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<html>

<head>
<title>
ADD, EXP, EXPAND
</title>
</head>

<h1 align=center>

ADD, EXP, EXPAND

</h1>

<hr size="3">

<font color=#880000>
<b>
NAME
</b>
<br>

</font>


ADD, EXP, EXPAND - add specified atoms to current selection.
<br><br>


<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>


ADD chain_identifiers/residue_serials/residue_names/atom_names
<br>
ADD residue_ranges
<br>
ADD residue_names
<br>
ADD ATO atomic_ranges
<br>
ADD ATOMS atomic_ranges
<br>
ADD keyword
<br>
ADD ELE chemical_symbol
<br>
ADD ELEMENT chemical_symbol
<br><br>


<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>


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:
<br><br>

(1) detailed selection;
<br>
(2) selection by residue serial numbers;
<br>
(3) selection by residue names;
<br>
(4) special selection (by keyword);
<br>
(5) selection by chemical symbol;
<br>
(6) selection by atom serial number.
<br><br>


<font color=#880000>
<b>
DETAILED SELECTION
<br>
</b>
</font>


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:
<br><br>
chain_identifiers/residue_serials/residue_names/atom_names.
<br><br>
Both uppercase and lowercase characters are accepted. Space ( ), comma (,)
and semicolon (;) may be used as separators.
<br><br>

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.
<br><br>
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.
<br><br>
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.
<br><br>
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:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

add a/*/*/*

</td>

<td align="left">

Add all atoms from chain A to current selection.

</td>

<tr>

<td align="left">

add * exc m/*/*/ca

</td>

<td align="left">

Add CA atoms from all chains except chain M.

</td>

<tr>

<td align="left">

add */*/*/* exc ca,c,n,o

</td>

<td align="left">

Add all atoms except CA, C, N and O.

</td>

<tr>

<td align="left">

add a/* exc 72-112/*/ca

</td>

<td align="left">

Add CA atoms from chain A, but exclude residues from 72 to 112.

</td>
</table>

<br>

<font color=#880000>
<b>
SELECTION BY RESIDUE SERIAL NUMBERS
<br>
</b>
</font>


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:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

add 1-100

</td>

<td align="left">

Add residues from 1 to 100 to current selection.

</td>

<tr>

<td align="left">

add 1-100 exc 20-40

</td>

<td align="left">

Add residues 1-100 but exclude 20-40.

</td>

<tr>

<td align="left">

add 1, 4, 8, 11-48 exc 20-32

</td>

<td align="left">

Add residues 1, 4, 8 and 11-48 but exclude 20-32.

</td>

</table>

<br>

<font color=#880000>
<b>
SELECTION BY ATOMIC SERIAL NUMBERS
<br>
</b>
</font>


To add a single atom by the atomic serial number, combine the command
ADD and the keyword ATO (ATOMS). For example, to add the atom number 102
to the current selection type:
<br><br>

add ato 102
<br><br>

The same keyword may be used to add a range of atoms or to add two or
more ranges. Examples:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

add ato 1-100

</td>

<td align="left">

Add atoms which have serial numbers in the range between 1 and 100.

</td>

<tr>

<td align="left">

add 1-20 40-50

</td>

<td align="left">

Add atoms which have serial numbers between 1 and 20 and between 40 and 50.

</td>

</table>

<br>


Do not combine the keywords EXC (EXCLUDE) and ATO (ATOMS).
<br><br>


<font color=#880000>
<b>
SELECTION BY RESIDUE NAMES
<br>
</b>
</font>


Three letters code should be used. Asterisk (*) and keyword EXC (EXCEPT) are
not accepted. Example:
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

add phe,tyr,trp

</td>

<td align="left">

Add PHE, TYR and TRP to current selection.

</td>

</table>

<br>

<font color=#880000>
<b>
SPECIAL SELECTION KEYWORDS
<br>
</b>
</font>


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.
<br><br>


<table border=2 cellspacing=2 cellpading=0>

<td align="left">

add *
<br>
add all

</td>

<td align="left">

Add all atoms to current selection, i.e. select all.

</td>

<tr>

<td align="left">

add abo
<br>
add above

</td>

<td align="left">

Add atoms above the plane.

</td>

<tr>

<td align="left">

add aci
<br>
add acidic

</td>

<td align="left">

Add acidic amino acids (GLU and ASP).

</td>

<tr>

<td align="left">

add ali
<br>
add aliphatic

</td>

<td align="left">

Add aliphatic amino acids (ILE, LEU and VAL).

</td>

<tr>

<td align="left">

add alt

</td>

<td align="left">

Add atoms at alternate positions.

</td>

<tr>

<td align="left">

add bad

</td>

<td align="left">

Add bad residues. A residue is treated as bad if the
<br>
peptide bond assigned to this residue is non-planar.
<br>
The peptide bond is non-planar if the omega angle is
<br>
different for 20 or more degrees from 0 or 180 degrees.

</td>

<tr>

<td align="left">

add bas
<br>
add basic

</td>

<td align="left">

Add basic amino acids (ARG, LYS and HIS).

</td>

<tr>

<td align="left">

add bel
<br>
add below

</td>

<td align="left">

Add atoms below the plane.

</td>

<tr>

<td align="left">

add cha
<br>
add charged

</td>

<td align="left">

Add charged amino acids (ARG, LYS, HIS, GLU and ASP).

</td>

<tr>

<td align="left">

add cis

</td>

<td align="left">

Add cis residues.

</td>

<tr>

<td align="left">

add com
<br>
add complement

</td>

<td align="left">

Add atoms which were not select previously.

</td>

<tr>

<td align="left">

add het
<br>
add hetero

</td>

<td align="left">

Add hetero atoms (heme groups, water etc.).

</td>

<tr>

<td align="left">

add pho
<br>
add hydrophobic

</td>

<td align="left">

Add hydrophobic amino acids
<br>
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).

</td>

<tr>

<td align="left">

add mai
<br>
add main_chain

</td>

<td align="left">

Add main chain atoms (CA, C, N and O).

</td>

<tr>

<td align="left">

add mod serial_number
<br>
add model serial_number

</td>

<td align="left">

Add model specified by serial_number.
<br>
NMR structure is a set of models. Example: add mod 1

</td>

<tr>

<td align="left">

add neg
<br>
add negative

</td>

<td align="left">

Add negatively charged amino acids (GLU and ASP).

</td>

<tr>

<td align="left">

add pat
<br>
add pattern

</td>

<td align="left">

Add the sequence pattern. The command
<br>
<a href="pat.html">
PAT (PATTERN)
</a>
is used to define the sequence pattern.

</td>

<tr>

<td align="left">

add pol
<br>
add polar

</td>

<td align="left">

Add polar amino acids
<br>
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).

</td>

<tr>

<td align="left">

add pos
<br>
add positive

</td>

<td align="left">

Add positively charged amino acids (ARG, LYS and HIS).

</td>

<tr>

<td align="left">

add seq
<br>
add sequence

</td>

<td align="left">

Add sequence fragments which match the sequence stored
<br>
to the sequence buffer. The sequence buffer should be
<br>
initialized before executing this command.

</td>

<tr>

<td align="left">

add sid
<br>
add side_chains

</td>

<td align="left">

Add atoms which belong to side chains (all except CA, C, N and O).

</td>

<tr>

<td align="left">

add sma
<br>
add small

</td>

<td align="left">

Add small amino acids
<br>
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).

</td>

<tr>

<td align="left">

add sph
<br>
add sphere

</td>

<td align="left">

Add atoms inside the sphere. Use the command
<br>
<a href="rad.html">
RAD (RADIUS)
</a>
to set the sphere radius.

</td>

<tr>

<td align="left">

add tin
<br>
add tiny

</td>

<td align="left">

Add tiny amino acids (GLY,ALA and SER).

</td>

<tr>

<td align="left">

add tm

</td>

<td align="left">

Add the transmembrane part
<br>
(useful for membrane proteins).

</td>

<tr>

<td align="left">

add tra
<br>
add trans

</td>

<td align="left">

Add trans residues.

</td>

<tr>

<td align="left">

add tri
<br>
add triplet

</td>

<td align="left">
If there are three (or more)
<font color="red"><b>positively charged</b></font>
residues in a fragment
<br>
of up to five protein residues, add these residues to the current set
<br>
of selected atoms. Detailed explanation may found in the article:
<br>
D. Juretic, L. Zoranic and D. Zucic,
<br>
Basic charge clusters and predictions of membrane protein topology,
<br>
<a href="http://pubs3.acs.org/acs/journals/toc.page?incoden=jcisd8&indecade=0&involume=42&inissue=3">
Journal of Chemical Information and Computer Sciences 42, No. 3,
</a>
<br>
620-632 (2002).
</a>
</td>

<tr>

<td align="left">
add 2c3
</td>

<td align="left">
If there are two (or more)
<font color="red"><b>charged</b></font>
residues in a fragment of
<br>
three residues, add these residues to the current selection.
</td>

<tr>

<td align="left">
add 2cz3
</td>

<td align="left">
If there are two (or more)
<font color="red"><b>charged or zwitterionic</b></font>
residues in
<br>
a fragment of three residues, add these residues to the current
<br>
selection.
</td>

<tr>

<td align="left">
add 2nz3
<br>
add 3c4
<br>
add 3cz4
<br>
add 3nz4
<br>
add 3c5
<br>
add 3cz5
<br>
add 3nz5
<br>
add 3p5
<br>
add 4c5
<br>
add 4cz5
<br>
add 4nz5
<br>
add 3c6
<br>
add 3cz6
<br>
add 3nz6
<br>
add 4c6
<br>
add 4cz6
<br>
add 4nz6
<br>
add 5c6
<br>
add 5cz6
<br>
add 5nz6
<br>
add 4c7
<br>
add 4cz7
<br>
add 4nz7
<br>
add 5c7
<br>
add 5cz7
<br>
add 5nz7
<br>
add 5p7
<br>
add 6p7
<br>
add 4c9
<br>
add 4cz9
<br>
add 4nz9
<br>
add 5c9
<br>
add 5cz9
<br>
add 5nz9
</td>

<td align="left">
Analogous to add 2c3 and add 2cz3, where c stands for
<font color="red"><b>charged</b></font>
,
<br>
cz for
<font color="red"><b>charged or zwitterionic</b></font>
, nz for 
<font color="red"><b>negative or zwitterionic</b></font>
<br>
and p for
<font color="red"><b>polar</b></font>
. The same selection criteria may be defined
<br>
using patterns, but these short keywords are more practical.
</td>

<tr>

<td align="left">
add 3p5
</td>

<td align="left">
If there are three or more
<font color="red"><b>polar</b></font>
residues in a fragment of five residues,
<br>
add these residues. The following residues are treated as polar:
<br>
ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
</td>

<tr>

<td align="left">
add 5p7
</td>

<td align="left">
If there are five or more
<font color="red"><b>polar</b></font>
residues in a fragment of five residues,
<br>
add these residues to the current selection. The following residues are
<br>
treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR,
<br>
TYR and TRP.
</td>

<tr>

<td align="left">
add 6p7
</td>

<td align="left">
If there are six or more
<font color="red"><b>polar</b></font>
residues in a fragment of five residues,
<br>
add these residues to the current selection. The following residues are
<br>
treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR,
<br>
TYR and TRP.
</td>

</table>

<br>

<font color=#880000>
<b>
EXPANDING SELECTION WITH
<br>
THE SPECIFIED CHEMICAL ELEMENT
<br>
</b>
</font>


To add certain chemical element to the selection, use the keyword ELEMENT
(short form: ELE) and the standard chemical symbol. To expand your selection
with iron atoms, for example, you should type the following command:
<br><br>

add ele fe
<br><br>

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.
<br><br>


<font color=#880000>
<b>
NOTES
<br>
</b>
</font>


(1) The command ADD resets the editing mode to default (no editing).
<br><br>


<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>


EXPAND does exactly the same job as ADD. SELECT overwrites the previous
selection. RESTRICT restrics the previous selection.
<br><br>


<hr size="3">

</html>