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.