P a r t III
The display options are accessible via the mouse when the Textport command >go is used. They are presented in eleven pop-up menus, which in some cases have been divided into submenus. The pop-up menus are activated when the cursor is driven up-screen to the top of the pop-up menu header. The submenus or functions can be accessed by dragging the mouse down, keeping the right button depressed. This will display the various options in yellow. To choose a function, drive the mouse along the menu until the function required is highlighted in yellow. Releasing the right button on the mouse will activate the function, which is then highlighted in green.
To turn off a function, drag the mouse to it and click the right button again. This action will make the function show up in yellow again and deactivate it.
The following eleven menus appear on top of the screen, working from left to right: Help, Main, Color, Geometry, Editing, Modeling, View, Plot, Tools, Surfaces, Molecules.
Philosophy of Use: The display options apply to the most recently picked molecule.
Display Options Table
CHAPTER 5
Help Menu:
Devices for Assistance
HELP MODE, HELP MOUSE, HELP DIALS.
Three options are available with which on-line information can be obtained. To get this information, choose the HELP MODE option and then click on any other option. Instead of activating this option, this will give information about it. To switch back to the normal mode, choose the HELP MODE option again.
The program makes use of the three mouse buttons, as well as combinations of them, which offers various alternatives. Active buttons are indicated in bold-faced letters.
The program can work without dials. In this case, activate the PSEUDO-DIALS option. The use of dials is summarized in the following scheme:
CHAPTER 6
Main Menu:
Saving and Special Views
CONTOUR, SAVE, SAVE ALL, CLEAR LABELS, NO INFO, CLEAR INFO, ORTHO VIEW, SPLIT STEREO, ALT STEREO, POLAR STEREO.
This menu provides options that are used to manage the items displayed and to save any changes made in the Heap File.
The CONTOUR option sets the new screen center at the most recently picked atom position. The maps and surfaces are recentered, as well as the molecular data in the sphere mode.
The SAVE option transfers the modified molecular data after it has undergone delete, insert, replace, frag-trans, torsion, and move, from the memory storage to the source disk data base. The entry is written above. If several molecules are stored in the memory (and displayed on the screen), only the most recently picked molecule is saved. To save all the molecules use SAVE ALL.
The SAVE ALL option transfers the modified molecular data from the memory storage to the source disk data base. This is the same option as SAVE, but in this case all the molecules loaded are saved.
The CLEAR LABELS options switches off any previously picked atom labels.
The NO INFO option dispenses with the atom information in the upper-left corner of the screen.
The CLEAR INFO option switches off the atom information in the upper-left corner of the screen.
The ORTHO VIEW option displays an orthogonal view of the current molecule, in the upper-right corner of the screen. It is useful for map fitting if no stereo device is available and for use with the ADD ATOM option.
The SPLIT STEREO option activates the split stereo mode. You can set the distance between the 2 views with the stereo dial (or pseudo-dial).
The ALT STEREO option renders operation in the alternate stereo mode possible. This mode requires special hardware (a stereo graphics board and special glasses). You can set the angle between the 2 views with the stereo dial (or pseudo-dial).
The POLAR STEREO option renders operation in the polarized stereo mode possible. This mode requires very special hardware (a stereo graphics screen). The orientation between the two views can be set with the stereo dial (or pseudo-dial).
CHAPTER 7
Color Menu:
Coloring the Molecule
SAME, ATOM TYPE, RESIDUE TYPE, SIDE CHAIN, FEATURE**, DEFINE**.
The Color menu and submenus are described on the following page. The Color menu comprises 4 options ,SAME, ATOM TYPE, RESIDUE TYPE, and SIDE-CHAIN, and 2 submenus, FEATURE and DEFINE. All these options can be applied to different molecular entities. In the special case of FEATURE, the choice of entities appears in response to calling one of the FEATURE submenu options. For the other options (SAME, ATOM TYPE, RESIDUE TYPE, SIDE-CHAIN, and the DEFINE submenu), the choice of entities appears immediately. The molecular entities
Molecular entities
Color MenuMolecular entities are as follows:
With the SAME option the molecular entities are displayed with a single color. You can choose the entity to be colored among those on the list (see above). You can choose one color out of 12 appearing in the menu.
The ATOM TYPE option displays atoms in color based on a list defined with the DEFINE submenu in the Color menu. Default colors are Carbon Yellow, Oxygen Red, Nitrogen Blue, Sulfur Green, Hydrogen White, and all other atoms Orange. You can choose the entity to be colored from the list of entities (see above).
Color Menu Table
The RESIDUE TYPE option colors residues depending on their type, as defined with the DEFINE submenu in the Color menu. Default colors are Acidic Red, Basic Blue, Aromatic Magenta, Cystein and Cystine Dark Green, Aliphatic Yellow, and Polar Light Green. You can choose the entity to be colored from the list of entities (see above).
The SIDE CHAIN option colors residue side chains based on a residue color list defined with the DEFINE submenu in the COLOR menu (the backbone color remains unchanged). Default colors are Acidic Red, Basic Blue, Aromatic Magenta, Cystein and Cystine Dark Green, Aliphatic Yellow, and Polar Light Green. You can choose the entity to be colored from the list of entities (see above).
FEATURE (submenu)
B-FACTORS, SECOND STRUCT, ACCESSIBILITY, HYDROPATHY.
The B-FACTORS option colors molecular entities depending on their crystallographic temperature factor. The B-factor range and color range can be defined using the B-FACT RANGE option from the DEFINE submenu. The default range is 0-20 but can be also modified with the Textport option BFACT-DEF. You can choose the entity to be colored from the list of entities (see above).
The SECOND STRUCT option colors secondary structures differently. The secondary structure distribution can be calculated in MENU TOOLS, with the SECOND STRUCT submenu either using the FAST option (fast and dirty) or DSSP, as described by C. Sander and W. Kabsch. The colors option of Helices, Beta-Sheets, Turns, and non-defined structures can be defined in the DEFINE option. When several molecules are displayed, this option works only on the last molecule to be picked (or by default, on the first molecule to be loaded).
The ACCESSIBILITY option colors the last-picked molecule based on the residue-accessible surface calculated by either the Textport option ACCESS or the ACCESS CALC option located in the SECOND STRUCT submenu of the Tools menu. Calculations are performed according to C. Sander and W. Kabsch. The accessibility range and color ramp can be defined using the ACCESS RANGE option from the DEFINE submenu.
The HYDROPATHY option colors the last-picked molecule depending on whether it is hydrophobic. For this purpose, calculations are carried out on a zone of the residue with the hydrophobic index given by Kyte and Doolitle. The size of the computation window can be modified using the HYDROPATHY Textport option. The color ramp can be modified by using the HYDR RANGE option from the DEFINE submenu.
DEFINE (submenu)
ATOM TYPE DEF, RES TYPE DEF, SECOND STRUC, B-FACT RANGE, HYDR RANGE, ACCESS RANGE, DIST COLOR, SAVE DEFINE.
Note that after each definition, color must be applied again to render the new definitions effective.
The ATOM TYPE DEF option defines the atom colors to be used in the ATOMTYPE display and atom radii to be used in CONNECT MOL and CPK display. New atom types can be added with NEW. The default colors can be recovered with DEF.END exits.
The RES TYPE DEF option defines the residue colors for the RESIDUE TYPE display. New residue types can be added in NEW. Default colors can be restored with DEF.END exits.
The SECOND STRUC option defines the colors in which the structure elements should be shown in the SECOND STRUC display: COIL, COLOR, HELIX COLOR, SHEET COLOR.END exits.
The B-FACT RANGE option defines the color ramp and the B-factor range.
The HYDR RANGE option defines the color ramp and the hydrophobicity range.
The ACCESS RANGE option defines the color ramp and the accessibility range.
The DIST COLOR option defines the color to be used with the DISTANCE dashed lines.
The SAVE DEFINE option saves in the HEAP all the modifications set up with DEFINE.
CHAPTER 8
The Geometry Menu:
Verifying the Geometry
DISTANCE, CLEAR DIST, ANGLE, CLEAR ANGLE, XYZ, DIHEDRAL, CLEAR ALL, RAMACHANDRAN, NEIGHBOR, H-BONDS, OCCUPANCY.
The options that come with this menu can be used to calculate and display the geometric characteristics of the molecule either on the left part of the screen and/or on the molecule.
With the DISTANCE option, you can measure the distance between 2 atoms. When the option is activated, the cursor arrow changes to <1, meaning that the first atom should be picked. When the first atom has been picked, <1 is replaced by <2, meaning that the second atom should be picked. The option is active until it is switched off. The atoms in each pair are linked by a dashed line, and the distance between the 2 atoms is displayed.
The CLEAR DIST option serves to remove the previously calculated distances and hydrogen bonds.
With the ANGLE option, you can measure the angles between three atoms. When this option is activated, the cursor arrow changes successively to <1, <2, <3, meaning that the first, second, and third atoms should be picked. The option is active until it is selected again, which cancels it. The atoms in the triangle are linked by dashed lines, and the angle value appears between pairs of atoms, opposite to the top angle.
The CLEAR ANGLE option serves to remove the previously calculated angles.
With the XYZ option, it is possible to display the Cartesian coordinates of the last-picked atom. Pick the option again to cancel it.
The DIHEDRAL option calculates and displays a dihedral angle between 4 atoms. When this option is activated, the cursor arrow changes successively to <1, <2, <3, and <4, meaning that the first, second, third, and fourth atoms should be picked. The angle value is displayed in the upper-left information area. Pick the option again to cancel it.
The CLEAR ALL option switches off any previously calculated distances and angles.
The RAMACHANDRAN option calculates the phi, psi, and omega conformations and angles and displays the Ramachandran plot corresponding to the last-picked residue. This option does not work with the first and last residues. A general Ramachandran plot is available with the RAM ALL option in the Plot menu. Pick the option again to cancel.
With the NEIGHBOR option it is possible to display all the contacts existing between the last picked atom and its neighbors. An atom is defined as being a neighbor if its distance from the picked atom is lower than the neighbor cutoff. The default cutoff is set at 4 but can be modified with the Textport order RAD NEIGHBOR. The contacts are displayed with dashed lines, and the distances are given between 2 atoms. Pick the option again to cancel it.
The H-BONDS option displays hydrogen bonds as dashed lines on the atoms displayed. Three types of atoms are defined: acceptor (N), donor (O), and acceptor/donor (OH,OG,OW). The distance range is between 2.6 and 3.5 . Hydrogen bonds are not possible within one residue or between two consecutive residues. This option runs only on molecules containing no hydrogen atoms.
OCCUPANCY
With the OCCUPANCY option, you can set the occupancy of the last picked atom to a new value. Those values are kept in memory, and you should activate SAVE to transfer them to the disk data base.
CHAPTER 9
Editing Menu:
Editing the Structure
DELETE, INSERT, REPLACE, SHEET/HELIX, ADD ATOM, [WAT]/CA, DEL ATOM, OPEN MODEL**, DATA BANK**, CONNECT MOL.
The Editing menu options can be used to modify the molecule by inserting, deleting, or replacing information. OPEN MODEL** and DATA BANK** mainly serve to construct small molecules, although they can be used on any protein structure.
With the DELETE option, it is possible to delete the last-picked residue in the molecular structure. This option works on the memory storage, and you must save the molecule if you want to keep the changes.
The INSERT option inserts a residue into a molecular structure. The new residue is inserted either before or after the last-picked residue. The residue must be chosen first on the menu. A Textport appears and a prompt asks for the name of the residue and its location, after or before the picked residue. The type of secondary structure can be chosen by using the SHEET/HELIX option on the same menu. SHEET works by default. The position of the side chain is given by the dictionary. This option works on the memory storage, and you must save the molecule if you want to keep the changes.
The REPLACE option replaces the last-picked residue in the molecular structure. The residue to be replaced must first be chosen on the menu. A Textport appears and a prompt asks for the position of the side chain: the previous one or the one defined by a dictionary. This option works on the memory storage, and you must save the molecule if you want to keep the changes.
The SHEET/HELIX option specifies the secondary structure of the inserted residue. The residues are inserted in the sheet or helical conformation whether this option is activated or not.
Editing Menu Table
Ignore in brackets [The ADD ATOM option adds a new atom which will be treated as a new residue, in the required position. This option is best accomplished with the orthogonal view displayed. With the left button on the mouse, pick the atom position required on the main view (x and y screen coordinates). A line will appear in the orthogonal view. With the left button on the mouse, pick the point on the line where you want to place the atom. Confirm the entry by picking yes or no. If you pick yes, a Textport will appear, and a prompt will ask you for the name of the residue. This option can work in a permanent way. If you choose so, the name of further residues will be set automatically by increasing th first name given. This option also works on the memory storage, and you must save the molecule if you want to keep the changes.]
Note: On November 28, 1996, Anne Gael wrote:
In the next release, I will implement both methods
The [WAT]/ CA option serves to choose the type of atom you want to add, using the ADD ATOM option in the same menu. A water molecule or an ALA residue (atom type CA) will be added whether this option is active or not.
THE DEL ATOM option deletes an atom in a molecular structure. Be careful with this option and keep in mind a possible dictionary/structure mismatch.
OPEN MODEL (submenu)
OPEN MODEL, CONSTRUCT**, USER DICT, COMMON, SUGARS, AM-ACIDS.
With the OPEN MODEL option, it is possible to obtain access to all the necessary tools for designing a new molecule. The construction takes place step by step by adding successive fragments. A dictionary is available containing some of the basic fragments you may need. To connect a fragment to your molecule, you should select a hydrogen atom on your molecule and a hydrogen atom on the new fragment (or vice versa). You can have your own dictionary (user dictionary), in which you can keep specific molecules (such as your own ones and any small ones which may be useful). When you activate this option for the first time within Turbo, the name of the user dictionary is requested.
CONSTRUCT (sub-submenu)
ADD FRAG, ADD ATOM H, REPLACE ATOM, DEFINE RESIDUE, DEFINE ANGLE, DEFINE DIST, DEFINE ATOM.
The ADD FRAG option serves to add a fragment to your molecule. First select a hydrogen atom on your molecule and a hydrogen atom on the appropriate fragment (or vice versa) to connect the new fragment to your molecule. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The ADD ATOM H option adds a hydrogen atom to any specific atom in your molecule. Select the atom to which you want to add a hydrogen atom (e.g., a carbon atom) before selecting the option. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The REPLACE ATOM option transforms your atom into one of another type. Select first the appropriate atom, before selecting the option. Then choose the new type of atom in keeping with the valence. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The DEFINE RESIDUE option serves to reorganize your molecule. First, select a set of atoms, using the BREAK BONDS option, then select this set by picking an atom, before selecting the option. Since the new name of the residue will be automatically calculated, the new type of residue is requested. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The DEFINE ANGLE option reshapes an angle. After selecting the option, determine the angle you want to reshape by picking the three atoms. The third atom and all the atoms connected to it will then be shifted to design the new angle. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The DEFINE DIST option reshapes a distance. After having selected the option, determine the distance you want to reshape by picking the two atoms involved. The second atom and all the atoms connected will then be shifted. This option works on the memory storage, and you should save the molecule if you want to keep the changes.
The DEFINE ATOM option renames the atom that you have picked.This option works on the memory storage, and you should save the molecule if you want to keep the changes.
DATA BANK (submenu)
SEARCH NAME, SEARCH CHEMIC, USER DICT.
The SEARCH NAME option provides access to the main dictionary. You have to give a string of letters to obtain all the molecules whose name contains these letters.
The SEARCH CHEMIC option grants access to the main directory. Once you have entered the chemical formula (or part of it), you will obtain all the molecules containing these atoms.
The USER DICT option will help you manage your own dictionary, i.e, LIST the contents, CREATE a dictionary, DELETE a dictionary, INSERT a molecule, and DELETE a molecule.
With the CONNECT-MOL option, the connectivity of the molecule can be recalculated. This step can be performed after FRAG ROT/TRANS, MOVE ATOM, REFI, and BREAK BOND, if necessary.
CHAPTER 10
The Modeling Menu
Modeling Menu: Designing the Molecule
BOND, BREAK BOND, FRAG ROT/TRANS, MOVE ATOM, REFINE, DGNL, DGNL PICK, TORSION**, RSR-WAT, RSR FULL.
The options of this menu can be used to modify and correct the geometry of the selected molecule.
The BOND option establishes a bond between two successively picked atoms. This option also works with bones points, but not with a mixture of bones and atoms. When this option has been activated, the cursor arrow changes successively into <1 and <2, which means that the first and second atoms should be picked.
The BREAK BOND option removes a bond between two successively picked atoms. This option works also with bones point, but not with a mixture of bones and atoms. When the option is activated, the cursor arrow changes to <1 and <2, which means that the first and second atoms have to be picked.
The FRAG ROT/TRANS option can rotate and translate a molecular fragment up to 10000 atoms in size. The fragment is defined as a set of connected atoms in the memory. If applied to Carbons Alpha, the rest of the atoms will follow. Therefore, to define a fragment, use the BOND and BREAK BOND options. The changes can be made using the dial (or pseudo-dial). The new position can be confirmed in memory or not by picking yes or no. The SAVE option in the Main menu should be used to save the new coordinates on the disk, and if necessary, the CONNECT-MOL option to reconnect your fragment.
The MOVE ATOM option serves to move a single atom. The new position can be confirmed or not by picking yes or no. The SAVE option in the Main menu should be used to save the coordinates on the disk, and if necessary the CONNECT-MOL option to reconnect your atom.
The REFINE option geometrically refines a stretch of residues. It uses the former Frodo routine REFI, but with a different user interface. The residues have to be described in the $TURBO_DIR/dict/dict.pdb file. You can select the stretch of residues by picking the first and last residues. The first residue cannot be a proline. This triggers REFINE, and each step is displayed on screen. The new position can be confirmed in memory by picking yes or refused by picking no, or you can start performing new operations on the same stretch by picking CONTINUE. You must use the SAVE option in the MAIN menu to save the coordinates on the disk, and CONNECT-MOL to reconnect your fragment if required.
The DGNL option extracts from the data base and display a 3-D molecular fragment that is homologous to a selected fragment of a loaded molecule. This option is based on diagonal distance matrixes and on the DGNL concept by Alwyn Jones, but it has been rewritten. You first have to define the fragment by picking the first and last residues (maximum 20 residues in the fragment). After the calculation, the information fields of the 10 best fragments (lowest in deviation) are displayed on the left side of the screen. These fields contain the name of the source protein, the sequence of the fragment, and the RMS deviation. You can display a fragment by picking its information field. If a map is attached to the molecule, the way in which the fragment fits in the density is displayed on a graph in the lower-left corner. A fragment can be stored in memory by picking yes. Picking no brings the option to an end. You must use the SAVE option in the Main menu to save the coordinates on disk.
The DGNL option can also be used on bones atoms as long as there is only one molecule entry on the screen. First "dummy" poly-ala entry needs to be prepared by reading the following file, $TURBO_DIR/dict/poly-ala.wh. You can then use DGNL in the same way, using REPLACE to obtain the requisite sequence.
The DGNL PICK option is the same as the DGNL option except that it can perform an insertion of some residues. Pick all the consecutive residues that define a first part of a fragment, then specify the number of residues to insert, then pick the consecutive residues that define the last part of the fragment. You must use the SAVE option to save the coordinates in the Heap file.
TORSION (submenu)
TORSION-PICK, TORSION-AUTO, DENS-SEARCH, DIST-SEARCH.
The TORSION-PICK option can modify up to 8 torsion angles defined between two selected atoms. When activating this option, the cursor becomes <1 and <2, prompting for the selection of the first and last atoms defining the torsion angle(s). The angles are then numbered, and each angle corresponds to one pseudo-dial on the lower-left part of the screen. The new position can be stored or not in memory by picking yes or no. Use the SAVE option in the MAIN menu to save coordinates on disk.
The TORSION-AUTO option modifies any of the torsion angles of the last residue picked. The torsion angles are automatically defined on both the main and side chains. The angles are numbered, and each angle corresponds to one pseudo-dial on the lower-left corner of the screen. The new position can be stored or not in memory by picking yes or no. Use the SAVE option in the MAIN menu to save the new coordinates on screen.
The DENS-SEARCH option automatically fits amino acids depending on their electron density map. This option runs on the last-picked residue. You can choose from among the twenty best positions. The position chosen can be accepted or refused by picking yes or no. Use the SAVE option within the MAIN menu to save the coordinates on disk.
The DIST-SEARCH option automatically fits amino acids depending on their atomic environment. This option runs on the last residue to be picked. You can choose between the twenty best positions. The position chosen can be stored in memory or not by picking yes or no. Use the SAVE option within the MAIN menu to save the coordinates on disk.
The RSR (Real Space Refinement) -WAT option fits an atom into a density map by seeking the nearest local maximum. This option is particularly useful for fitting water molecules. If several density maps are displayed, you will be asked for the one in which you would like to fit the atom.
The RSR-FULL option fits a set of atoms (a maximum of 100) into the density by seeking the nearest local maximum. If several density maps are displayed, you will be asked for the one in which you would like to fit the set of atoms. If only one map is displayed, the fitting will be processed on it.
CHAPTER 11
The View Menu:
Representing the Structure
SPHERE, CA, BACKBONE, CA-SIDE-RES, CA-SIDE-NAME, NO HYDROGEN, SMALL CIRCLE, LABEL ATOM**, COMPACT SELE**, COMPACT-DO-IT, MAP SPHERE.
This menu contains both options and submenus. These options and those contained in the submenus are used to set the type of representation of the selected molecule and the atom labeling.
The SPHERE option displays the molecular contents of a sphere, the size of which is defined by the radius. This radius can be set with the RADIUS SPHERE Textport option.
The CA option selects and links the Alpha Carbon atoms of the last molecule to be picked. The maximum possible distance at which two consecutive atoms can be linked is 6.3 .
The BACKBONE option selects the backbone atoms (main chain) of the last molecule to be picked.
The CA-SIDE-RES option selects and displays amino acid side chains when the CA or BACKBONE option has been activated. When one of these options has been activated, a list of amino acids shows up in the pull-down menu. You can then pick the amino acids required and conclude with END.
The CA-SIDE-NAME option selects and displays amino acid side chains in terms of their position in a sequence when either the CA or BACKBONE option has been activated. When one of these options has been activated, a Textport appears from which it is possible to select the residue names. You must end the list by a period (.).
View Menu Table
The NO HYDROGEN option removes the hydrogen atoms display from molecules. This option does not remove the hydrogens from memory, but you can do that with the DELETE ATOM Textport option.
The SMALL CIRCLE option presents atoms in the forms of filled depth-cued circles, the radii of which are 1/10 of the corresponding atom. This mode is a "pseudo balls and sticks" display, which makes interactive handling possible.
LABEL ATOM (submenu)
LABEL TYPE**, DEF FONT, COLOR LABEL
LABEL TYPE (sub-submenu)
The LABEL TYPE option allows one to choose among various modes of displaying atom labels. These modes are as follows :
T1 / T3 mean one-letter code/ 3 codes giving the residue type. NAM is the name of the residue, ATO is the name of the atom, MOL is the name of the molecular entry, and DOM is the number of the domain to which the residue belongs, if it exists.
The DEF FONT option modifies the label font. In the Textport that appears, you can choose the size and font names. This option is useful to set pictures or photos of screens.
The COLOR LABEL option can be used to change the color of the labels.
COMPACT SELE (submenu)
CPK, BALL & STICKS, COMPACT ROT, CURVE LINE, CURVE PATCH, STRUC REP, STRUC MENU, RESET STR MENU.
This submenu contains options used when displaying a compact view of the loaded molecule.
The CPK option displays the last-picked molecule in the form of lighted compact spheres. From the menu which appears, you can choose the complexity (number of faces) and the size of the spheres. The radii of atoms (and so spheres) can be modified with the ATOM TYPE DEF option of the DEFINE submenu, which is located in the Color menu.
This option displays the last-picked molecule as lighted "balls and sticks". In the appearing menu you can choose the type (B & S White, B & S Colored, STICKS ONLY) and the size of the "sticks". The radii of atoms (and so balls) can be modified with the ATOM TYPE DEF option of the DEFINE submenu found in the Color menu.
The COMPACT ROT option serves to work interactively in the compact display mode. When this option has been activated, you can use the dials (or pseudo-dials) to move the molecule around.
The CURVE LINE option displays a curved line calculated from the Alpha Carbons positions.
The CURVE PATCH option displays a curved surface calculated from the Alpha Carbons positions.
With the STRUC REP option, secondary structures can be displayed in the vector mode in the form of cylinders, arrows, and ribbons. The COMPACT-DO-IT option will then transform this view into compact display.
This option recovers the default values of the STRUC MENU features.
The COMPACT-DO-IT option calls up a compact view based on the previously selected modes.
The MAP SPHERE option displays the map only around the displayed atoms. Use the Textport order RADIUS MAP to define the radius you want.
CHAPTER 12
The Plot Menu:
Graphs and Postscripts
WRITE MATRIX, GRAPHICS**, RAMA ALL, ALL MODE, SEQUENCE, SET VIEW**.
This menu's options enable the user to obtain hard copies of the displayed molecule(s) and to display some of the information built up by residue.
Most of these options create Postscripts files (GRAPHICS' options, PLOT, RAMA ALL). For the PLOT option, keep in mind that the thickness of the lines can be adjusted by making color selections using the SAME color map. The uppermost line is the thickest (red very thin, white very thick). These ASCII Postscript files can be named and fed into a Postcript laser printer. To send a file on UNIX workstation to a laser printer, follow this procedure:
WRITE MATRIX
The WRITE MATRIX option writes the current orientation matrix on disk.
GRAPHICS (submenu)
GRAPH B-F ALL, GRAPH B-F M/S, DIFF B-F ALL, DIFF B-F M/S, GRAPH.
The GRAPH B-F ALL option displays the B-factors per residue (all the atoms except hydrogens) of a single molecule on a graph. A Postscript output file can be generated.
Plot Menu Table
The GRAPH B-F M/S option displays the B-factors per residue (main and side chain except hydrogens) of a single molecule on a graph. A Postscript output file can be generated.
The DIFF B-F ALL option displays the difference of B-factors per residue (all the atoms except hydrogens) of the last two molecules picked.
The DIFF B-F M/S option displays the difference of B-factors per residue (main and side chain except hydrogens) between the last two molecules picked. A Postscript output file can be generated.
The GRAPH option displays the RMS deviation per residue on a graph after superimposition performed by the RIGID2 option (Tools menu) and by the Textport options COMPARE or DEVIATION. While running RIGID2, you will be asked for a deviation file name. This file must be an input to the Textport option GR-RMS-DEV. For the other options, GRAPH displays automatically the result. Two graphs can be displayed simultaneously. The option works with the GR-RMS-DEV Textport option.
The RAMA ALL option displays the full Ramachandran plot of the last molecule to be picked. You can generate a Postscript file with this plot. This file can be named and sent to a Postscript laser printer.
The ALL MODE option gives access to some options for displaying all the molecules that have been loaded. The following display options are available in the ALL MODE: all the options in the Color menu working on whole molecules, CA, BACKBONE, CA-SIDE-RES, CA-SIDE-NAM, NO-HYDROGEN, NO-PSEUDO, PSEUDO-HYDS, RAMA ALL.
The SEQUENCE option displays the sequence of the last-picked molecule. You may go backward or forward with the different commands or use the lift to display the entire sequence.
SET VIEW (submenu)
PLOT, PLOT FRAME, TITLE, PHOTO, SCREENSAVE, SCREENSAVE ALL, WHITE BACK
The PLOT option writes the model displayed on a Postscript file. The Textport appears and prompts you to give a file name.
Warning: The size of the SPLIT STEREO view is wrong and does not fit the PLOT FRAME.
The PLOT FRAME option displays the plotting frame (size of the paper). You can modify the position of the frame by selecting its lower-left corner with the mouse's left button and by moving it interactively.
Warning: The size of the SPLIT STEREO view is wrong and does not fit the PLOT FRAME; it should be set to 2-3 centimeters on screen.
The TITLE option displays up to ten titles on the screen. When defining a title, one is asked to give the title itself, the type and size of the font, whether or not the title should be displayed with an arrow, and the width of the arrow. The title and the arrow can be moved separately by dragging on the little green box at the end of the arrow. Please note that some fonts may not be available in the required size. This depends on the fonts provided by your computer. The TITLE option is useful to set pictures or photos of screens.
The PHOTO option removes the boxes from the titles and arrows so that a photo of a screen can be taken.
The SCREENSAVE option captures an image (rgb format file) of Turbo. Give a name to your rgb file and then prepare the view to capture the image (CPK views, SECOND STRUCT, or whatever you would like). When ready, drag the mouse while keeping the left button depressed to define the area that you want.
The SCREENSAVE ALL option works the same way as SCREENSAVE but captures a view of the entire screen. When ready just activate the left button.
The WHITE BACK option lets you work on a white background instead of a black one.
CHAPTER 13
The Tools Menu:
The Workshop
RIGID 2, SCAN, MAPS**, BUILDING**, BONES**, SYMMETRY**, NCS**, NMR**, TRAJECTORY**, SECOND STRUCT**.
This menu contains submenus, which in turn contain options for displaying the electronic density maps, the bone maps, the symmetric molecules and NMR features, and the dynamic trajectories.
The RIGID 2 option refines the fit between two molecules that are already quite similar. This option works in the same way as RIGID (see this Textport option), except that a rough fit has to already exist.
The SCAN option displays the different dynamic conformations one after another. You must first have loaded the conformations, using the TRAJECTORY Textport option. You can set the speed and the way you want to scan molecules (forward, backward, one way, or in a loop) by using the tape-recorder-like commands. Other features are available under the display TRAJECTORY submenu in the Tools menu.
MAPS (submenu)
Tools MenuMAPS
With the MAPS option, you can display the maps' management menu. The 5 map entries with their 5 possible levels are listed. You can manage the display of the maps and levels by picking on DEF. In this case, Textport appears and asks you to give the new parameters (the levels, the color associated with each level, the box size, and the contour direction). You can change the MAP COLOR by picking COL in the box on the right.
Tools Menu Table
BUILDING (submenu)
MAKE FRAGS, HIDE FRAGS, ALIGN FRAGS, ADD TPPR, MULTI REPLACE, TOOLS BOX**, CA LABELS.
The MAKE FRAGS option connects the CA atoms which are less than 5 angstroms apart. This cutoff is the default and can be modified with the DIST CA Textport option. If present, the map will help the process of fragment building. Connections outside the density are not allowed. The density cutoff is chosen as the first displayed level. If several maps are displayed, choose one with the WORK MAP Textport option. Those fragments will be aligned further with the target sequence in the ALIGN FRAGS option.
The HIDE FRAGS option disables the display of the previously built fragments.
The ALIGN FRAGS option performs the alignment of previously built CA fragments on the target sequence. These fragments must have been built with the MAKE FRAGS option, and the target sequence must have been loaded with Textport's LOAD SEQUENCE order. The 10 best alignments are proposed, and results are presented along the sequence with a color code: green for correct matchings, red for wrong matchings, and yellow if both residue types belong to the same group (short, medium, long, or aromatic). To accept an alignment, click CONFIRM, and all residues will be ordered and named after the target sequence. This options works on the memory storage, and you must save the molecules if you want to keep the changes. Note that you can work with either the right or middle mouse buttons. The left button will end the alignment screen.
The ADD TPPR option fits a Trigonal Planar Pseudo Residue in the electron density map. After activating the option, activate one of the two BUILD MODE buttons that appear on the right of the screen. Click on the density map where you would like to add the pseudo residue with the left mouse button. The pseudo residue comes at this place and is automatically fitted by a special algorithm of Real Space Refinement. If you choose the BM1 button, RSR will be performed with both rotation and translation. If you choose the BM2 button, RSR will be performed with only a rotation. For the first residue you add, you have to specify the name (suffix included), and the following residue names will be increments of this first one. TPPRs are added on the last molecule. This option Works on the memory storage, and you should save the molecule if you want to keep the changes.
The MULTI REPLACE option replaces a set of Trigonal Planar Pseudo Residues by real residues. The TPPRs must first have been aligned with the target sequence, so that the atoms are named after N, CA, C, and CB.The first step of the replace algorithm is to create the backbone oxygens. This step is achieved by rotating a virtual peptidic bond on the CA (i) CA (i +1) axis and searching for the best fit in the density map, for the N, C, O of this virtual bond. They are then replaced by residues according to their types. The side-chain orientation is given by the CB position of the former TPPR. One cycle of refine is automatically performed.
If there is one mismatch between the set of residue types and the target sequence, you will be asked to correct the TPPR types. This option is also suitable for Molecular Replacement. You have to change the residue types of your residues with the CA LABELS option, and the side chain will thus be changed. The MULTI REPLACE option works on the memory storage, and you should save the molecule if you want to keep the changes.
TOOLS BOX (sub-submenu)
RESI ROT/TRANS, RSR MAIN, RSR SIDE, ROTAMERS.
The RESI ROT/TRANS option works as the FRAG ROT/TRANS option does, but the whole last-picked residue is automatically selected. The modifications are made by using the pseudo-dials visible on the left side of the screen. This option works on the memory storage, and you should save the molecule if you want to keep it changed.
The RSR MAIN option fits the backbone (N, CA, C, O, CB) of the last-picked residue into the density by seeking for the nearest local maximum. The side chain follows the movement of the C Alpha atom. You can choose the map that you would like to fit in with the WORK-MAP Textport option. If only one map is displayed, the fittting will be performed on it.
The RSR SIDE option fits the side chain of the last-picked residue into the density by seeking for the nearest local maximum. The main chain remains unchanged. You can choose the map you would like to fit in with the WORK-MAP Textport option. If only one map is displayed, the fitting will be performed on it.
The ROTAMERS options proposes all different rotamers of an amino acid as they have been defined by J.W. Ponder and F.M. Richards. This option runs on the last-picked residue. The chosen position can be accepted or refused in memory by picking YES or NO and can be modified by using the left pseudo-dials. The figure noted for each proposed rotamer is its frequency in the Ponder and Richards protein panel.
In the label window, you may change the residue type of the last-picked residue by clickingf with the right mouse button on the appropriate place. Note that this type is important for the ALIGN FRAGS option. You can also add a comment to the residue, but the comment must not be longer than 60 characters. Comments may be listed or dumped in an ascii file via the LIST COMMENTS and MAKE COMMENTS Textport orders, respectively.
BONES (submenu)
BONES ON/OFF, 8 CELLS, BONES MAIN, BONES SIDE, UNDEFINED, BONES SAVE, BONES C ALPHA, CREATE CA, CREATE TPPR.
This is not a menu or submenu but a new feature. A new label window now appears when a bones point is selected. In this label window you may change the name (or label), the bones type, or the residue type of the last-picked bones point by clicking with the right mouse button on the appropriate place. The bones type is one of the four following types: C ALPHA, MAIN, SIDE, UNDEFINED; choose one in the appearing pop-up menu. The residue type is one of the 20 amino acids or one generic type such as Short, Medium, Long, or Aromatic. You can give a name to the C ALPHA bones points. The name consists of a number and a letter, which can be considered as a fragment label. If adjacent and connected C ALPHA points exist, a name will be proposed for the last-picked point. If you would like to keep the changes, you should ask for the BONES SAVE option.
The BONES ON/OFF option toggles on and off the bones map display.
The 8 CELLS option calculates and displays the bones map of 8 cells.
The BONES MAIN option displays only the bones identified as belonging to the main chain.
The BONES SIDE option displays only the bones identified as belonging to the side chains.
The UNDEFINED option displays any bones that have not been identified as belonging to either the main chain or the side chains.
The BONES SAVE option saves on disk the status and the connectivity of the bones map.
The BONES C ALPHA option displays only the BONES identified as C ALPHA points. In the label window, you may change this bones type as well as the residue type and label by clicking with the right mouse button on the appropriate place.
The CREATE CA option creates residues (of only one CA atom) at the location of the bones points identified as C ALPHA. Define a fragment by picking the first and last bones point.
The CREATE TPPR option creates Trigonal Planar Pseudo Residues at the location of the bones points identified as C ALPHA. They are automatically fitted by a special algorithm of Real Space Refinement. Define a fragment by picking the first and last bones point.
SYMMETRY (submenu)
SYM NEIGH, 1 CELL, 27 CELLS, 1 BOX, 27 BOXES, CELL CONTENT, DEL SYM, NO SYMM.
The SYM NEIGH option displays all symmetry and translation-related molecules within radius R from the origin molecule. The R radius can be adjusted with Textport's RAD SYM order.
The 1 CELL option displays all the symmetric related molecule of the defined space group according to the definitions of the international tables. This option requires the CA view mode.
The 27 CELLS option displays all the symmetric related molecules of the defined space group with all the translations along the cell axis. This option requires the CA view mode.
The 1 BOX option displays a representation of the cell.
The 27 BOXES option displays 3*3*3 representations of the cell.
The CELL CONTENT option displays all the symmetric related molecules of the defined space group, but relevant translations have been applied to place them into the cell. This options requires the CA view mode.
The DEL SYM option cancels the display of the most recently picked symmetry-related molecule.
The NO SYMM option switches off the symmetry display.
NCS (submenu)
APPLY MATRIX, AUTO APPLY, NCS MAPS, PRINT NCS.
With this option, you can display the Non-Crystallographic Symmetries. You have to define the symmetries with Textport's DOMAIN and NCS options.
With this option, you can also display the Non-Crystallographic Symmetries, and you first have to define the symmetries with Textport's DOMAIN and NCS options. In this option's case, however, the display is automatic: Only symmetries related to the centered residue will be displayed.
The NCS MAPS option allows you to diplay the symmetric box of a map if Non-Crystallographic Symmetries are defined for the protein. Symmetries defined for the last picked molecule are applied if APPLY MATRIX is activated. Symmetries defined for the centered molecule are applied if AUTO APPLY is activated. You can define different levels and colors than those in the original map box. Furthermore, you can ask for map difference or average density. The map difference is represented by the absolute value of the difference, and, in addition, only positive values are considered. The average density represents the average between all symmetric boxes and the original one.
The PRINT NCS option allows you to display the rotation matrix and translation of the different Non-Crystallographic Symmetries defined, in Textport. Give a file name if you want your matrix to be printed in a file.
NMR (submenu)
NMR ON/OFF, VIOLATIONS, COL REST ATO, COL REST RES, DISPLAY RES, PSEUDO HYDS, NO PSEUDOS.
The NMR ON/OFF option toggles on and off the constraints display. The constraints are displayed as colored lines according to the following code:
The colors will change interactively when you activate the FRAG ROT TRANS and TORSION options in the MODELING menu.
The VIOLATIONS option displays only the constraints which have been isolated (value> maximum value range +0.2) (Red lines). 0.2 is the default tolerance. You can set it with Textport's TOLERANCE option.
The COL REST ATO option colors the atoms depending on the constraints. Yellow means that there is no constraint with this atom; the colors range from blue (few constraints) to red (many constraints).
The COL REST RES option colors the residues depending on the number of contraints. Yellow means that there are no contraints with the residue; the color ranges from blue (few contraints) to red (many constraints).
The DISPLAY RES option displays only the contraints applying to the most recently picked residue.
The PSEUDO-HYDS option generates pseudo-hydrogens. These artificial atoms can be used instead of protons in cases where there is no stereospecific assignment. They can be created with protons previously generated using the nmr paramameter files of XPLOR.
The NO PSEUDOS option serves to alternatively switch on and off the pseudo-hydrogen display.
TRAJECTORY (submenu)
DEFINITION, STATIC, DYNAMIC.
The DEFINITION option defines the dynamic conformations you want with the TRAJECTORY option. The program will prompt you to give the name of the trajectory files and the way you want to display the different conformations (see Textport's TRAJECTORY option for details).
The STATIC option displays all chosen conformations. When picking an atom, the conformation number is given in the information pad.
The DYNAMIC option highlights the molecular dynamic trajectory. When this option is activated, the following command pad apppears in the lower part of the screen:
Where MODE is: step by step / one way /auto reverse / loop, and NUM is the number of the displayed conformation.
SECOND STRUCT (submenu)
HELIX, SHEET, TURN, COIL, FAST CALC, DSSP CALC, ACCESS CALC.
The SECOND STRUCT option displays on the screen only some secondary structure elements (e.g. Helices,Turns, and so on). The default color of these elements can be changed with the display option SECOND STRUCT of the DEFINE submenu (Color menu).
Tools MenuSECOND STRUCT HELIX, SHEET, TURN, COIL
1/ Serves to select these secondary structures, once they have been defined by either FAST CALC or DSSP CALC for display.
2/ If the CHANGE option is selected, the secondary structure type of the most recently picked residue is set to the chosen secondary structure HELIX, SHEET, TURN, or COIL.
The FAST CALC option calculates the secondary structures using the fast and dirty algorithm based on inter-CA distances. This option works on the memory storage, and you should activate the SAVE option to keep the result.
The DSSP CALC option calculates the secondary structures. The algorithm used here is from Kabsch and Sander's DSSP program, with minor modifications. This option works on the memory storage, and you should activate the SAVE option to keep the result.
The ACCESS CALC option calculates the water-accessible surface by residue. The algorithm used is also from Kabsch and Sander's DSSP program, with minor modifications. This option works on the memory storage, and you should activate the SAVE option to keep the result.
CHAPTER 14
The Surface Menu:
The Landscape
SURF MENU, NO SURF, SAME COLOR, COLOR SURF, NEW VDW SURF, ADD VDW SURF, VDW MENU, COLOR VDW.
This menu contains options to calculate and display Van der Waals surfaces and submenus in which the different loaded surfaces, Van der Waals, Connolly, and Spline surfaces may be selected or switched on and off. Connolly surfaces must have been previously calculated (with programs supplied in the $TURBO_DIR/ms subdirectory) and loaded with the Textport LOAD SURFACE order. Van der Waals surfaces, on the other hand, are interactively calculated.
The SURF MENU option displays the surface menu. You can switch each loaded molecular surface on/off. You can also select a surface with the menu.
The NO SURF option switches off the surface display.
The SAME COLOR option colors the selected surface with a single color. This makes the surface display more interactive. If the surface is already colored, however, and depending on the type of atom or residue, there will be a mismatch when you activate this option.
The COLOR SURF option switches the system over to the color surface mode. All the subsequent color options will be applied to the selected surface.
With the NEW VDW SURF option, a Van der Waals surface can be generated around the defined atoms. Before defining the set of atoms, the first and last residues of the required stretch should be picked.
The ADD VDW SURF option can add a new Van der Waals surface around the defined atoms. To define the set of atoms, you should pick the first and last residues of the desired zone. Each VDW surface is numbered and can be switched on or off in the VDW MENU.
The VDW MENU option switches on or off each Van der Waals surface. You can select a surface within this menu.
The COLOR VDW option switches the system over to the color Van der Waals surface mode. All the subsequent color options will be applied to the selected VDW surface.
CHAPTER 15
The Molecule Menu:
Displaying Loaded Molecules
This menu contains the loaded molecules
Moleculesloaded
Moleculesdisplay. With this menu, the loaded molecules can be displayed or not depending on whether their name is highlighted or not. There is no limit to the possible number of entries, but only the names of the first eight loaded molecules are displayed. If you have loaded more than eight molecules, you can have access to the others via the "updown" option on this menu. For each molecular entry, you can manage the display of zones by picking the Z-knob.