FREAD: PDB [WH].

The FREAD option reads structural data from ASCII disk files with the Wayne Hendrickson (WH) or Protein Data Bank (PDB) formats when the coordinates are fractional. You have to enter the cell parameters before reading your molecule. For example:

LIST: ATOMS BONES [HEAP] MAP MOLECULE RESIDUES SURFACE.

With the LIST option you can generate a list of information from memory data (atoms, residues, molecules), disk data (heap), or file information (bones, map, surface). This option works on the molecule selected. For example:

LOAD: BONES MAP [MOLECULE] NMR SEQ SURFACE.

The LOAD option loads molecules (from the heap disk storage), bones, maps, NMR constraints and surface (from the respective files). For example:

MAKE: ACCESS MS PDB SS [WH] XPDB.

With the MAKE option, you can write ASCII files on a disk with Wayne Hendrickson, Protein Data Bank, and Connolly Molecular Surface (MS) formats or with a special PDB format for the XPLOR program (XPDB). The coordinate source is the memory storage. For residue accessibility (ACCESS) and secondary structure (SS), the information is dumped onto the disk under a classical ASCII file. The name is requested on the screen. For example:

The symmetry number is based on the Turbo system of numbering. (Pick any atom belonging to the molecule in question to find out its number.)

The MAKE XPDB option asks for an additional information to meet the generate.inp format requirements of XPLOR, i.e., >segment name. If you are not working on a multichain protein, just hit RETURN, otherwise give the segment name (up to 4 characters).

RAD: BONES MAP NEIGHBOR [SPHERE] SYMMETRY.

The RAD option defines the radius of several objects: BONES for the bones map, MAP to display the map around the displayed atoms, NEIGHBOR for the GEOMETRY NEIGHBOR option, SPHERE for the View menu option,and SYMMETRY for the SYMMETRY NEIGHBOR option. For example:

READ: ACCESS PDB SS [WH].

The READ option reads structural data from ASCII disk files with Wayne Hendrikson or Protein Data Bank formats. For residue accessibility (ACCESS) and secondary structure (SS), the information can be read from the Turbo ASCII file previously recorded on the disk, or from the ACCESS or SS file with the Turbo format. For Example:

SELECT: [MOLECULE].

With the SELECT option you can select the current molecule if it is already loaded in the memory. Several options (LIST,ZONE, among others) make use of the current selected molecule. For example:

UNLOAD: BONES MAP [MOLECULE] SEQ SURFACE.

ACCESS, ACON, BALL & STICKS, B-FACTOR, BFACT-DEF, BF-AVERAGE, CHANGE-NAME, COL_RAMP, COMPARE, COMPSEQ, CONNOLLY, CONTOUR, CP-HEADER, CPK, DEVIATION, DIST-CA, DOMAIN, DUPLICATE, END, GO, GR-ACCESS, GR-BF-DIFF, GR-PC-REFI, GR-RESET, GR-RMS-DEV, HELP, HYDROPATHY, INFOS, MAKE-DGNL, MAKE-DNA, NCS, NEIGHBOR, NMR-RIGID, NMR-SPECT, OCCUPANCY, PSEUDO-DIALS, READMULT, READ-NMRPDB, RENAME, RIGID, SAVE-E, SETLINEWIDTH, SLAB-DISPLAY, SOLVENT, SPLINE, SYMMETRY, SYSTEM, TOLERANCE, TRAJECTORY, TRANSLATE, VDW-DENSITY, WORK-MAP, ZONE.

ACCESS

The ACCESS option calculates the accessibility of each residue for a given protein, with respect to the solvent. You can further color the protein accordingly to the accessibility to the solvent. Acessibility scores are not saved until you activate the display option SAVE. You can keep accessibility scores in an ascii file by using the Textport order MAKE ACCESS (and read them with the Textport order READ ACCESS).

ACON

The ACON option centers the selected atom to display the current molecules, maps, surfaces, and so on. The input is the name of the residue and that of an atom (CA or first atom is by default). For example:

BALL & STICKS

The BALL & STICKS option defines zones that are to be displayed as "balls and sticks". The non-selected parts keep the status previously defined, using the COMPACT SELECT screen option in the View menu. For example:

B-FACTOR

The B-FACTOR option allows one to change the B-factor values of atoms, for a range of residues. For example:

BFACT-DEF

The BFACT-DEF option defines the range of B-factors used by the FEATURE BFACT option in the display Color menu: For example:

BF-AVERAGE

The BF-AVERAGE option provides the averages of the B-factors for the whole residues, the backbone, and the side chain. This option works for a range of residues. For example:

CHANGE-NAME

The CHANGE-NAME option changes the name of the molecular entry in the heap.

COL_RAMP

The COL_RAMP option displays on the screen the color ramp used for the BFACT, HYDROPATHY, or ACCESSIBILITY color features of the display Color menu.

COMPARE

The COMPARE option compares 2 different zones. The molecules required must be loaded before running this option. For example:

You can display 2 graphics at the same time with the GRAPH option in the Plot menu. You can choose the graphic you want by giving the appropriate graph number. The deviation file gives the RMS deviation per residue. This file can be used as an input in the GR-RMS-DEV option.

COMPSEQ

The COMPSEQ option searches in the selected protein sequence the pattern that you specify. For example:

CONNOLLY

The CONNOLLY option reads a Connolly Surface File. Surface points can be attributed to the nearest atom. This option can be therefore rather time consuming. The output file name is file.ts if the input file name is file.srf. For example:

CONTOUR

The CONTOUR option centers the current molecules, maps, surfaces, and so on. The inputs are the XYZ coordinates of the point required. For example:

CP-HEADER

The CP-HEADER option copies some information from one molecular entry to another. The former molecular entry can belong to another heap file. You can copy map information, space group and cell parameters, zones, or non-crystallographic symmetry information.

CPK

The CPK option defines zones to be displayed as icosahedra. The non-selected parts keep the status previously defined using the COMPACT SELE screen option in the View menu. For example:

DEVIATION

The DEVIATION option calculates the RMS between two structures without carrying out any fitting on these molecules. The program prompts you to give the file name of the two molecules, as well as the name of the output file and the kind of deviation file you want. Type 1 deviation file contains the RMS values (in Postscript form) and can be used with the GRAPH option. Type 2 file contains the RMS values in the ASCII format, which are thus ready to print.

DIST-CA

The DIST-CA option defines the ideal distance between 2 C Alpha atoms. This is important for the LIST MOL Textport option, the CA display option, and the MAKE FRAGS option from the ab initio construction part. The default is set to 5 angstroms.

DOMAIN

The DOMAIN option allows you to specify the different domains of your molecule, e.g., monomers, fragments, and so on. One domain can include different zones. These domains can be colored with different colors, and they are required for Non-Crystallographic Symmetries. For example:

ND is the number of the domain that you want to modify. To add a domain in the list, give a new ND number. Be careful with this step because if you do not accurately use the above-mentioned syntax, previously defined domains will be removed.

DUPLICATE

The DUPLICATE option duplicates a molecular entry from the heap disk data base and files it under another name for further use and modification. For example:

END

The END option ends a Turbo session.

Ex: end

GO

With the GO option, you can leave Textport and start the interactive session.

Ex: go

GR-ACCESS

The GR-ACCESS option reads an accessibility output file and displays the corresponding graphics. Since Turbo-Frodo can display 2 graphics simultaneously, you must choose the one you want (graph number). For example:

You can display the graphics with the GRAPH option in the Plot menu. Be careful because the XPLOR accessibility output file does not have the same format as the MAKE ACCESS order, since if it had the same format, the MAKE ACCESS output cannot be used here.

GR-BF-DIFF

The GR-BF-DIFF option reads a B-factor diff output file to display the corresponding graphics. Since Turbo-Frodo can display 2 graphics simultaneously, you must choose the one you require (graph number). For example:

You can display the graphics with the GRAPH option in the Plot menu.

GR-PC-REFI

With the GR-PC-REFI option, you can read an XPLOR PC refinement output file and display the corresponding graphics. Since Turbo-Frodo can display 2 graphics at the same time, you must choose the one required (graph number). For example:

You can display the graphics with the GRAPH option in the Plot menu.

GR-RESET

The GR-RESET option initializes all the graph.

GR-RMS-DEV

The GR-RMS-DEV option reads a deviation file to display the corresponding RMS deviation graphics. Turbo-Frodo can display 2 graphics simultaneously, and again, you should choose the required graphics (graph number). For example:

You can display the graphics with the GRAPH option in the Plot menu.

HELP

The HELP option provides information about all the Textport options. To obtain access to this help, you must have the doc_text_port.txt files in the $TURBO_DIR/doc subdirectory. For example:

help rigid

HYDROPATHY

The HYDROPATHY option makes it possible to enter the window (number of residues) with which the hydropathy index will be computed. The default is 5 residues.

INFOS

The INFOS option provides access to some predefined parameters. For example:

---------

---------

HYDROPATHY :size of the window is 5 residues

---------

VDW DENSITY : 20 dp A2

---------

PSEUDO -DIALS are turned ON

---------

TOLERANCE : 0.2 A acceptable violation of NMR distance constraints.

---------

MAKE-DGNL

The MAKE-DGNL option creates a new DGNL data base. First, you should generate a heap data base (called dgnl.heap), selecting your own structures. Second, you should stop the program and start it again with another heap file (for example, test.heap). Third, you should activate MAKE-DGNL. The program prompts you to give the name of the heap that contains the new DGNL data base (dgnl.heap if you called it so). This option calculates the distance matrix, and the output is diag.mtx. To be used in further Turbo-Frodo sessions, the two files, dgnl.heap and diag.mtx, must be moved to the $TURBO_DIR/dict directory. For example:

...

DGNL > molecule 17: TOXIN

MAKE-DNA

The MAKE-DNA option generates the DNA molecule corresponding to the user's specifications. For example:

NCS

The Non-Crystallographic Symmetries handling option, or NCS, serves to define the symmetry operation between two domains, read a matrix file for a given pair, read the pairs, read rotation matrix and translation from another heap entry, as well as remove previously defined pairs.

1-Define an operation symmetry

You will be asked for a pair of domains. These domains are listed and must be defined with Textport's DOMAIN option. To define the symmetry, you can refer to the RIGID option for help. The rotation matrix and translation, as well as pairs, are systematically saved in the heap.

2-Remove previously defined symmetries

You will be asked for a pair of domains. Note that this pair will be removed from the heap.

3-Read a matrix file

Give the name of the matrix file. The format is the same as the one produced by the display option PRINT NCS. However, you can add spaces, lines, and comments if they are specified by a `#'.

4-Read a matrix from another heap entry

You will be asked for a molecule name. Make sure that defined domains are well defined and relevant.

NEIGHBOR

The NEIGHBOR option generates a file containing all the contacts, below a cutoff value, between 2 zones in 1 or 2 differents structures. For example:

NMR-RIGID

The NMR-RIGID option performs least-square rigid body fitting between a family of structures (source) and a single molecule (target). Please refer to the RIGID option (see below) for instructions about using NMR-RIGID.

NMR-SPECT

The NMR-SPECT option generates peak and ref files from a prot file. These files are used in the NMR assignment program EASY. For example:

OCCUPANCY

The OCCUPANCY option modifies or not the atom occupancy depending on the value of the B-factor. For example:

PSEUDO-DIALS

The PSEUDO-DIALS option turns off the screen pseudo-dials instead of a real dial service. For example:

pseu

> Do you want to use the pseudo-dials ([y]/n)y)? y

READMULT

The READMULT option reads several pdb files in a unique command. It prompts you to give the name of a text file, which must be created in the following manner:

READ-NMRPDB

The READ-NMRPDB option reads the special PDB files that contain several NMR structures. Enter a generic name for this set, and the different molecular entries will be named after it. For example:

The different molecules will be named TOXIN0, TOXIN1, TOXIN2, and so on. You can use the LOAD ALL order to load all the molecules.

RENAME

The RENAME option renames a molecular entry sequence. There are three possibilities: Change the starting count number, add a suffix, or both. You must load and select the molecule of interest before running this option. The changes are made in the memory. To save them, use the SAVE option in the Main menu. For example:

RIGID

The RIGID option performs a rigid body superimposition of a molecule (source) on another molecule (target). Both molecules have to be loaded in the memory. Source and target names are requested. At least three fitting points have to be given for the program to work properly. Note that in this unique case, the chain label, if it exists, has to be given before the residue name. For example:

The program will fit the two molecules using the alpha carbons of the two molecules that are less than the given cut-off, i.e., 10 , apart.

>RMS of 41 CA: 2.65

The residues of the 41 molecules were closer than the cut-off and were therefore used to fit the two molecules. The resulting RMS value was 2.65 .

>max distance CA selected (<CR< to finish): 2

> RMS of 25 CA: O.80

Another fit has been performed using alpha carbons which at this stage were closer than 2.0  (only 25 out of the 41 present in the sequence, which led to a better fit (RMS=0.80 ).

SAVE-E

The SAVE-E option saves the work environment of the selected molecule, thus saving the different zones defined and those that are activated. This option also saves the orientation matrix, scale, slab, zval, and intensity map. Since different orientation matrices cannot be active simultaneously, the first molecule loaded when running Turbo-Frodo is important: Only its matrix will be applied.

SETLINEWIDTH

The SETLINEWIDTH option allows you to change the width of displayed lines. Note that antialiasing is supported only with a width of 1.

SLAB-DISPLAY

The SLAB-DISPLAY option displays the dimension of the clipping world.

SOLVENT

The SOLVENT option defines a residue with a residue type so that it will not be taken in connectivity calculation (CONNECT).

SPLINE

The SPLINE option reads a Spline Connolly Surface File. Surface points can be to the closest neighboring atoms attributed. This option can be therefore rather time consuming. The output file name is file.ts if the input file name is file.spl. For example:

In this case the output file name is toxin.ts. The file can be used as input with the LOAD SURFACE option. To create the .spl file you have to use the 2 following programs, prep_spl and make_spl, which are located under the $TURBO_DIR/ms subdirectory. The input of prep_spl is a Connolly Surface File (.srf).

SYMMETRY

The SYMMETRY option prompts you to give the molecule space group and cell parameters. Most of the protein space groups have been defined. You need to enter only the name of the space group, not all symmetry operations relative to this space group.

SYSTEM

The SYSTEM option returns to UNIX and executes UNIX orders. To leave this option, enter lo. A more efficient way to return to UNIX is to clone the window (that is, open another window).

TOLERANCE

The TOLERANCE option sets the acceptable violation of NMR distance restraints. The default value is set at 0.2 . When displaying the NMR restraints using the NMR ON/OFF display option (within the NMR submenu), a distance larger than the restraints but smaller than the restraint plus the tolerance will be displayed in orange, while the distance larger than the restraint plus the tolerance will be displayed in red.

TRAJECTORY

The TRAJECTORY option prompts you to give the name of the trajectory file extracted from the XPLOR dynamic calculation and then permits you to choose any of the conformations displayed. This option works provided the corresponding molecule has been loaded. To calculate conformations with XPLOR you should insert these commands into your XPLOR input file:

TRANSLATE

The TRANSLATE option applies a translation (i.e., a lateral shift) to the selected molecule. This option works provided the corresponding molecule has been loaded. This option applies to the memory storage, and you must save the molecule if you want to keep the changes. For example:

VDW-DENSITY

The VDW-DENSITY option chooses Van der Waals surface points with 20, 40 or 80 dots per square angstroms (20 points by default).

WORK-MAP

Use this option to specify the map on which you would like to work. Several options, such as RSR, TORSION DENS SEARCH, DGNL, or MAKE FRAGS, must be told to which map they have to refer. Note that if there is only one map displayed, the options will work on it, and DGNL and MAKE FRAGS may work without map at all.

ZONE

The ZONE option displays a large number of residue zones. These zones can be given different colors. (See the ZONE Option in the Color menu). For example:

You can modify a previously defined zone by using the following syntax:

Ex: zone=NZ RANGE. (Note that in this specific case, you have to type the equal sign.) NZ is the number of the zone that you want to modify. To add a zone in the list, give a new NZ number. Be careful with this step because if you do not accurately use the above-mentioned syntax, previously defined zones will be removed. Use the display Zone menu (located in the Molecule menu) to manage the display of the different zones.