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