# 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 ATO atomic_ranges
SEL keyword
SEL ELE chemical_symbol
SELECT chain_identifiers/residue_serials/residue_names/atom_names
SELECT residue_ranges
SELECT residue_names
SELECT ATOMS atomic_ranges
SELECT keyword
SELECT ELEMENT chemical_symbol
DESCRIPTION
Select specified atoms. Atoms are selected according to the specified cryteria. Six types of selection are available:
(1) detailed selection;
(2) selection by residue serial numbers;
(3) selection by residue names;
(4) special selection (by keyword);
(5) selection by chemical symbol;
(6) selection by atom serial number.
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 ATOMIC SERIAL NUMBERS
To select a single atom by the atomic serial number, combine the command SEL (SELECT) and the keyword ATO (ATOMS). For example, to select the atom number 102 type:
sel ato 102
The same keyword may be used to select a range of atoms or two or more ranges. Examples:

sel ato 1-100 | Select atoms which have serial numbers in the range between 1 and 100.
sel 1-20 40-50 | Select atoms which have serial numbers between 1 and 20 and between 40 and 50.

Do not combine the keywords EXC (EXCLUDE) and ATO (ATOMS).
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 pat sel pattern | Select the sequence pattern. The command PAT (PATTERN) is used to define the sequence pattern.
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 tm | Select the transmembrane part (useful for membrane proteins).
sel tra sel trans | Select trans residues.
sel tri sel triplet | If there are three (or more) positively charged residues in a fragment of up to five protein residues, select these residues. Detailed explanation may be found in the article: D. Juretic, L. Zoranic and D. Zucic, Basic charge clusters and predictions of membrane protein topology, Journal of Chemical Information and Computer Sciences 42, No. 3, 620-632 (2002).
sel 2c3 | If there are two (or more) charged residues in a fragment of three residues, select these residues.
sel 2cz3 | If there are two (or more) charged or zwitterionic residues in a fragment of three residues, select these residues.

sel 2nz3
sel 3c4
sel 3cz4
sel 3nz4
sel 3c5
sel 3cz5
sel 3nz5
sel 3p5
sel 4c5
sel 4cz5
sel 4nz5
sel 3c6
sel 3cz6
sel 3nz6
sel 4c6
sel 4cz6
sel 4nz6
sel 5c6
sel 5cz6
sel 5nz6
sel 4c7
sel 4cz7
sel 4nz7
sel 5c7
sel 5cz7
sel 5nz7
sel 5p7
sel 6p7
sel 4c9
sel 4cz9
sel 4nz9
sel 5c9
sel 5cz9
sel 5nz9

Analogous to sel 2c3 and sel 2cz3, where c stands for charged ,
cz for charged or zwitterionic , nz for negative or zwitterionic
and p for polar . The same selection criteria may be defined
using patterns, but these short keywords are more practical.

sel 3p5 | If there are three or more polar residues in a fragment of five residues, select these residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
sel 5p7 | If there are five or more polar residues in a fragment of seven residues, select these residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
sel 6p7 | If there are six or more polar residues in a fragment of seven residues, select these residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.

SELECTING CHEMICAL ELEMENTS
To select certain chemical element, use the keyword ELEMENT (short form: ELE) and the standard chemical symbol. To select iron, for example, you should type the following command:
sel ele fe
In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain. By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. Note that symbols J and Q are not used in the periodic table of elements.
NOTES
(1) The command SELECT resets the editing mode to default (no editing).
(2) The keyword TM may be used to select the transmembrane part of the protein. In addition to the atoms which lay between two planes which define the membrane, some outside atoms will be taken into account, if they don't lay more than two anstroms from the nearest plane. This should ensure that some hydrophobic residues close to the edge will not be excluded from the selection.
RELATED COMMANDS
ADD expands the previous selection. RESTRICT restrics the previous selection.