RES, RESTRICT

NAME
RES, RESTRICT - restrict the current selection.

SYNOPSIS
RES chain identifiers/residue serials/residue names/atom names
RES residue_ranges
RES residue_names
RES keyword

DESCRIPTION
Restrict the current selection. Atoms which do not satisfy the specified cryteria are excluded from selection. Four types of restriction cryteria may be used:

(1) detailed restriction;
(2) restriction by residue serial numbers;
(3) restriction by residue names;
(4) special restriction (by keyword).

DETAILED RESTRICTION
In this case four data types are specified simultaneously: chain identifiers, residue serial numbers, residue names and atom names. It is not possible to specify atomic serial numbers. The string should contain exactly three slashes, separating different data types:

chain identifiers/residue serials/residue names/atom names.

Both uppercase and lowercase characters are accepted. Space ( ), comma (,) and semicolon (;) may be used as separators.

Chain identifiers are single alphabetic characters. Asterisk (*) may be used to specify all chains. The keyword EXC (EXCEPT) may be used to exclude one or more chains from restriction.

Residue serial numbers consist of digits. Minus may be used to specify a range of residue serial numbers. For example, 1-100 specifyes residues from 1 to 100, including these two. Asterisk (*) may be used to specify all residue serials. The keyword EXC (EXCEPT) may be used to exclude serial numbers or ranges from restriction.

Residue names are expected in three letters code. Asterisk (*) may be used to specify all residue names. The keyword EXC (EXCEPT) may be used to exclude one or more names from restriction. Non-standard names are accepted.

The names of atoms are expected as used in the input file; do not replace them with pure chemical symbols. C alpha, for example, should be specified as CA or ca (case is not important), if coordinates are read from PDB file. Asterisk (*) may be used to specify all atoms, while EXC may be used to exclude some atoms from this specification. Examples:

res a///*	Leave only atoms which belong to chain A.
*res exc m///ca**	Leave only CA atoms which belong to chain M.
*res ///* exc ca,c,n,o**	Remove CA, C, N and O atoms from the selection.
*res a/ exc 72-112//ca*	Leave only CA atoms which belong to chain A, but exclude residues 72-112.

RESTRICTION BY RESIDUE SERIAL NUMBERS
In this type of selection restriction, residue numbers, residue ranges or residue names may be specified. The restriction cryteria should contain no slashes. Keyword EXC (EXCEPT) is accepted, but asterisk (*) will be missintepreted. Minus may be used to specify residue ranges. Comma (,), semicolon (;) and space ( ) may be used as separators. Examples:

res 1-100	Leave only atoms which belong to residues from 1 to 100.
res 1-100 exc 20-40	Leave only atoms which belong to residues 1-100, but exclude 20-40.
res 1, 4, 8, 11-48 exc 20-32	Leave atoms which belong to residues 1, 4, 8, 11-48 but exclude residues 20-32.

RESTRICTION BY RESIDUE NAMES
Three letters code should be used. Asterisk (*) and keyword EXC (EXCEPT) are not accepted. Example:

res phe,tyr,trp

Restrict selection to PHE, TYR and TRP.

SPECIAL RESTRICTION KEYWORDS
Some special keywords may be combined with RES to specify residues or atoms according to some properties. A single keyword should be used; asterisk (*) and keyword EXC (EXCEPT) are not accepted. COM (COMPLEMENT) may be specified, but restriction to complement means that nothing will be left in the selection. Examples:

res * res all	Leave the selection unchanged (trivial, useless).
res abo res above	Restrict to atoms above the plane.
res aci res acidic	Leave only acidic amino-acids in the selection (GLU and ASP).
res ali res aliphatic	Leave only aliphatic amino acids (ILE, LEU and VAL).
res alt	Restrict to atoms at alternate positions.
res bad	Restrict selection to bad residues. A residue is treated as bad if the peptide bond assigned to this residue is non-planar. The peptide bond is non-planar if the omega angle is different for 20 or more degrees from 0 or 180 degrees.
res bas res basic	Leave only basic amino acids (ARG, LYS and HIS).
res bel res below	Restrict to atoms below the plane.
res cha res charged	Leave only charged amino acids (ARG, LYS, HIS, GLU and ASP).
res cis	Restrict selection to cis residues.
res com res complement	Leave only atoms which were not select previously.
res het res hetero	Leave only hetero atoms (heme groups, water etc.).
res pho res hydrophobic	Leave only hydrophobic amino acids (ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
res mai res main_chain	Leave only main chain atoms (CA, C, N and O).
res mod serial_number res model serial_number	Restrict to a model specified by serial_number. NMR structure is a set of models. Example: res mod 1
res neg res negative	Leave only negatively charged amino acids (GLU and ASP).
res pol res polar	Leave only polar amino acids (ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
res seq res sequence	Restrict to sequence fragments which match the sequence stored to the sequence buffer. The sequence buffer should be initialized before executing this command.
res pos res positive	Leave only positively charged amino acids (ARG, LYS and HIS).
res sid res side_chains	Leave only atoms which belong to side chains (all except CA, C, N and O).
res sma res small	Leave only small amino acids (GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
res sph res sphere	Restrict to the atoms inside the sphere. Use the command RAD (RADIUS) to set the sphere radius.
res tin res tiny	Leave only tiny amino acids (GLY,ALA and SER).
res tra res trans	Restrict selection to trans residues.

RELATED COMMANDS
SELECT overwrites the previous selection. ADD expands the previous selection.