Other windows related to project

New Group window

Select data files window

4. Micrograph window

File selection

Ethan parameters

Zoom and Pan controls

Micrograph Toolbox

Close button closes micrograph window and passes particle radius and cutout box size (if they were set) to the group.

5. Mosaic window

File selection

Maps and delete boxes

Particle control buttons

Delete button

6.Example session

1. Run spade.
2. Set the data directory. In directories frame click on the right "Browse" button. A file selector window will appear. Suppose your micrograph mrc files are located in /home/user/data directory. You can eithere type this path in the entry field at the bottom window, or use naviagtion controls to get to that particular place in the file system. Press OK.
3. Create new group. Press "large +" button on the left of main project window. A window will appear prompting for name of this group. Type the name of the group into the entry field. It's good to use infomative group names, that is names that in some way describe the future contents of the group. Suppose the group will contain micrographs produced on 28.09.00, so the date can be used a group name. Type it in, press OK.
4. Add micrograph files to the group. Click on the group name, "small +" button will become active. Click on it, another window will appear shoung the list of all mrc files contained in the directory that was set in 2. Suppose there are severeal files in the list, 1.mrc 2.mrc etc. Suppose the files you want are 1.mrc 3.mrc and 5.mrc. Hold "ctrl" button on the keyboard down and on the names of the files that should go into this group. When you have selected the files (3 in our example) release "ctrl" and click ok. You will now see that the file have been added to the group in the main window.
5. Set radius and box size. This can be done in two ways. If you already know the radius of a particle (in pixels), you will click on the group name to activate it, you will then see that two tabs at the bottom of "Files" frame have become active. Suppose you know that radius of you particles is 40 pixels. Eneter this number into the Radius tab. A good choice of box size is usually the diameter of the particle plus few pixels, say 90. In no case should the box size be less then twice the radius. Enter the appropriate value in the "Box" tab.

   If the radius of the particle is not known apriori, it will have to be determined from one of the micrographs. Click for example on 1.mrc, you will see that the "eye" button in the center of main window was become active, press it. You will see a new window displaying the given micrograph. If the micrograph is large you might have to zoom in, to find a particle that is well represebtative of the others. In order to zoom, click on the "looking glass" button on the left side of the micrograph. Then select a region of the micrograph by first cliking upper left corner, hold the mouse button down and drag it to the right bottom corner, when it is done relese mouse botton. Remeber that the micrograph viewer will not zoom closer then 1:1 with the screen resolution. If you want to jump imeddiately to closest possible view press "1:1" button in the "Zoom & Pan" frame. When you think the view of particles is good, select the radius. Press the "radius" button (located just below the "looking glass" button), position mouse cursor on the outer edge of one particle. Press and hold mouse button, drag it so that the green circle exactly covers the particle, release the button. You will now see that in "Radius" tab, in "Ethan Params" frame there appeared a value, this is the radius of the circle you have just produced in pixels. Now you have to set the box size. This procedure is similar to setting the radius. Press "box" button (located under radius button) then drag the box above one of the particles so that it covers the whole particle. Notice that the box size is now set in the "Ethan Params" frame. You can change box size and radius any number of times. When you are satisfied with the values, clock "close" button int he upper right corner of the window.

6. Save project Now is a good time to save your project. From the "Project" menu select "Save as ..." a file selector window will open, type in the name you want to give to your project. Just like the group names it's a good policy to give projects meaningful names, for example take the name of the particle. Standard extension of SPADE project file is ".spa" but don't have to type that, the program will auomatically append it. You still can if you choose to.
7. Process micrographs. By now the project should be ready for processing, files selected and parameters set. Micrograph are processed in groups, so click on the name of the group to select it, check that "Radius" and "Box size" tabs have meaningfull values. Press "->" button in the middle to preocess files.
8. Examine output Ethan output needs to be checked. Select now the first file from the processed group. Press mosaic button (on the right of the main project window). In the mosaic window you will see all particles extarcted from the given micrograph. Select all the damaged or otherwise inappropriate particles by clicking on them. When this is done, click "->" button to move the these particles to the bin. Once they are there click "Delete" button in lower righgt corner to remove the paricles and their respective files. Click "close" button, repeat this procedure for all micrograph files. At the end of this process you should get a set of consequetively numbered mrc files all of the same size and each contianing a good particle.