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Miscellaneous Analysis Commands

This node describes commands used for controlling the analysis facility. See section Open File Command -- OPEN, for a description of the OPEN command which is also accepted by the analysis facility, and see section Set Delimiter Command -- DELIM, for a description of how to change the command delimiter. The GEPOL command, see section GEPOL Command -- Set GEPOL Defaults, may also be specified in the analysis facility.

SET -- Modify Analysis Facility Variables

Syntax

SET [INUNIT unit-number] [PRUNIT unit-number]

    [LINESZ integer] [PAGESZ integer]
            
    [ASURf real] [RH2O real]

Function

INUNIT sets the unit number of the unit where analysis commands are read from. This allows other command files to be read. This command uses the stream switching arrays available in the main part of CONGEN. The file read in must start with a title. To return back to the previous stream, the END command, see section END command, will suffice or hitting the end of file on the stream. Note that if you return from the stream which was current when the analysis facility starts, you will return back to the main program.

PRUNIT sets the unit number of the outputs of any commands which produce voluminously. PRINT, HISTO, PLOT, 2DPLOT, CORREL, and SEARCH are commands in that class. Initially, INUNIT is 5 and PRUNIT is 6. LINESZ gives the number of characters on a line for PRUNIT. Various commands have certain minimum limits on the value for LINESZ, and will adjust the value they use accordingly. The upper limit is what the printers can handle. PAGESZ gives the number of lines on a page.

ASURF controls the accuracy of the Lee and Richard's accessible surface algorithm. The default value is 0.05. Smaller values will improve the accuracy at the expense of speed. RH2O specifies the radius of the probe sphere. The default value is 1.4 A. See section Static Properties of Atoms, for more information.

TWIST -- Preparing to Compute Peptide Twist

Syntax

        TWIST [COMPare]

Function

The TWIST command rewrites the PSF used in the analysis facility in order to create virtual dihedrals spanning the alpha and beta carbons in the backbone of a protein. For residue i, the dihedrals formed are CB(i) -- CA(i) -- CA(i-1) --- CB(i-1). If a residue is a glycine, then no entry is made for it. The old list of dihedrals is destroyed (so be forewarned!), but only in the analysis facility. The PSF used by the top level of CONGEN is still intact so exiting the analysis facility and reentering it will restore the dihedrals list.

The COMPARE option controls which analysis PSF is used. When this keyword is omitted, then the main PSF is used; otherwise, the comparison PSF is used.

Once this command has been executed, then the twists can be obtained by a BUILD TORSION GEOMETRY command, and subsequent processing of the table by the analysis facility.

END command

Syntax

END

Function

This terminates a set of analysis commands. If the current stream is not unit 5, the next stream to read from is popped from the stream stack, see section STREAM Command. Otherwise the analysis facility terminates, and control reverts to the main program.

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