Misc
Getting started
General help--
NAMOT2 is an interactive graphic tool for building and manipulating
nucleic acid structure. It allows the user to build structures
from various libraries or read structures for the user to manipulate.
Specific help is located in the other help files.
File.
The options in the file menu provide most of the input/output
functions.
Open...:This is used to input files. NAMOT2 accepts either
PDB, AMBER,
or parameter formats.
Generate...:Generates WC or single stranded DNA/RNA.
- Pick the number of strands by clicking the left mouse button
over the appropriate box.
- Pick the general form the same way.
- Enter the sequence as one letter code in lower case with no
spacing(i.e. gcgcgc )
- Entering return(or clicking "Apply" for the Motif interface) will
tell the program to begin processing the file.
Write..:This is used to output coordinates. NAMOT2 produces
PDB, AMBER,
or parameter formats.
Close..:This deletes all molecules being worked on.
Quit..:This causes the program to exit.
Geometry.
Unit Controls.
The unit controls allow the user to alter Dx,Dy,Dz,
tilt,roll,and twist. The affect controls whether a change is
compensated for in the next unit, or whether the remaining part of the
helix is altered. The start and end fields take Helix:Unit
as the specifier. Wild cards are not allowed. "View" causes the
values for the parameter specified to be displayed in the data window.
Ribose Controls:
The ribose controls allow the user to alter W,q,and chi.
Starting and ending fields take helix:unit:base as a specifier.
View has the same functionality as described above.
Phosphate Controls:
The phosphate controls allow the user to alter the
pseudo-torsional angle about the phosphate, see the references
for more data. Starting and ending fields take helix:unit:base as
a specifier. View has the same functionality as described above.
Base Controls
The base controls allow the user to alter Sx,Sy,Sz,
propeller twist, opening and buckle. It is not recommended that
the user alter anything other than buckle and propeller twist.
Starting and ending fields take helix:unit:base as a specifier.
View has the same functionality as described above.
The CPK option toggles CPK for the entire molecule. Note that it
uses an exclusive OR to toggle, which means that if
the user already has a portion of the molecule in
CPK form, that will become wireframe, while the rest
becomes CPK. See commands.
The Label unit option toggles the appearance of the unit level
information on the right side of the main canvas.
See commands.
The Reset option makes all atoms visible, makes all atoms
wireframe represention, zeros out the distance list,
resets the color to the original color, and rescales the view.
Printing
The only option under Printing is Screen dump. This produces an
Encapsulated Postscript raster plot of the view. The file name will
be "screen_dump.ps".
Rotation
The axis of rotation is given by the coordinate system on the upper left
of the display. Below that is the orientation panel(On XView interfaces).
To select an axis of rotation, click on one of the boxes under the coordinate
system. Then enter an angle via the keyboard. Once you press return, the
molecule should undergo the rotation. Pressing and holding the return
results in the repetitive execution of the rotation. Positive and negative
rotations are allowed.
The view can also be rotated with the mouse
and the command line.
Inside the graphics window the mouse has several special features.
See appendix three for a detailed description
of mouse features.
Commands
See chapter 5
Add unit:
This popup adds a unit to the view. The units are kept in a
library that the user can modify. The user can pick the unit
from the menu of the first ten entries in the unit library,
or can use the Unit field to input the unit name by hand.
The user is also able
to get the parameters to specify the form of the helix for
w-c units, by selecting the form from the menu on the upper right.
The user can specify the parameters by hand in the fields
provided. The helix and unit field, can be used to add a
unit into the middle of the helix, if nothing is specified,
the unit will be added to the end of the last helix. The
attachments field specify the placement of the group in the
Molecule->Chain->Group structure, thus establishing
the backbone connection. The specifier is in the form:
Molecule:Chain:Group.
For example to add a unit into unit 2 of helix 1 and maintain
proper backbone connectivity, the attachment would be:
1:1:2 1:2:3.
The "Apply" button causes the changes to take place.
Also see, "generate" under file help.
Add Helix
This popup creates or adds a helix to the view. The helices are
kept in a user modifiable library. The helix is chosen from the given
menu. Fields are provided that allow the user to set the parameters
for the first unit(remember that these will refer to the global
frame).
The "helix" and "unit" fields are present to allow a helix to be
added in the middle of another helix.
The "start Attachments:" field allows the users to specify the
backbone connection as mentioned in the add unit
help.
The "Apply" Button executes the the changes.
Make unit:
This is perhaps the most course of the "Advanced..." popups.
The Bases are chosen by typing them on the "Bases:" field
separated by a space. All the parameters must be entered.
The Alpha field should be used to define the orientation of
the base. There should be no reason to use this menu frequently.
"Help": Gives general help on NAMOT2 in categories.
Misc functions:
"Help": Gives general help on NAMOT.
- red
- blue
- yellow
- green
- white
- orange
- cyan
- magenta
- grey
- black
- usr(this is a user defined color:see
set usr-rgb)