Commands for Running MASIA
This section summarizes MASIA commands to run the program WITHOUT using the GUI.
MASIA is not CPU-time extensive so it should be run in interactive mode. After entering the command MASIA, the following will be displayed on the screen:
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* MASIA *
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An easy way for looking at alignments
Program Version 1.0
MASIA>
The prompt MASIA> always appears when the user should type in a new command. Upper or lower case letters should be matched with command definitions as discribed below. Commands begining with the character "@" (e.g., @conses) are considered as a macro file which should be found in the pathway defined in masia.par. If a command line contains the character "*" followed immediately by an integer N, the command will be executed N times repeatedly. For example, the command
MASIA> property *4 name=all-KP art=eis equivalent with the combination of the following commands
MASIA> property name=all-KP art=e MASIA> property name=all-KP art=e MASIA> property name=all-KP art=e MASIA> property name=all-KP art=e
In the following, command strings appear in boldface, and corresponding parameters to be defined by the user are in italic. Options followed to specific commands are put in bracket [...]. If options are absent, the program uses default values. The length of commands may not exceed 80 characters (columns).
proplib file=stringreads the property library. The string is the relative pathway of the property library file. Without specification, the default library file as specified in the include file masia.par will be read. Properties from user’s definitions can be easily integrated in the file if written in the correct format.
reads the exchange matrix of the probability for amino acid substitutions in families of structural related proteins. The string is the relative pathway of the exchange matrix file. Generally, the default library file as specified in the include file masia.par will be read.
reads the input file of multiple sequences alignment. The string is the pathway and name of the file. MASIA recognizes the extension name of input file .aln as the format of program CLUSTAL W and .msf as the format of program PILEUP.
specifies the structural characteristics to be predicted by MASIA. The string(4) defines corresponding name of the structural characteristic of protein. For secondary structure prediction (SSP) string(4) has four choices: alph, beta, turn, and coil, and for hydrophobic or hydrophilic prediction of individual residue the string(4) has two choices: insd and outs. These specific name will be used by translation program TRANSLATE to generate distance constraints and dihedral angle constraints for distance geometry calculations. grpcrit specifies the criterion for structure/property prediction from the analysis of "groups" which follow the curent command. The default value of grpcrit equals 1.00. abbrev specifies the abbreviation character to be printed in output file *.mas. The default characters for alph, beta, turn, coil, insd, and outs are H, B, T, C, i, and o, respectively.
combines with the following property and step commands to define the structure of rule for secondary structure and property predictions. grpw specifies the weight factor (default value is 1.00) of the group to be used for characteristic analysis. y is the number of positions to be checked, and x the number of positions to be fulfilled for the group. The defaults of x and y are 1. print command defines the abbreviation character to be printed in output file *.mas. crit is the criterion of recognition of the results from following property commands. The default value is crit=1.00.
specifies a property to be read from the property library. The string(15) should be consistent with the property name in library file. art sets the method to be used for searching significant conservation of property from the multiple sequences. In this version there are three methods implemented: art=d – dominant criterion; art=s – probability entropy criterion; art=e – statistical expectation criterion. cut sets the cutoff of frenquency of appearence in multiple sequences. look specifies the character to be searched for. The default of look is the character of the first group of the property as defined in property library file. stepw (default value is 1.00) defines the weight factor of the property for the first step execution.
looks for fulfilled patterns of properties according to the structure of a rule. stepw defines weight factor of corresponding property at current step. hstep sets horizontal steps, and vstep sets vertical steps. look command is the same as previous description. Default parameters are asigned automatically as: stepw=1.00 hstep=1 vstep=1 look=abbreviated character of first group of the property. step command always follows a set of property commands, and the number of step commands in a characteristic may not exceed the number of properties that belongs to the characteristic.
generates result file with extension name .res or with a file name as defined by string. title prints a one line comment in the output file.
generates predicted results file with extension name .mas or with a file name as defined by string. title prints a one line comment in the output file.
generates comparison file with extension name .cpr or with a file name as defined by string. title generates one line comment in the output file. When using this command the file (with extension .sec) of secondary structure and inside/outside lists which are derived from known x-ray or NMR structure sholud be given in the working directory.
generates topology file with extension name .top or with a file name as defined by string. titile generates one line comment in the output file.
makes the initialization of the program.
writes a list of all commands of MASIA with a short description of each command on the screen.
terminates the running of program MASIA.