ADD, EXP, EXPAND

NAME
ADD, EXP, EXPAND - add specified atoms to current selection.

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

DESCRIPTION
Add specified atoms to current selection. Atoms are added according to the specified cryteria. The command EXPAND does exactly the same job as ADD. The essential difference between ADD and SELECT is that ADD does not overwrite the previous selection. 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:

add a///*	Add all atoms from chain A to current selection.
*add exc m///ca**	Add CA atoms from all chains except chain M.
*add ///* exc ca,c,n,o**	Add all atoms except CA, C, N and O.
*add a/ exc 72-112//ca*	Add 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:

add 1-100	Add residues from 1 to 100 to current selection.
add 1-100 exc 20-40	Add residues 1-100 but exclude 20-40.
add 1, 4, 8, 11-48 exc 20-32	Add 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:

add phe,tyr,trp

Add PHE, TYR and TRP to current selection.

SPECIAL SELECTION KEYWORDS
Some special keywords may be combined with ADD 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.

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

RELATED COMMANDS
EXPAND does exactly the same job as ADD. SELECT overwrites the previous selection. RESTRICT restrics the previous selection.