The Batch file edit form

Spire can present a batch file in a graphical form, with entry boxes for the user to enter or verify values. This only works if the batch file has a proper batch file header. If your batch file does not have a properly written header, Spire will try to inform you about errors it encountered. After making the desired changes to the form, and hitting the Save button, Spire will write the new values into the procedure file.

Below is a batch header that produces the form on the right. Note the three sections for Registers, Input files, Output files (you can have as many filename sections as you want, but only one register section).

x91 = 1 ; the first particle number x87 = 2 ; overview number x59 = 0.75 ; peak separation distance ; ----------- Input files -------------- FR G [params]../params ; parameter file FR G [filenums]../filenums ; file numbers FR G [mic]../Micrographs/mic{****x55} ;micrographs FR G [refvol]../reference_volume ; reference volume FR G [noise]./noise ; noise file ; ----------- Output files -------------- FR G [ser]win/ser ; template for particle images FR G [sndc]coords/sndc{****x55} ; coordinate doc files ; -------------- END BATCH HEADER ---------------

Sections: each section must begin with a comment line that has text enclosed in a row of minus signs, such as
; ------ Input files -----
Sections are outlined in the form with the section heading in the upper left corner.

Registers: the comment is used as a label, the register's value appears in the entry box.
Only assignments of the form X11 = 1.234 are acceptable, with a floating point number on the right side of the equal sign. Assignments that are functions of already set registers (e.g., X22 = X11 + 1) are not shown in the form.

Filename sections: the comment appears as a button label, the symbolic parameter's text value appears in the entry box.
The button label, when pressed, allows the user to browse for a file.
Note: this replaces a relative path name with the full absolute file path name in the batch file, e.g. ../filenums.hcc can become /usr13/bbaxter/projects/hcc/filenums.hcc (see below).

Be careful of batch files that have template file names, e.g., win/ser will be expanded by Spider to win/ser000066. In this case you do not want to replace the text with a specific file name.
If the filename includes Spider's file numbering convention (e.g., mic{****x11}) Spire will attempt to keep the register in the filename.

• Save: write the values currently in the batch form into the batch file.
• Save as: write the current values into a batch file with a new name.
• Editor: open up the batch file in a text editor (specified in the Options menu - under Preferences). Important! If you make changes in a text editor, exit the batch form via the Cancel button, or else Spire will not save the changes you want
• Execute!: close the window and run the batch file in Spider. (Same as running it from a Dialog.)
• Cancel: close the window without making any changes to the batch file text.