O version 6 works with a set of pull down menus. They are activated by the mouse buttons in much the same way as working with any other kind of windowing system.
The windowing system can be activated in two ways. In one way, the mouse is moved to one of the panes making up the window and then the left mouse button is depressed. If the pane is a parent of another window, the child window will be expanded. If the mouse is kept down, and moved to any item in the expanded window, further panes can be expanded (if they exist). Releasing the mouse over a windowed item, activates the particular item. Alternatively, a pane can be expanded by a press and release. The window will stay expanded, and then another item can be pressed and released.
Each pull-down menu in the O windowing system must be described in the O database. This allows the user to decide on things like colour and text. Note that the actual activity to be carried out is not a function of the text but of the position within the pane. The distributed descriptions are in the menu.o file.
Some panes can be stripped off and positioned elsewhere within the 3D graphics window. These panes are identified by having a line drawn around their boundary. Clicking on the small, red square in the top, left corner, strips the child window so that it can be moved around. The square changes colour to green, and another small square appears in the top, right corner. Clicking and keeping the mouse depressed on the new square, causes the pane to follow the mouse pointer as it is moved. Clicking on the left square again, causes the pane to disappear, and to return to the control of the windowing system.
Here are the highest level pull-downs, used in O 6.2
Controls - frequently used commands such as Save/Quit/Yes/No
Display - create molecular related objects
Graph - create graphs and Ramachandran plots
Rebuild - commands frequently used when building a structure
Bones - skeleton related commands
Density - related commands, contoruing, Real Space Refinement, Template building
Menus - various menus (object list/user menu ....).
These are frequently user control commands that map to their equevalent
O commands. The Quit commands can also be activated by hitting the ESC key.
Some items in this windom map directly to an O command. Others do not, or activate further windows. Here are the commands:
Molecule name - this activates a new window that allows
one to define a new active molecule. If a molecule has been defined, it
is named in this item entry.
Ca atoms - creates a Ca object from the current molecule. the object name is <mol>ca
Sphere atoms - creates a an object of atoms that are within the presently defined distance from the screen centre. The object name is <mol>sph
Sphere ID- creates a an object of atoms that are within the presently defined distance from the screen centre. The object name is <mol>sph
All atoms - creates an obect of all atoms contained in the the current molecule. The object name is <mol>all
Objects on - turns all 3D objects on
Objects off - turns all 3D objects off
Delete object - activates another pull-down window that contains the names of each displayed 3D object. Activates on of these items, deletes that particular object. This window can be torn off and placed somewhere else in the 3D window
Paint mol. - activates another pull-down window that allows one to paint either the current molecule or molecular ojects
Sketch mol.- activates another pull-down window that allows one to create sketch objects
Display Paint Pulldown (980215)
This pull-down contains a series of commands that are
used to paint molecules, molecular objects, and to define the active colour.
Although the user is able to change the text displayed within this window,
as well as the colours, most of the actions cannot be changed. The colours
defined within this pull-down can be modified and extended to include new
ones. This requires the user to edit the o datablock , .paint_display,
that describes this pull down - it is quite obvious how you do it but remember
to update the number of lines as defined in the header of this atablock.
Most items in this windom map directly to an O command. Here are the commands:
Paint - the name of the pull-down. It does not activate a command.
Paint by atom - paints the atoms in the current molecule according to their atom type.Carbons are painted yellow, nitrogens blue, oxygens red, sulphurs green. Here is the macro that gets activated
@pt_by_atom t 1 50
pai_case ; 4 6 7 8 16 yellow blue red green
Paint red->blue - paints the atoms in the current molecule according to their internal residue count. Colouring is red to blue. Here is the macro that gets activated
@pt_red_blue t 1 50
paint_ramp ; ; red blue
Paint blue->red- paints the atoms in the current molecule according to their internal residue count. Colouring is red to blue. Here is the macro that gets activated
@pt_blue_red t 1 50
paint_ramp ; ; blue red
Paint by B- paints the atoms in the current molecule according to their itemperature factors. Low B's are blue, high ones are red. Here is the macro that gets activated
@pt_by_b t 1 50
paint_ramp atom_b ; blue 1 0 0
Paint object - paints an object the current active colour. The object is specified by the user identifying an atom in the desired object.This only affects the colour in the object not in the <mol._atom_colour datablock.
Paint obj. zone - paints a zone in an object the current active colour. The zone is specified by the user identifying two atoms in the desired object. This only affects the colour in the object not in the <mol._atom_colour datablock.
Paint obj. atom -paints an atom in an object the current active colour. The atom is specified by the user identifying the atom in the desired object. This only affects the colour in the object not in the <mol._atom_colour datablock.
The remaining items in the window allow the user to set the active colour. These can be added to, by the user correctly modifying the datablock .paint_display
The datablock is distributed with the following colours as standard
red
yellow
green
blue
magenta
cyan
white
Display Sketch Pull-down (980115)
This pull-down contains a series of commands that are
used to generate sketch objects. Although the user is able to change the
text displayed within this window, as well as the colours, the actions cannot
be changed.
These items map directly to one or more O command. They use the currently defined sketch setup values. Here are the commands:
Sketch - the name of the window. It does not activate any command
Sticks - makes a stick object, The object is defined by identifying an atom in the object
Balls small - makes a cpk object where each atom has a small radius. The object is defined by identifying an atom in the object. The radii are defined by reading in the O file radii.o in the users O data directory
Balls VdW- makes a cpk object where each atom has a Van der Walls radius. The object is defined by identifying an atom in the object. The radii are defined by reading in the O file cpk_radii.o in the users O data directory
Cartoon 2ry colours - makes a sketch cartoon that is coloured according to the secondary structure. The yasspa command must be run first.
Cartoon atom colours- makes a sketch cartoon that is coloured according to the colour of each Ca atom The yasspa command must be run first. Use the paint pull-down to quickly set up pretty cartoon colours.
Add tapeworm - adds a tapeworm to the current sketch object. The zone must be defined by identifying the start/end residues.
Add ribbon - adds a ribbon to the current sketch object. The zone must be defined by identifying the start/end residues.
Add rattler - adds a rattler to the current sketch object. The zone must be defined by identifying the start/end residues.
Add arrow - adds an arrow to the current sketch object. The zone must be defined by identifying the start/end residues.
Add cylinder - adds a cylinder to the current sketch object. The zone must be defined by identifying the start/end residues.
Add spiral - adds a spiral to the current sketch object. The zone must be defined by identifying the start/end residues.
Undo - removes the last defined sketch item from the current sketch object
This pull-down contains a series of commands to generate graphs Although the user is able to change the text displayed within this window, as well as the colours, the actions cannot be changed.
Most items in this windom do not map directly to an O command. Here are
the commands:
Molecule- activates a pull down containing the names of all molecules in the database. The one selected becomes the current molecule.
Y Db - chooses the datablock from the selected molecule that will be plotted along the y-axis when graphed.
X Db - chooses the datablock from the selected molecule that will be plotted along the x-axis when graphed.
Graph it - Plot the chosen Y/X Db datablocks against one another.
Ramachandran - draws a Ramachandran plot. The restricted area of Kleywegt & Jones (1996) is superimposed on the plot. This area represeents ~20% of the drawing but should contain 98% of the residues.
Chooses the datablock from the selected molecule that will be plotted
along the y-axis when graphed.
The program lists all of
the database entries adssoiated with the molecule. Many of these would not
be suitable for plotting. If the user chooses a residue property, the X
Db must also be a residue property. If an atomic property is chosen, the
X Db must also be atomic.
This offers the same choice as Y Db, to sdpecify the X-axis when graphed. If the user chooses "Index", the horizontal axis will be a cardinal integer corresponding to either a residue or an atom count, depending on the property being plotted along the y-axis.
Plot the chosen datablocks against one another. In the current version, the points are linked and not coloured if the x-axis is "Index". Otherwise, a scatter plot is drawn and coloured. For an atomic property, the colour is the atomic colour. For a residue property it is the colour of the CA atom (if the residue has one), or the first atom in the residue (if there is no CA atom). If one of the points is identified, the macro on_graph_pick is activated. In the distribution, this is an entry in the user's database
@on_graph_pick t 1 50
cen_atom ${.id_m} ${.id_r} ${.id_a}
which centres the 3D picture on the identified atom
This window contains a Ramachandran plot showing the main-chain phi and psi angles in a scatter diagram. The window can be torn-off and repositioned.
Each residue is represented as a diamond (glycine residues) or a square.
The colour is that of the CA atom of the residue. In the example here, the
colour goes from red at the N-terminus, to blue at the C-terminus
The restricted area of Kleywegt & Jones (1996) is superimposed on the plot. This area represeents ~20% of the drawing but should contain 98% of the residues.
When a symbol is identified, the macro on_rama_pick is activated. In the O distribution, this is an entry in the user's database
@on_rama_pick t 1 50
cen_atom ${.id_m} ${.id_r} ${.id_a}
and moves the screen centre to the identified atom. The user is free to customize this macro, e.g. to draw the electron density around the place of interest, together with an object showing all atoms that are close by.
When the Ramachandran plot is drawn for the first time, O creates an entry in the database called <mol>_residue_rama that contains phi and psi values for each amino-acid in the structure. If these angles are changed later (e.g. by the torsion commands or by pep_flip), the entries in the datablock are not (yet) automatically updated. Therefore, to see the result of changing the main-chain, the user should deletete this entry in the data-base, and then reactivate the command or move the open plot window.
Rebuild Pull-down Overview (980218)
The Rebuld pull-down provides a means for a user to activate a series
of commands that are usefull when carrying out a rebuild of a structure.At
present, each pane in this window is a parent to another window containing
the actual O commands.
Grab - activates the Grab commands
Torsion - the torsion and flip peptide commands
Regularize - the model regularization commands
Database - the main-chain, side-chain O database commands
Trig - distance, angle, phi/psi, H-bond information
Mutate - a menu to mutate the currently defined molecule
This pull-down allows access to the 4 Grab commands
grab atom - to move singel atoms
grab group - to move a group of connected atoms
grabfragment - to move a group of atoms defined in a fragment
grab residue - to move those atoms in a residue
In residue - all torsion angles within the residue are affected. Needs an entry for the particular residue type in .torsion_information
General via bonds - the user must explicitly define the connected bonds that are affected. If the identified atoms are connected via 3 bonds, one angle is defined. If 4 bonds, then 2 angles etc
Flip peptide - flips the direction of the carbonyl oxygen, keeping the plabe orientation
Show phi/psi - when atoms are identified, the residue tosrion angles are displayed
Regularization Pull-down (980218)
Allows access to the Refi commands
Define zone - regularizes within a zone
Continuous - continuously refines the coords within a defined zone
Fix an atm - prevents an atom moving during regularization. The atom remains fixed after regularization
Clear an atom - clears a fixed atom
Clear all group -clears fixes of all atoms in a group
Access a subset of the O database main-chain, side-chain commands
Rotamer to build - to seelect a new rotamor for a residue
Rotamer to show - to look at the rotamers for each amino acid
Define zone - to seach the database for the most similar structures
Auto main-chain - build the main-chain from penta-peptide
Auto side-chain - build side-chain from top rotamer
Activates various trig. information commands, to specify:
distances
angles
atom contacts
residue contacts
main-chain hyderogen bonds
all hydrogen bonds
A residue can be mutated to another residue type, or can be deleted.
All objects made from the molecule are delted and a new one made centred
on the CA of the mutated residue
Residue inserts have to be made with the Mutate_insert command
Overview Bones pull-down (980215)
This pull-down contains a series of commands that are
used to generate and interect with the skeleton options in O. It can also
be used to modify the molecular connectivity.. Although the user is able
to change the text displayed within this window, as well as the colours,
the actions cannot be changed.
Some items in this windom map directly to an O command. Others do not, or activate further windows. Here are the commands:
Skeleton - this activates a new window that allows one to define a new active skeleton. If a skeleton has been defined, it is named in this item entry.
Make bond - connect 2 atoms (from a skeleton or regular molecule) with a bond
Break bond - break a bond between 2 atoms( from a skeleton or regular molecule).
Undo bond - undo the last bond break 9or make?) operation
Set to class - activate another ull-down menu. The latter contains a list of cardinal numbers that correspond to the class code to be set. The identified atoms must be connected and not be linked by a circular connection
Move atom - activates a move atom command.
Add branch - insert a branch skeleton atom at the identified atom. Such branches are usefull for providing indicators for where Ca atoms could be placed.
Prune - makes a connected set of skeleton atoms look like a skeleton Ca trace. This is done by keeping atoms that have branch points, and those that can be placed at 3.8 A separation from each other. The rest are are not inlcuded in the connection list.
Draw all - draw all skeleton atoms withi the current radius of the screen centre. The object is called <mol>msc
Draw main draw just main-chain skeleton atoms (i.e. not class 2 atoms) withi the current radius of the screen centre. The object is called <mol>mc
Radius drawn - activates a new pull-down menu that can specif the radius for drawing skeleton objects
Symmetry - draws a symmetry copy of a skeleton object. The unit cell and space group data must be in the database for the relevent skeleton molecule (use symm_setup)
Baton mode - activates a new menu that allows one to change the baton mode. Baton mode switches can be used to follow skeletons, set the baton for building alpha helices or beta strands.
Bones Baton Pull-down (980215)
This pull-down allows one to change the baton mode.
The baton mode controls the orientation and position of the di-peptide when
Baton_build is active. If the mode setting is alpha, the coordinates
of the last 4 CA atoms are taken and a least squares comparison made with
a regular alpha-helix. The di-peptide is then placed in the position of
the 4th and 5th residues of the helix. The di-peptide is then translated
so that it does not appear separated from the Ca trace that has just been
built. If the mode is beta, the comparison is made with residues from a
regular beta-strand. If the mode is 2ry, a comparison is made with both
alpha and beta structures, and the one closest to the last 4 residues is
used to position the di-peptide. In all three modes, if 4 residues have
not been built, the mode defaults to a 'standard' orientation for the peptide.
This can also be achieved by defining mode ? or any other non-recognized
character string. The option may also be a skeleton molecule. The program
uses the current connectivity of this molecule to place one end of the di-peptide
on a line joining 2 bones atoms, if these atoms exist. If more than one
pair of atoms exists, the program creates a list of suggestions. Multiple
calls to this command cause the peptide to be placed at different positions
within this list. The order of items in the list is determined by the bones
status of the pair of skeleton atoms; pairs of class 1 atoms first, followed
by pairs of non-class 2, followed by mixed 2/other etc, and by the direction
of building.
This option, therefore, makes it easy to follow a skeleton or to build standard secondary structure elements.
Density Pulldown Overview (980204)
This pulldown allows the user to control any of the 5 maps that can
be handled by the Fm contouring commands, as well as the Real Space Refinement
options available with the Fm cpmmands. The pulldown also allows the user
to control model building using secondary structure templates.
The user can also use local density averaging to produce the enhanced alpha helix Christams trea affect. This is to aassist in determining chain directionality.
Density Slider Control (980204)
Each of the five maps that can be used with the F(ast)m(ap) system has an associated window (accessible from the Density Pulldown) that can control the contouring.
Each slider window allows the user to control a maximum of 3 different levels for the particular map. The first slider controls the radius used for the contouring, and then for each level (maximum of 3 levels): Contour level in sigma units, Red component of contour object, Green component of contour object, Blue cmponent of contour objcet.
On a modern workstation, the sliders give the user real time control of their contouring.
Density Secondary Structure Template Unit Pulldown (980204)
At present this pull down contains a list of 4 secondary structure templates that can be used for fast template building with the Density Pulldown systems.
The templates correspond to molecules in the O DB and have the following names:
alph9 - alpha helix of 9 alanine residues
alph7 - alpha helix of 7 alanineresidue
beta7 - beta strand of 7 alanine residue
beta5 - beta strand of 5 beta residues
The current template being used is indicated in the parent pulldown frame (alph9 above)
Density Template Action Pull-down (980218)
Fit <2ry unit> - identify a skeleton atom, the secondary unit defined in the pane will then undergo a full 3D search to best fit the currently defined density. This unit will be made in the TRACE molecule and drawn on the screen. The current template being used is indicated in this first frame.
Remove template - identify an atom in the TRACE molecule, and that group of residues will be removed
Trim template - identify a residue in the TRACE, and it will be removed
Combine 0 (1,2,3 ....) gap - to combine two templates into one. Identify the C-terminal residue in the first template, and the N-terminal residue in the second template. Depending on the gap chosen, the program will search the database for the speciifed size. HItting Yes accepts the result, NO returns to the 2 templates.
Allows the user to specify which of the 5 maps that
can be used in the Fm_* system is to be used in the Density action pulldown
controlling RSR functions and template building.
This window controls which action is to be carried out.
Possible actions are
Real Space Refinement of a group of connected atoms - identify one atom to define the group
Real Space Refinement via rotamer definition - identify one atom to define the residue
Real Space Refinement via torsional search - identify 2 connected atoms to define the angle
Add a new secondary structure template - identify an atom to act as the pivot point for a full 3D search of the template. The template used, is the one last defined in the template window.
This pull-down contains a series of items that generate new windows,
most of which can be torn from the parent pull-down. Although the user is
able to change the text displayed within this window, as well as the colours,
the actions cannot be changed. Here are the items
Objects - lists the current 3D objects
User menu - draws a window that can be filled with the user's own personalized set of items. Items in this menu come from the .menu datablock and can include text colouring commands. For example, the following datablock
.menu t 9 50
colour_text green
Yes
No
colour_text red
Save
Quit
colour_text yellow
Grab_atom
Grab_group
The first group are drawn in green, the next in red, the next in tellow
Fake dials - creates a window that can be used to change the 20 dials. Move the mouse into the relevent dial, depress and slide left/right
Graphics - creates a window to change rarely used graphics
states; set on or off stereo, line smoothing, depth cueing. More frequently
used graphics settings are changed with the F keys.