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<html>

<head>
<title>
SEL, SELECT
</title>
</head>

<h1 align=center>

SEL, SELECT

</h1>

<hr size="3">

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


SEL, SELECT - select specified atoms. Overwrite the previous selection.
<br><br>


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


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


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


Select specified atoms. Atoms are selected according to the specified
cryteria. Six 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">


sel a/*/*/*

</td>

<td align="left">


Select all atoms from chain A.

</td>

<tr>

<td align="left">


sel * exc m/*/*/ca

</td>

<td align="left">


Select CA atoms from all chains except chain M.

</td>

<tr>

<td align="left">


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

</td>

<td align="left">


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

</td>

<tr>

<td align="left">


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

</td>

<td align="left">


Select 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">


sel 1-100

</td>

<td align="left">


Select residues from 1 to 100.

</td>

<tr>

<td align="left">


sel 1-100 exc 20-40

</td>

<td align="left">


Select residues 1-100 but exclude 20-40.

</td>

<tr>

<td align="left">


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

</td>

<td align="left">


Select 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 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:
<br><br>

sel ato 102
<br><br>

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


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

<td align="left">


sel ato 1-100

</td>

<td align="left">


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

</td>

<tr>

<td align="left">


sel 1-20 40-50

</td>

<td align="left">


Select 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">


sel phe,tyr,trp

</td>

<td align="left">


Select PHE, TYR and TRP.

</td>

</table>

<br>

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


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.
<br><br>


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

<td align="left">
sel *
<br>
sel all
</td>

<td align="left">
Select all atoms (select all).
</td>

<tr>

<td align="left">
sel abo
<br>
sel above
</td>

<td align="left">
Select atoms above the plane.
</td>

<tr>

<td align="left">
sel aci
<br>
sel acidic
</td>

<td align="left">
Select acidic amino acids (GLU and ASP).
</td>

<tr>

<td align="left">
sel ali
<br>
sel aliphatic
</td>

<td align="left">
Select aliphatic amino acids (ILE, LEU and VAL).
</td>

<tr>

<td align="left">
sel alt
</td>

<td align="left">
Select atoms at alternate positions.
</td>

<tr>

<td align="left">
sel bad
</td>

<td align="left">
Select 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">
sel bas
<br>
sel basic
</td>

<td align="left">
Select basic amino acids (ARG, LYS and HIS).
</td>

<tr>

<td align="left">
sel bel
<br>
sel below
</td>

<td align="left">
Select atoms below the plane.
</td>

<tr>

<td align="left">
sel cha
<br>
sel charged
</td>

<td align="left">
Select charged amino acids (ARG, LYS, HIS, GLU and ASP).
</td>

<tr>

<td align="left">
sel cis
</td>

<td align="left">
Select cis residues.
</td>

<tr>

<td align="left">
sel com
<br>
sel complement
</td>

<td align="left">
Select atoms which were not selected previously.
</td>

<tr>

<td align="left">
sel het
<br>
sel hetero
</td>

<td align="left">
Select hetero atoms (heme groups, water etc.).
</td>

<tr>

<td align="left">
sel pho
<br>
sel hydrophobic
</td>

<td align="left">
Select hydrophobic amino acids
<br>
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
</td>

<tr>

<td align="left">
sel mai
<br>
sel main_chain
</td>

<td align="left">
Select main chain atoms (CA, C, N and O).
</td>

<tr>

<td align="left">
sel mod serial_number
<br>
sel model serial_number
</td>

<td align="left">
Select model specified by serial_number.
<br>
NMR structure is a set of models. Example: sel mod 1
</td>

<tr>

<td align="left">
sel neg
<br>
sel negative
</td>

<td align="left">
Select negatively charged amino acids (GLU and ASP).
</td>

<tr>

<td align="left">
sel pat
<br>
sel pattern
</td>

<td align="left">
Select 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">
sel pol
<br>
sel polar
</td>

<td align="left">
Select polar amino acids
<br>
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
</td>

<tr>

<td align="left">
sel pos
<br>
sel positive
</td>

<td align="left">
Select positively charged amino acids (ARG, LYS and HIS).
</td>

<tr>

<td align="left">
sel seq
<br>
sel sequence
</td>

<td align="left">
Select 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">
sel sid
<br>
sel side_chains
</td>

<td align="left">
Select atoms which belong to side chains (all except CA, C, N and O).
</td>

<tr>

<td align="left">
sel sma
<br>
sel small
</td>

<td align="left">
Select small amino acids
<br>
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
</td>

<tr>

<td align="left">
sel sph
<br>
sel sphere
</td>

<td align="left">
Select 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">
sel tm
</td>

<td align="left">
Select the transmembrane part
<br>
(useful for membrane proteins).
</td>

<tr>

<td align="left">
sel tra
<br>
sel trans
</td>

<td align="left">
Select trans residues.
</td>

<tr>

<td align="left">
sel tri
<br>
sel 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, select these residues. Detailed
<br>
explanation may be 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">
sel 2c3 
</td>

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

<tr>

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

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

<tr>

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

<td align="left">
Analogous to sel 2c3 and sel 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">
sel 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>
select 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">
sel 5p7
</td>

<td align="left">
If there are five or more
<font color="red"><b>polar</b></font>
residues in a fragment of seven residues,
<br>
select 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">
sel 6p7
</td>

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

</table>

<br>

<font color=#880000>
<b>
SELECTING CHEMICAL ELEMENTS
<br>
</b>
</font>


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:
<br><br>

sel 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 SELECT resets the editing mode to default (no editing).
<br><br>

(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.
<br><br>

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


ADD expands the previous selection. RESTRICT restrics the previous selection.
<br><br>


<hr size="3">

</html>