SEL, SELECT

NAME
SEL, SELECT - select specified atoms. Overwrite the previous selection.

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

DESCRIPTION
Select specified atoms. Atoms are selected according to the specified cryteria. Four types of selection are available:

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

DETAILED SELECTION
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 selection 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 select all chains. The keyword EXC (EXCEPT) may be used to exclude one or more chains from selection.

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 selection.

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 selection. 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 select all atoms, while EXC may be used to exclude some atoms from selection. Examples:

sel a///*	Select all atoms from chain A.
*sel exc m///ca**	Select CA atoms from all chains except chain M.
*sel ///* exc ca,c,n,o**	Select all atoms except CA, C, N and O.
*sel a/ exc 72-112//ca*	Select CA atoms from chain A, but exclude residues from 72 to 112.

SELECTION BY RESIDUE SERIAL NUMBERS
To select all atoms in a single residue, a residue range or in a number of residues and residue ranges, a simple syntax may be used. The selection string 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:

sel 1-100	Select residues from 1 to 100.
sel 1-100 exc 20-40	Select residues 1-100 but exclude 20-40.
sel 1, 4, 8, 11-48 exc 20-32	Select residues 1, 4, 8 and 11-48 but exclude 20-32.

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

sel phe,tyr,trp

Select PHE, TYR and TRP.

SPECIAL SELECTION KEYWORDS
Some special keywords may be combined with SEL (SELECT) to select residues or atoms according to some properties. It is also possible to select the complement, i.e. all atoms which were not selected previously. A single keyword should be used; asterisk (*) and keyword EXC (EXCEPT) are not accepted.

sel * sel all	Select all atoms (select all).
sel abo sel above	Select atoms above the plane.
sel aci sel acidic	Select acidic amino acids (GLU and ASP).
sel ali sel aliphatic	Select aliphatic amino acids (ILE, LEU and VAL).
sel alt	Select atoms at alternate positions.
sel bad	Select 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.
sel bas sel basic	Select basic amino acids (ARG, LYS and HIS).
sel bel sel below	Select atoms below the plane.
sel cha sel charged	Select charged amino acids (ARG, LYS, HIS, GLU and ASP).
sel cis	Select cis residues.
sel com sel complement	Select atoms which were not selected previously.
sel het sel hetero	Select hetero atoms (heme groups, water etc.).
sel pho sel hydrophobic	Select hydrophobic amino acids (ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
sel mai sel main_chain	Select main chain atoms (CA, C, N and O).
sel mod serial_number sel model serial_number	Select model specified by serial_number. NMR structure is a set of models. Example: sel mod 1
sel neg sel negative	Select negatively charged amino acids (GLU and ASP).
sel pol sel polar	Select polar amino acids (ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
sel pos sel positive	Select positively charged amino acids (ARG, LYS and HIS).
sel seq sel sequence	Select sequence fragments which match the sequence stored to the sequence buffer. The sequence buffer should be initialized before executing this command.
sel sid sel side_chains	Select atoms which belong to side chains (all except CA, C, N and O).
sel sma sel small	Select small amino acids (GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
sel sph sel sphere	Select atoms inside the sphere. Use the command RAD (RADIUS) to set the sphere radius.
sel tin sel tiny	Select tiny amino acids (GLY, ALA and SER).
sel tra sel trans	Select trans residues.

RELATED COMMANDS
ADD expands the previous selection. RESTRICT restrics the previous selection.