Pull-down Overview (980215)
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 ....).
Controls Pull-down (980215)
 
   These are frequently user control commands that map to their equevalent O commands. The Quit ommands can also be activated by hitting the ESC key

 
Display Overview (080207)
 
 

 This pull-down is used to create molecular objects, to control which onjects are dispalyed, to colour atoms or objects, to make cartoons and to set the active sequence.

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 Pull-down (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
Graph Overview (080207)
 
This pull-down contains a series of commands to generate graphs. 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.
Sequence - activates another pull-down that allows the user to define the 'active sequence'. The sequence slider is used to control what is drawn in the graph window, and by a number of other commands to define a position in the sequence.

The ODBs that are getting graphed are listed in the pull-down. If the x-coordinate of the value being plotted has a very large range (e.g. if one plots the atomic B-factors, for example), only a suitably defined window of values is plotted. Changing the position of the central residue in the sequence slider causes this window to shift. If a graph is drawn and the user decides to change the molecule or one of the ODBs, the graph will get updated provided the relevant ODBs exist in the molecule. In the Ramachandran plot, a green cross is drawn for the central residue in the sequence-slider. If a plot is visible and the molecule is changed, the plot of the new molecule is drawn. Defining the molecule on the Graph pull-down sets the the molecule controlled by the Build_mol and Molecule_name commands. The Build_mol controls a number of things, including the sequence-slider pull-down, the insert pull-down, and the defaults used by many other commands accessed via the terminal.
Graph Molecule
Select a molecule for graphing from the possible molecules loaded in the O database. Defining the molecule on the Graph pull-down sets the the molecule controlled by the Build_mol and Molecule_name commands. The Build_mol controls a number of things, including the sequence-slider pull-down, the insert pull-down, and the defaults used by many other commands accessed via the terminal.
Graph Y Db (080112)
 
 
Chooses the datablock from the selected molecule that will be plotted along the y-axis when graphed.
The program lists all of the atomic and residue database entries associated 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.
In this example, the user wants to look at the temperature factors and has selected the residue B-facors for graphing. Atomic properties can be converted to residue-based properties with the Db_a2r_average command.
Graph X Db (980215)
This offers the same choice as Y Db, to specify 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.
Graph It (080112)
 

 
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 O 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.
In the above, the average B-factors within each residue are plotted (created with the command Db_a2r_average from the atomic B-factor proerty). Becaue the molecule is farilry large, only a window of 200 residues is shown. This window is controlled by the sequence slider. In the next graph, the slider has been moved to a new position.



Ramachandran Plot (101025)
 
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 represents ~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.
Sometimes a user may want to see where a particular residue is located on a Ramachandran plot. This is easily accomplished by using the Slider pull-down to indicate the residue of interest, which then shows up on the Ramachandran plot as a small green square.

Sequence Slider(101025)
 
 


 

 The user interacts via two vertical slider lines, and a vertical list of resdiues. The first slider corresponds to the complete sequence of the molecule (called NCS1 in this example), while the second is an enlargement of 100 residues. The < & > signs allow the user to move 100 residues forward and backwards in the molecule. The current range is indicated beside each <,> sign (A6 to A105 in the example on the left, and A168 to A267 on the right)). Sliding along the first vertical line, maps out a new range of residues in the second.

The active residue is highlighted in green text. It can be changed with either slider or by clicking on one of the 4 adjacent residues.

The molecule is defined via the Graph molecule pull-down or with the Build_mol command.

This pull-down is used by the Graph pulldowns, some of the Decor commands (Decor_fix, Decor_free), and some of the template based commands (SST_merge, Build_slider).

This pull-down can also be used to easily set the screen centre, If centring is on, clicking on one of the sliders or residue names will centre on the central atom of the chosen residue. The default setting, however, is centring off, but the mode can be toggled on or off by clicking on the 'Centre on or 'Centre off' text at the bottom left of the 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

.
Here are the various parents:
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
Grab Pull-down (980218)
 

 
This pull-down allows access to the 5 Grab commands
grab atom - to move singel atoms
grab group - to move a group of connected atoms
grab fragment - to move a group of atoms defined in a fragment
grab residue - to move those atoms in a residue
grab build - the multipurpose grab building command
Torsion Pull-down (980218)
 

 
In residue - all torsion angles within the residue are affected. Needs an entry for the particular residue type in the stereochemistry dictionary
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 atom - prevents an atom moving during regularization. The atom remains fixed after regularization
Clear an atom - clears a 'fixed' status code for an atom
Clear all group -clears fixes of all atoms in a group
Database Pull-down (980218)
 

 
Access a subset of the O main-chain, side-chain database 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
Trig. Pull-down (980218)
 

 
Activates various trig. information commands, to specify:
Distances
Angles
Neighbour atom - atomic contacts
Neighbour residue - residue contacts
Hb main-chain - main-chain hydrogen bonds
Hb all - all hydrogen bonds
Mutate (980218)
 
 

 A residue can be mutated to another residue type, or can be deleted from this pull-down. All objects made from the molecule are deleted and a new one made centred on the CA of the mutated residue

Residue inserts have to be made with the Mutate_insert command


 

Rebuild/Insert Pull-down (041228)

This pull down inserts a new residue at the end of the molecule defined in the sequence slider menu. The molecule name can be defined with the Build_molecule command. The new residue is given the name X<number of residues in the molecule>. This command builds the coordinates of the new residue at the current screen centre (defined by the contents of .active_centre).

The pull-down can be ripped off. It contains the names of a few kinds of residues that might need to be added during refinement. It does not include amino-acids and nucleotides, for example. This pull-down is created by the O DB called .rebuild_ins and can, of course, be changed by the user. The distributed entry is in menu.odb and contains the following:

.rebuild_ins t 18 50

origin -0.7 .50

pane_size .150 0.05

step 100

colour_background black

colour_text magenta

colour_inverse_background red

colour_inverse_text green

moveable

text <Mol>

text HOH

text SOL

text MG

text CL

text SO4

text NAD

text GLC

text GAL

text XYL

This results in the creation of the following pull-down:

pd_rebuild_insert.tiff The first line in the pull-down is the molecule where the insert is made (A in this case). Each residue type in the pull-down must have a complete set of stereo-chemical definitions to allow for the construction of the 3D coordinates using the Build_residue command.

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. Some items in this window map directly to an O command. Others do not, or activate further windows.

Here are the commands:
Bones - 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.Users are recomended to use Grab_build !
Bones Class Pull-down (980215)
   The class values refer to skeleton codes that are associated with each atom in a skeleton molecule. Once activated, the user must identify 2 connected skeleton atoms. All atoms in the connection list are then set to the appropriate skeleton class and coloured accordingly.


Bones Baton Pull-down (980215)
This option has been superceded by the Grab_build command.
 

 
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 Pull-down (000104)
 
 

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 (E.D. Fit) available with the Fm commands. The pulldown also allows the user to control model building using secondary structure templates.

In this example, there are 2 maps that have been loaded, MIR and AV. The one being used for the E.D. fit options is AV

The user can also use local density averaging to produce the enhanced alpha helix Christmas tree affect. This is to assist in determining chain directionality.



Density Slider Control (000104)
 
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. Only one level can be changed in the example on the left. 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 Map Pull-down (, 020801)
 
   This allows the user to select which FastMap will be used for some command to be selected later. In the above, two maps have been loaded into the FastMap system and the AV map has been selected.


Density 2ry unit Pull-down (000104, 020714, 020801)
At present this pull-down contains a list of 5 secondary structure templates that can be used for fast template building with the Density Pulldown system.
   The current template being used is indicated in the parent pull-down frame (alph9 above). Ab RNA template is availbale but has been clipped from the image

 
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 alanine residue
beta7 - beta strand of 7 alanine residue
beta5 - beta strand of 5 beta residues
RNA5 - an RNA helix of 5 cytosine residues
The beta strands are shorter than the alpha helices because they are often twisted in real proteins
Density Template Pull-down (000104)
 
  This pull-down controls the functionality of the template secondary structure building sub-system in O. With this system, the user is able to quickly construct main-chain sections from the templates in a special molecule TRACE that is used by the sub-system. These can, at the user's discretion, be incorporated into a target molecule representing the molecule of interest. The latter step requires knowledge of where we are in the sequence

 
Here are the various commands:
Fit with ... -Add a new secondary structure template to the TRACE molecule - 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 '2ry unit' window, in this case A9.
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
Reverse - identify a part of the TRACE molecule, and the relevent residues in the group containing the id'ed atom will be reversed in direction.
Merge - identify an atom after preparing the sequence pull-down. The residue identified in the TRACE is merged to the current residue indicated in the sequence pull-down The other main-chain atoms from that TRACE group are merged into their equivalent position in the target protein.
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.
Density Map Pull-down (000104)
 
 

 Allows the user to specify which of the 5 maps that can be used in the Fm_* system is to be used in theE.D. Fit pulldown (controlling RSR functions) and the Template pull-down (controlling template building).

In this example, there are 2 maps loaded (MIR & AV), and the one being used is AV.



Density E.D. Fit Pull-down (050801)
 
 pd_ed_fit.tiff  This window controls which real-space refinement action is to be carried out, using the FastMap RSR commands, in the map defined by the Density Map pull-down.

Possible actions are:
RSR group - Real Space Refinement of a group of connected atoms, identify one atom to define the group
RSR rotamer - Real Space Refinement via rotamer definition, identify one atom to define the residue
RSR torsion - Real Space Refinement via torsional search, identify 2 connected atoms to define the angle
RSR zone - Real Space Refinement of a zone of residues, identify start and end residue to define the zone
RSR residue - Real Space Refinement of a single residue, identify residue
Menus Pull-down (980215)
 
   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 yellow
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.


This macro is called when using Baton. I'm playing around here with GoLive to see if I can use Frames correctly.