The Start program as radio buttons select the mode in which the program will be run; the two choices are equivalent to starting the program at the command line with "3dmod" or "3dmodv".

The Use previous directory for file chooser if no files entered yet checkbox controls whether a file chooser dialog (browser) will open in the directory last visited with a browser in the previous session of 3dmod. It has no effect if image or model file names were entered at the command line, because the browser directory is set from the path to the first such file. If the option is not checked and there are no incoming file names, the file chooser will open in the current directory from which 3dmod was run.

The four lines for specifying input files allow you either to type file names into the text boxes or to open a file chooser to select the files, using a Select button. The first line is used to specify either image files, when running the program as "3dmod", or model files, when running as "3dmodv". There are several special features for this line:

• Multiple files can be selected.
• Multiple file names can always be separated by semicolons, and they can usually be separated by spaces. When the names are returned from the file chooser, they will be separated by spaces if they do not contain any spaces themselves. When you type names into the edit box, you can separate them by spaces if they are just filenames with no directory paths. If you enter any directory paths with the names, you must separate multiple names with semicolons.
• The wild card characters * and ? can be used for file name entries; * matches any set of characters and ? matches a single character.

The line for specifying a piece list file will also accept multiple filenames, up to one per image file. Multiple montages are allowed only when they constitute an image pyramid. Filenames can be separated by semicolon or space, unless they contain spaces.

The rest of the items in the window correspond to options documented in the 3dmod or 3dmodv man pages. Specifically:

• The Load image subset group corresponds to the -x, -y, and -z options.
• The Open group specifies which windows to open initially, and activates the -Z, -xyz, -S, and -V options.
• The Bin by spin boxes correspond to the -b option.
• Scale image intensities corresponds to the -s option.
• When files must be scanned to find scaling radio buttons correspond to the -J option and override identical choices in the Scaling tab of the 3dmod Preferences dialog.
• Modify MRC header with values from scan corresponds to the -K option.
• The Use cache entries correspond to the -C option, or to the -CT option if Cache images as tiles or strips is checked. Placing a 0 in the field for the cache size will activate the cache with a size big enough to hold all the image data.
• Cache images as tiles or strips corresponds to the -CT option.
• Fill cache upon startup activates the -F option.
• Image files form a pyramid at multiple resolutions correspomds to the -py option.
• Flip Y and Z size by rotating around X activates the -Y option.
• Load non-byte data in as 16-bit integers activates the -I option.
• Show RGB images as grayscale activates the -G option.
• Read EER file with super-resolution corresponds to the -es option and takes values from -3 (to give a 1K image) to 2 (for the full 16K image).
• Read EER file with ... Z summing corresponds to the -ez option and specified how many frames to sum for each displayed image.
• Do not load single-image files as sections or volume stack as times activates the -T option.
• Load model without scaling activates the -m option.
• Load FFT without mirroring activates the -M option.
• Load montage as single frames activates the -f option.
• Load montage pieces and the three alignment choices correspond to the -A option.
• The Show images and montage spin boxes correspond to the -P option.
• The Overlap pieces spin boxes correspond to the -o option.
• Model View window size options let you set the size of the window when running as 3dmodv and correspond to the 3dmodv -s and -f options.

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