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<html>
<head>
<title>
EDI, EDIT
</title>
</head>
<h1 align=center>
EDI, EDIT
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
EDI, EDIT - edit structure
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
<table border=1 cellspacing=1 cellpading=0>
<td align="left">
<font color=#004400>
<b>
SHORT FORM
</b>
</font>
</td>
<td align="left">
<font color=#004400>
<b>
LONG FORM
</b>
</font>
</td>
<tr>
<td align="left">
EDI OFF
<br>
EDI ATO
<br>
EDI BON atom1 atom2
<br>
EDI CLI
<br>
EDI DIM
<br>
EDI MAI
<br>
EDI OME
<br>
EDI PHI
<br>
EDI PSI
<br>
EDI SID
<br>
</td>
<td align="left">
EDIT OFF
<br>
EDIT ATOMS
<br>
EDIT BOND atom1 atom2
<br>
EDIT CLICK
<br>
EDIT DIMENSIONS
<br>
EDIT MAIN
<br>
EDIT OMEGA
<br>
EDIT PHI
<br>
EDIT PSI
<br>
EDIT SIDE
</td>
</table>
<br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
The command EDI (EDIT), combined with one of associated keywords (except OFF),
switches the program to editing mode. This will work for garlic version 1.2
or later. The keyword OFF may be used to switch the program to default mode
(no editing). The command EDIT should always be combined with one of the
keywords. The most comfortable keyword is CLI (CLICK): after executing the
command EDI CLI (long form: EDIT CLICK), use the pointer (mouse) to pick
one bond (torsion angle) for editing. Click the left mouse button.
<br><br>
The keywords ATO (ATOMS) and DIM (DIMENSIONS) are reserved for special
purposes and should not be used to edit real molecular structures, unless you
want to introduce (or to fix) some distortion. These keywords may be used to
prepare some artificial structures, made from quarkonium and jellium atoms.
<br><br>
To avoid the accidental modification of the structure, a little sea creature
will be visible at the position of the chosen bond or atom. If editing
(moving) more than one bond (atom), the creature will be drawn at the position
of the first bond (atom). If editing bonds (torsion angles), you will see
a little seahorse. If editing atoms (keyword ATOMS) or dimensions
(keyword DIMENSIONS) you will see a little squid. Why I have chosen these
animals? Seahorse is a poor swimmer but has excellent maneuverability.
Squid known hot to use jet propulsion for fast translation. These little
creatures will warn you that you are working in editing mode. They will
disappear after executing the command EDIT OFF.
<br><br>
<table border=1 cellspacing=1 cellpading=0>
<td rowspan=3 align="center">
<img src="seahorse.gif">
</td>
<td align="left">
The squid will be visible if using
<br>
keywords DIMENSIONS or ATOMS
<br>
and the seahorse will be visible if using
<br>
keywords BOND, BOND, CLICK,
<br>
MAIN, OMEGA, PHI, PSI or SIDE.
</td>
<tr>
<td align="center">
<img src="squid.gif">
</td>
</table>
<br>
<font color=#880000>
<b>
EDIT OFF
<br>
</b>
</font>
The keyword OFF may be used to switch the program to default mode (no editing,
just viewing). The editing symbol (seahorse - if editing bonds or squid -
if editing atoms) will disappear from the screen.
<br><br>
<font color=#880000>
<b>
EDIT ATOMS
<br>
</b>
</font>
The command EDIT ATOMS (short form: EDI ATO) may be used to translate selected
atoms. Normally, you will not use the keyword ATOMS if working with a real
molecular structure. This keyword is intended for usage with artificial
structures, consisting of polygonal lines. In rare cases, you may use this
command to distort the molecular structure, for example to test your own
molecular dynamics program. Do not use this keyword unless you really know
what you are doing!
<br><br>
The translation of atoms is done by using the keys /, *, +, -, 5 and 0 on
numeric keypad.
<br><br>
<font color=#880000>
<b>
EDIT BOND atom1 atom2
<br>
</b>
</font>
The command EDIT BOND (short form: EDI BON) should be followed by serial
numbers of two atoms which form the bond. The keyword BOND may be used in
scripts, to specify a single bond angle for editing. In interactive mode,
the keyword CLICK is much more comfortable. Garlic will not allow the editing
of the specified bond angle in two cases:
<br>
(1) If the specified two atoms do not form an ordinary covalent bond.
Disulfide bonds are not counted as such.
<br>
(2) If these atoms form a covalent bond, but this bond in part of a closed
structure (a ring).
<br><br>
The bond rotation may be done by using the keys 7 and 9 on numeric keypad.
Garlic is capable to recognize the bond angle. For dihedral angles phi and
psi, an auxiliary plot will be drawn to the bottom right corner of the main
window. For dihedral angle omega, the auxiliary plot will be drawn to the
bottom of the main window.
<br><br>
<font color=#880000>
<b>
EDIT CLICK
<br>
</b>
</font>
The command EDIT CLICK (short form: EDI CLI) is the most comfortable way to
chose a single bond angle for editing. Just execute this command and click
a single bond. If this bond is as an ordinary covalent bond and if it is not
part of some closed structure (a ring), the bond angle editing will be
allowed. The seahorse will appear close to the place where the click
occurred. Use the keys 7 and 9 on the numeric keypad to change the bond angle.
<br><br>
The keyword CLICK may be used to pick both the main chain bonds as well as
side chain bonds. It may not replace the commands MAIN and SIDE, because
these two keyword activate the simultaneous editing of two dihedral angles.
<br><br>
Be sure to select all atoms (residues) before using the command EDIT CLICK!
<br><br>
In some cases, a small auxiliary plot will appear in the main window. This
means that you have chosen one of the main chain dihedral angles for editing.
More details about these auxiliary plots may be found below (see EDIT MAIN).
<br><br>
<font color=#880000>
<b>
EDIT DIMENSIONS
<br>
</b>
</font>
The command EDIT DIMENSIONS (short form: EDI DIM) may be used to resize
the selected portion of the structure. Normally, you will not use the
keyword DIMENSIONS if you are working with a real molecular structure.
The translational controls should be used to change each of three dimensions
independently: 0 and 5 may be used to change the depth of the structure,
/ and * to change the width and + and - to change the height of the structure.
To resize the structure proportionally change all three dimensions
consecutively. Be careful with the command EDIT DIMENSIONS!
<br><br>
<font color=#880000>
<b>
EDIT MAIN
<br>
</b>
</font>
Change the main chain dihedral angles phi and psi, for all selected residues.
A residue is treated as selected if the first atom of this residue is selected.
Click
<a href="dihedrals.html">
here
</a>
for detailed definitions of dihedral angles.
<br><br>
The current pair of values and the allowed regions for phi and psi will be
visible in the auxiliary Ramachandran plot, in the bottom right corner of
the main window. The current position in the Ramachandran plot may be
recognized as the small, yellow square with red outline. The favorable
regions are colored blue, with the more favorable regions colored dark blue.
Two dark blue squares represent the positions of alpha helix and beta strand.
Note that these conformations may be unfavorable in some cases (pre-proline
in alpha helix, for example). There are four different types of auxiliary
Ramachandran plot, describing residues with different steric constraints:
<br><br>
<table border=1 cellspacing=1 cellpading=0>
<td align="center">
glycine
</td>
<td align="center">
proline
</td>
<td align="center">
pre-proline residues
</td>
<td align="center">
all other residues
</td>
<tr>
<td align="center">
<img src="gly_hint.gif">
</td>
<td align="center">
<img src="pro_hint.gif">
</td>
<td align="center">
<img src="prepro_hint.gif">
</td>
<td align="center">
<img src="generic_hint.gif">
</td>
</table>
<br>
Be sure to read something about the revision of Ramachandran steric constrains:
<a href="http://xray.bmc.uu.se/~gerard/rama/ramarev.html">
http://xray.bmc.uu.se/~gerard/rama/ramarev.html
</a>
<br><br>
<font color=#880000>
<b>
EDIT OMEGA
<br>
</b>
</font>
Change the angle omega.
Click
<a href="dihedrals.html">
here
</a>
for detailed definitions of dihedral angles.
Most of residues in a protein are in trans conformation, with omega value
of about 180 degrees. A small fraction of residues may be found in cis
conformation, with omega value of about 0 degrees. The cis conformation is
typical for proline. The auxiliary plot at the bottom of the main window
shows the current omega value (yellow vertical line with red outline) and
the statistical distribution of omega values, across the range between
-180 degrees and +180 degrees. The blue peaks represent the most probable
values. Note that -180 degrees is equivalent to +180 degrees; two prominent
peaks in the auxiliary plot are actually two parts of the same (trans) peak.
The central (cis) peak is almost invisible.
<br><br>
<img src="omega_hint.gif">
<br><br>
<font color=#880000>
<b>
EDIT PHI
<br>
</b>
</font>
Change dihedral angle phi.
Click
<a href="dihedrals.html">
here
</a>
for detailed definitions of dihedral angles.
The angle phi may be changed by using the keys 7 and 9 on numeric keypad.
The operation will be done for every selected residue. A residue is treated
as selected if the first atom of this residue is selected. An auxiliary
Ramachandran plot (described above in EDIT MAIN section) will be visible in
the bottom right corner.
<br><br>
<font color=#880000>
<b>
EDIT PSI
<br>
</b>
</font>
Change dihedral angle psi.
Click
<a href="dihedrals.html">
here
</a>
for detailed definitions of dihedral angles.
The angle psi may be changed by using the keys 7 and 9 on numeric keypad.
The operation will be done for every selected residue. A residue is treated
as selected if the first atom of this residue is selected. An auxiliary
Ramachandran plot (described above in EDIT MAIN section) will be visible in
the bottom right corner.
<br><br>
<font color=#880000>
<b>
EDIT SIDE
<br>
</b>
</font>
Edit the side chain dihedral angles chi1 and chi2. Four numeric keys are
used to change dihedral angles: 4 and 6 to change chi1 and 2 and 8 to change
chi2. The command EDI SID (EDIT SIDE) is suitable for asparagine,
aspartic acid, histidine, isoleucine, leucine, phenylalanine, proline,
tyrosine and tryptophan.
<br><br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) The commands REPLACE, CREATE, LOAD, DISCARD, CATCH, SELECT, ADD and
RESTRICT are switching program to default editing mode (no editing).
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
The command
<a href="set.html">
SET
</a>
may be used to set dihedral angles directly. It is more precise than the
command EDIT. The commands ADD, RESTRICT and SELECT (short forms: ADD, RES
and SEL) may be used to select one or more residues for editing. As it will
be difficult to combine script execution and interactive rotational controls
(numeric keys), the command ROTATE (short form: ROT) may be used to change
dihedral angles in scripts, after executing the command EDIT.
BONDS REFRESH may be used to fix bad bonds, which may sometimes be generated
after executing the command CREATE.
<br><br>
<hr size="3">
</html>
|
