3dmod Startup Window
When 3dmod is started with no arguments or with the -O argument, this dialog
is opened to provide the ability to select many of the options that can be
controlled with command-line arguments. In addition, input files can
be selected with a file chooser.
The Start program as radio buttons select the mode in which the
program will be run; the two choices are equivalent to starting the
at the command line with "3dmod" or "3dmodv".
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
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
- 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
- Show RGB images as grayscale activates the -G option.
- Load single-image files as separate times activates the
- 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
- The Overlap pieces spin boxes correspond to the -o option.