EDI, EDIT

NAME
EDI, EDIT - edit structure

SYNOPSIS

SHORT FORM	LONG FORM
EDI OFF EDI ATO EDI BON atom1 atom2 EDI CLI EDI DIM EDI MAI EDI OME EDI PHI EDI PSI EDI SID	EDIT OFF EDIT ATOMS EDIT BOND atom1 atom2 EDIT CLICK EDIT DIMENSIONS EDIT MAIN EDIT OMEGA EDIT PHI EDIT PSI EDIT SIDE

DESCRIPTION
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.

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. An example of such structure is the model of the vascular system of human brain . Quarkonium and jellium are described here .

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.

	The squid will be visible if using keywords DIMENSIONS or ATOMS and the seahorse will be visible if using keywords BOND, BOND, CLICK, MAIN, OMEGA, PHI, PSI or SIDE.

EDIT OFF
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.

EDIT ATOMS
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. The model of the vascular system of human brain is an example of artificial structure, made from quarkonium and jellium atoms. Do not use this keyword unless you really know what you are doing!

The translation of atoms is done by using the keys /, *, +, -, 5 and 0 on numeric keypad.

EDIT BOND atom1 atom2
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:
(1) If the specified two atoms do not form an ordinary covalent bond. Disulfide bonds are not counted as such.
(2) If these atoms form a covalent bond, but this bond in part of a closed structure (a ring).

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.

EDIT CLICK
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.

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.

Be sure to select all atoms (residues) before using the command EDIT CLICK!

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).

EDIT DIMENSIONS
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!

EDIT MAIN
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 here for detailed definitions of dihedral angles.

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:

glycine	proline	pre-proline residues	all other residues

Be sure to read something about the revision of Ramachandran steric constrains: http://xray.bmc.uu.se/~gerard/rama/ramarev.html

EDIT OMEGA
Change the angle omega. Click here 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.

EDIT PHI
Change dihedral angle phi. Click here 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.

EDIT PSI
Change dihedral angle psi. Click here 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.

EDIT SIDE
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.

NOTES
(1) The commands REPLACE, CREATE, LOAD, DISCARD, CATCH, SELECT, ADD and RESTRICT are switching program to default editing mode (no editing).

RELATED COMMANDS
The command SET 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.