Chapter 5-Command line

• add-add elements to the structure
• delete- deletes certain elements
• modify -Alters parameters
• query- displays information about the molecule
• set- set the given variable
• view-view the specified parameters
• write- output the data in the various formats
• misc-Misc. commands.

add

add bond <spec1> <spec2>

Adds a bond from atom1 to atom2. NAMOT2.1

add unit <unit name> <form name> <helix number> <unit number> <Attach info> <Strand direction info> <Dx> <Dy> <Dz> <Tilt> <Twist> <Roll>

Adds the unit with the specified parameters to structure specified.

add helix <helix name> <Dx> <Dy> <Dz> <Tilt> <Twist> <Roll> <s_attach info> <d_attach info>

Adds the helix to the structure.
dx,dy,dz,tilt,twist,roll-the parameters to position the first unit of the helix
s_attach-How the starting end of the helix is attached in the M:C:G structure.
d_attach-How the ending portion of the helix is attached in the M:C:G structure.

add to_monitor <atom specifier>

Adds the atom to the Four structure. The four structure controls which atoms are used in the position, distance, angle, torisional, display about the data window. This command appears in NAMOT2.1.2

delete

delete bond <spec1> <spec2>

deletes the bond from atom1 to atom2. NAMOT2.1

delete dis <spec1> <spec2>

Deletes the specified distance monitoring.

delete helix <helix number>

Deletes the specified helix.

delete mol <molecule number>

Deletes the specified molecule.

delete text <text number>

Deletes the specified text.

modify

modify base <parameter> <start> <end> <change>

Change an intra-unit parameter for the specified base.
<parameter> can be: "Sx", "Sy", "Sy", "pt", "op", or "bu".
The <start> and <end> specifiers should be in H:U:B format.
<change> is a floating point number.

modify phos <parameter> <start> <end> <change>

Change a phosphate parameter for the specified phosphate(s).
<parameter> can be: "Phi","ang1", or "ang2".
The <start> and <end> specifiers should be in H:U:B format.
<change> is a floating point number.

modify sug <parameter> <start> <end> <change>

Change a sugar parameter for the specified sugar(s).
<parameter> can be: "W","q", or "chi".
The <start> and <end> specifiers should be in H:U:B format.
<change> is a floating point number.

modify unit <parameter> (g|l) <start> <end> <change>

Change a unit parameter for the specified unit(s).
<parameter> can be: "Dx","Dy", "Dz", "tilt", "twist", or "roll"
Specify "g" or "l" to apply a Global or Local change.
The <start> and <end> specifiers should be in H:U:B format.
<change> is a floating point number.

query

query angle <spec1> <spec2> <spec3>

Finds the angle between the given atoms

query dist <spec1> <spec2>

Finds distance between the given atom pair.

query fatm4 <spec1> <spec2> <spec3> <spec4> <distance> <angle> <torsional>

This function moves the fourth atom into the position specified by the length, angle, and torsional. The order of the specifying atoms is important. spec1 spec2 spec3, will define the torsional angle; spec2 spec3 will define the angle; and spec3 will define the distance used to place spec4. If spec4 is "-", the routine will just return the coordinates that the fourth atom would be located.

query pos <spec>

Finds the x,y,z for the specified atom.

query rms <moln1> <moln2> <C:G:A specifier>

Calculates the RMS difference between the specified atoms. NAMOT2.1

query strand

Determines the strand directions.

query tors <spec1> <spec2> <spec3> <spec4>

Finds the torsional angle between the given atoms.

query vdw

Provides the information of the worst VDW contact plus a measure for total bad VDW contacts. If Di is defined to be the distance of the Ith atom pair minus the sum of their VDW radii, and Di=0 if Di > 0), the sum of Di gives the measure for the total bad VDW contacts. As of versions released after Dec 19, the intra-base vdw contacts are ignored in calculating the totals and highest.

set

set ambient <value>

Sets the ambient light levels for determining shades. value ranges between 0 and 100. The default is 60.

set ang1 <spec> <angle>

Changes the O3'-P-O5' angle of the specified phosphate by angle

set ang2 <spec> <angle>

Changes the P-O5'-C5' angle of the specified phosphate by angle

set AutoAd (on|off)

Sets the flag to decide if automatic adjustment of the phosphate angles should be performed. This command appears with NAMOT2.0.8

set AutoResize (on|off)

Determines whether or not NAMOT automatically resizes the image after certain operations(add unit and recalculate structure). This is not fully implemented yet, many other operations should check this flag. This command appears with NAMOT2.1.5

set background <color>

Sets the background color.

set color <spec> <color>

Sets color for the specified region.

set color_mode

Sets to color viewing.

set depth_cueing (on|off)

NAMOT can depth-cue images by line thickness now. The default is off. NAMOT2.1

set dim <size>

Sets the window size. This will allow you to use the 700x700 NAMOT and when you get ready to print you can: set dim 600, and have a printable image. "set dim" can not be used to set the the screen size above the original dimensions. NAMOT2.1

set DISPAd (on|off)

Turns off/on the displacement vector adjustment, must be done before starting. This has no effect on bases that are being WC adjusted. This command appears in NAMOT2.0.8

set font <textn> <font>

This features sets the specified text to the specified font. The font should be in the X11 font format. "xlsfonts" can be used to determine the fonts availible on your XServer. An example of a font specifier is: "-adobe-helvetica-medium-r-normal--14-*" NAMOT2.1

set foreground <color>

Sets the foreground color.

set hush (Original)

Prevents the display of messages.

set hush <level> (versions of NAMOT2 more recent than 1-17-95)

Prevents the display of messages based on level of severity. The levels are: INFO, REQUESTED, WARNING, and ERROR. INFO toggles the display of informational messages such as the molecule primary and secondary structure. REQUESTED toggles the presentation of information that the use specifically asks for on the command line. WARNING and ERROR toggle warning and error messages such as backbone breakage. Without any arguments, "set hush" toggles the display of INFO messages.

set hush <level> (on|off)(NAMOT2.0.7 and up)

Prevents the display of messages based on level of severity. The levels are: INFO, REQUESTED, WARNING, and ERROR. INFO toggles the display of informational messages such as the molecule primary and secondary structure. REQUESTED sets the presentation of information that the use specifically asks for on the command line. WARNING and ERROR set warning and error messages such as backbone breakage. Without any arguments, "set hush" toggles the display of INFO messages.

set icenter <atom specifier>

Moves the image so that the specified atom is in the center of the display window. This command appears in NAMOT2.1.2

set invis <spec>

Sets the specified atoms to invisible. The Scaling will adjust when this is done so that the image fills the screen. To make invisible atoms visible use this command again. (Its an exclusive OR)

set ioffs <x> <y>

Sets the offset of the image, in angstroms. This command appears in NAMOT2.1.2

set label_atom <spec>

Labels the specified atoms with their names. NAMOT2.1

set label_atom_font <font>

Sets the atom label text to the specified font. The font should be in the X11 font format. "xlsfonts" can be used to determine the fonts availible on your XServer. NAMOT2.1

set label_bp_font <font>

Sets the Label base pair text to the specified font. The font should be in the X11 font format. "xlsfonts" can be used to determine the fonts availible on your XServer. NAMOT2.1

set label_dis_font <font>

Sets the distance monitoring text to the specified font. The font should be in the X11 font format. "xlsfonts" can be used to determine the fonts availible on your XServer.

set label_unit (on|off)

This variable controls the display of the unit level on the right side of the screen.

set mono_mode

Sets the viewing to black and white

set NoAutoAd (on|off)

Sets the flag to decide if automatic adjustment of the phosphate angles should be done. This command disappears with NAMOT2.0.8

set NoDISPAd (on|off)

Turns off/on the displacement vector adjustment, must be done before starting. This has no effect on bases that are being WC adjusted. This command disappears with NAMOT2.0.8

set NoRotAd (on|off)

Turns off/on the new mapping, and uses the old mapping that was used in NAMOT1. This command disappears with NAMOT2.0.8

set NoWCAd (on|off)

Turns off/on WC adjustment, must be done before starting. This command disappears with NAMOT2.0.8

set phos <spec> <type>

Sets the phosphates specified to a type found in the phosphate library. The specifier must be in H:U:B form.

set protected <molecule>

Prevents independent rotation and translation of the molecule, but allows rotations of the global environment. This is useful for manipulating rigid bodies, to help make sure you don't manipulate the wrong one by mistake.

set qual (on|off)

This forces the DrawSphere routine to use "sqrt()" instead of the integer approximation lookup tables. This causes a significant decrease in performance.As of NAMOT2.0.6

set radius <spec> <radius>

Sets the Space-filling radius of the specified atoms to radius

set ref <helix number> <unit specifier>

Sets the reference unit for the specified helix to the unit. This is only used in the building code, so the user must be careful to set the unit specifier to zero and recalculate before dumping parameters.

set RotAd (on|off)

Turns off/on the new mapping, and uses the old mapping that was used in NAMOT1. This command appears in NAMOT2.0.8

set sliding_p (on|off)

toggles the behavior of the phosphate auto adjust. With this set off, NAMOT first tries to make the phosphate with the existing angle values if it cannot make the phosphate with existing angles, then it attempts to adjust the angles to make it. If turned on, NAMOT automatically changes the angles as the distance changes without first trying the current values. This command appears in NAMOT2.0.10

set space <spec>

Sets the specified atoms to CPK. To make CPK atoms wireframe use this command again. (Its an exclusive OR)

set spot <atom> <distance>

Sets the atoms within distance of atom to visible. Note that this is not a toggle. This command appears in NAMOT2.1.1

set sugar <spec> <type>

Sets the sugars specified to a type found in the sugar library. The specifier must be H:U:B.

set text <x> <y> <text>

Places the text at the coordinates x,y. These coordinates are image x.y that can be found by clicking any mouse buttons over the area.

set thick <moln>

This command replaces "set thick". Indvidual molecules can be set to thick mode. If any molecule is set thick, the distance monitoring lines are all set thick.

set usr-rgb <red> <green> <blue>

Sets the rgb value for the color "usr". The values should range from 0 to 255.

set uz <unit specifier>

positions the molecule so that the specified unit is set to the global coordinates 0,0,0 and in its inertial frame.

set WCAd (on|off)

Turns off/on WC adjustment, must be done before starting. This command appears in NAMOT2.0.8

set WCAdfirst (on|off)

Turns off/on WC adjustment of the first unit in a helix. By default this if turned off. This command appears in NAMOT2.0.10

set zoom <factor>

This is a multiplier. A negative zoom will mirror image the structure. This command appears in NAMOT2.1.2

view

view base <parameter> <start> <end>

Print the specified parameter to the data window.
parameter:"sx", "sy", "sz", "pt", "opening", "buckle"
start: the starting base in H:U:B form.
end: the ending base in H:U:B form.

view hub

Print the H:U:B structure of the molecules in NAMOT. This command appears in version 2.1.6

view mcg

Print the M:C:G structure of the molecules in NAMOT. This command appears in version 2.1.6

view phos <parameter> <start> <end>

Print the specified parameter to the data window.
parameter:"phi", "ang1", "ang2"
start: the starting base in H:U:B form.
end: the ending base in H:U:B form.

view sugar <parameter> <start> <end>

Print the specified parameter to the data window.
parameter:"W", "q", "chi"
start: the starting base in H:U:B form.
end: the ending base in H:U:B form.

view unit <parameter> <start> <end>

Print the specified parameter to the data window.
parameter:"dx", "dy", "dz", "tilt", "twist", "roll"
start: the starting base in H:U form.
end: the ending base in H:U form.

write

write AMBER <file name>

Writes out an AMBER 4 file of the molecules in the program.

write base-lib <name>

Writes out the contents of the base.lib file in a user readable format

write gen_list <mol 1> <mol 2> <C:G:A specifier>

Generates the atom list that "align" and "query rms" would generate and dumps it to a file, "gen_list" NAMOT2.1

write helix <helix> <name>

Writes out a helix library entry for the specified helix. the name cannot have any spaces. The helix is specified by number.

write history <file name>

Writes out the history into the specified file., If a file name is not provided the history is written to "history" (Added with NAMOT2.0.7)

write param <h|m> <file name>

This writes out the parameters in either human or mmachine readable formats. If The format is not specified, the file is written out in human readable format.

write pdb <file name>

Writes out a pdb file of the molecules in the program,

write pdb-orig <file name>

Writes out a pdb file of the molecules in the program, but in the original orientation. This only works for cases where the molecule has been rotated only in the global frame. If the molecule has been rotated in its own frame, this command will include those rotations when it outputs the coordinates.

write ppm <file name>

Writes out a ppm file as "name" in the directory from which NAMOT2 was launched. PPM is a good standard graphics format that can be converted to any number of other formats using freely available programs. This format is recommended if you anticipate processing the image with another program.

write ps <file name>

Writes out a postscript file in the directory from which NAMOT2 was launched. Regardless of the current view on the screen, NAMOT2 will attempt to write the postscript file as vector postscript. This is suggested to achieve the best quality wireframe.

write ps-lit <name>

Writes out a postscript file as indicated name in the directory from which NAMOT2 was launched. This is suggested for situations where you don't anticipate modifying the image later with an external program and want a literal dump of the screen.

write tiff <name>

Writes out a TIFF format file as indicated name in the directory from which NAMOT2 was launched. This file is approximately 1/3 the size of a PPM file. (Added with NAMOT2.0.10)

write unit <helix> <unit> <name>

Writes out a unit library entry for the specified unit. the name cannot have any spaces. Helix and unit are specified by number.

write unit-lib <file name>

Writes out the contents of the unit.lib file in a user readable format. If file name is not supplied the information will be written to "unit-lib"

Misc commands

align <moln> <moln> <C:G:A specifier>

Aligns the specified parts of molecule one and molecule 2 by the method of McLachlan(J Mol Bio(1979) 128,49-70) NAMOT2.1

bond <moln>

This command is useful for displaying partial structures, in particular structures where only the phosphates or base centers are known. Since these points are too far apart to be classified as bonds, NAMOT has a null bond pointer for that molecule and knows to display the "atoms" as spheres. The bond function connects adjacent atoms(in the order that in which they were read in.) with a bond. NAMOT2.1

close

Closes and deletes the current molecules.

curve <pitch> <radius> <Dz> <Omega> <number of units>

Creates superhelices given pitch and radius. Both pitch and radius have to be supplied. The other parameters will be set to 3.4,34 if not specified and the curving will be caried out on all units. This does not work with the default NAMOT settings. WCad, RotAd, and DISPAd have to be turned off. NAMOT2.1

echo >string<

echos the string to the data window. (Added with NAMOT2.0.7)

execute >file name<

Runs the commands in the specified file. (Added with NAMOT2.0.7)

generate (s|d) (d|r) (a|b|z) >seq...<

Generate a single stranded or duplex for the specified arguments
Specify "s" or "d" to create a single or double stranded molecule
Specify "d" or "r" to create a ribo or deoxyribo nucleic acid
Specify "a","b", or "z" to generate a specific form, not that "z" only works with alternating cg/gc pairs.
(Added with NAMOT2.0.7)

genolig (s|d) (d|r) (a|b|z) <seq...> <repeat number>

This takes all the arguements of "generate" and adds a number after the sequence. This number is the number of times to concatonate the sequence together. This allows the user to create long sequences with ease.

ligate <chain specifier>

Causes NAMOT2 to add a bridging phosphate to the start and end of a chain. Added with NAMOT2.0.8

link <Chain 1 specifier> <Chain 2 specifier>

links chains one and two.

load <format> <type> <file>

loads file according to format and type. Format can either be "PDB", "AMBER",or "param". Type can be "rigid" or "na". If the format is "param" the the type will be ignored.

move chain <M:C> <moln>

Moves the specified chain to the molecule "moln" to the last chain in the molecule NAMOT2.1

nick <M:C:G>

This causes a break in chain structures after the specified group. The new chain is inserted after chain "c" in molecule "m". This command appears in version 2.1.6

prep

Prepares the data structures required for VDW calculations.

quit

Terminate the program.

recalculate

Recalculate the nucleic acid parameters of the structures in NAMOT. This can be useful in situations where the nucleic acids have been positioned using rigid body rotation and translation.

repeat <n> <command>

repeat the specified commands "n" times. (Added with NAMOT2.0.7)

reset

Resets the image flags and data structures. (Added with NAMOT2.0.7)

rotate <molecule> <axis> <amount>

rotates the specified molecule(s) by the prescribed amount. The axes are as given in the drawing window on the top right of the interface. the amount is in degrees. A "*" in the molecule field causes rotation about the global geometrical center of all molecules.

rotatm <specifier> <molecule> <axis> <amount>

rotates the specified molecule(s) by the prescribed amount about the specified atom. The axes are as given in the drawing window on the top right of the interface. the amount is in degrees. A "*" in the molecule field causes rotation about the global geometrical center of all molecules. Note:it is not advised that this option be used to rotate NA structures

rotorig <molecule> <axis> <amount>

rotates the specified molecule(s) around the global zero.

sleep <n>

Sleep the program for the specified number of seconds. (Added with NAMOT2.0.7)

trans <molecule> <x> <y> <z>

moves the specified molecule by the prescribed amount.
example: trans 1 0.0 1.0 0.0
would translate molecule 1 by one angstrom in the +y.

version

Returns the NAMOT2 version being used.