Frequently Asked Questions
My MRC images from Digital Micrograph/eTomo/Other Microscopy Package don't seem to load in 2dx.
This can be caused by the "MRC" file not fully being to the standard of the MRC file format loading library provided with the image2000 MRC release. As a result, images in MRC format from eTomo, Digital Micrograph and possibly others can occasionally not be correctly read by the MRC programs that run underneath 2dx.
We suggest that people having issues loading MRC images should try TIFF images instead. These will be transformed by the MRC program tif2mrc.for into a correct MRC format file, which then can be processed by 2dx. TIFF also supports 16-bit images, so that you will not suffer any resolution loss when using this format.
Mac OSX: How to I launch the program
You can either find the program and double-click it. If you installed it into the default location in /usr/local/2dx, then you could open that directory by typing in the terminal window (Terminal is a program is Applications/Utilities):
That should open a Finder window. You can then drag the applications into the dock, to find them easier next time.
Alternatively, you can open the programs from the terminal command line:
If you installed the programs elsewhere, replace /usr/local/2dx with that location.
2dx_image does not recognize my image file
2dx_image recognizes TIFF files and/or MRC files. The file type is recognized by the ending. TIFF files should have a file-name like <FILENAME>.tif . We recommend a filename that is composed of an alphanumerical part describing the protein name (e.g. 2 to 4 letters), then two digits describing the nominal tilt angle (e.g. 30), then 8 digits describing the image number (e.g. 12345678). The file would then be named something like AMTB3012345678.tif. Such a file would be transformed into an MRC format file, called AMTB3012345678.mrc.
MRC format files are also recognized by the file name ending, which needs to be "mrc". This is valid for all MRC map formats, including the FFTs<a class="new visualNoPrint" href="http://localhost:8080/Plone/documentation/FrequentlyAskedQuestions/createform?page=FFTs" title="create this page">?</a>, which within the 2dx scripts are often called <name>.fft.mrc.
2dx_image does not allow me to change the scripts
When you double-click on the script name, 2dx_image will open that script and also all sub-script that the first-level script may use. Those scripts will be opened in a platform-dependent editor. On Mac OSX that would be TextEdit<a class="new visualNoPrint" href="http://localhost:8080/Plone/documentation/FrequentlyAskedQuestions/createform?page=TextEdit" title="create this page">?</a>, for example. If you have installed 2dx in the default location /usr/local/2dx, then they might be only readable for a normal user, but you would not neccessarily have write permission there. If you want to change these scripts, or add your own scripts, then simply make the script directories writable for yourself.
You can do this by typing in the terminal
sudo chmod -R ugo+w scripts-custom scripts-standard proc
That would make those directories and all file in them writable for the user, group and others.
I cannot reach certain variables
The central pane of 2dx_image shows the variables. This pane has the title Processing Data, and can be in the Standard mode, where it displays only the most important variables, or it can be in the Advanced mode, where it displays all variables. You can switch between the two modes with the two buttons at the left end of that title bar.