sequence in each entry in the database. By turning
on EXHAUSTIVE_SEARCH, QUEST is instructed to find every
location of the target sequence.
NO_OF_CHAINS If this command is used, QUEST will only search entries with
number of chains in a given range. For example, you may say
that the number of chains must be "> 3".
The recognised symbols are:
<> or .NE. "not equal to"
= or .EQ. "equal to"
<= or .LE. "less than or equal to"
< or .LT. "less than"
>= or .GE. "greater than or equal to"
> or .GT. "greater than"
Ð "between" (two numbers are required)
NO_OF_RESIDUES If this command is used, QUEST will only search chains with
number of residues in a given range. For example, you may
say that the number of residues must be ">=20".
The recognised symbols are:
<> or .NE. "not equal to"
= or .EQ. "equal to"
<= or .LE. "less than or equal to"
< or .LT. "less than"
>= or .GE. "greater than or equal to"
> or .GT. "greater than"
Ð "between" (two numbers are required)
FULL_CHAIN For brevity, the default text output from PDB sequence
searches shows only the portions of each chain which match
the target sequence.
The FULL_CHAIN command instructs QUEST to show the complete
sequences of chains matching the target sequence.
FULL_ALL For brevity, the default text output from PDB sequence
searches shows only the portions of each chain which match
the target sequence.
The FULL_ALL command instructs QUEST to show the complete
sequences of all chains, regardless of whether they match the
target sequence.
DELETE-LAST Removes the last residue from the sequence, or from the
definition if you are within PDEF.
DELETE-ALL Resets either the sequence or the definitions completely.
DEFINE-SEQUENCE Declares that the sequence is complete, and returns to the
PDB-SEARCH menu. The QUESTÉ command may then be selected to
start the search. See also FIND-SEQUENCE below.
FIND-SEQUENCE Declares that the sequence is complete, and immediately
starts searching for the sequence.
Volume 2 Chapter 10 Search Menu *PDBSEQ.