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Scanning Transmission Electron Microscopy Facility

PCMass Manual: Tutorial 3

Tutorials >>  1 2 3 4 5 6 7

Customize a Model and Adjust Selection Parameters
  1. Select a model from the existing list that is similar to your particle or filament of interest. Note that models are displayed with the same magnification and contrast as the current image.
  2. Place the mouse cursor over a typical particle. Adjust the circle radius with <t> / <y> or rectangle length with <l> / <;>. Observe the difference image to the right of the zoomed particle and the fitting parameters to the right of the difference image. dX & dY are offsets of the model relative to the center of the pixel under the pointer. If there are greater than 2.0, they will appear on a red warning background. Adjust the mouse or use the arrow keys to get closer to center. T is the rotation angle of the best-fit model. The parameters of interest are SZ and HT, which are magnification and amplitude scale factors of the model relative to the current particle. If these are outside the selection range, they will appear on a red background (see below to change selection cutoffs). VS is a variable subunit, usually at the center of a sphere or rod meant to give an indication of “hollowness” of the feature. BK is the background value interpolated to the center of selected particle.
  3. If the model particle does not seem to converge on the correct size and orientation, try another model. If no models seem appropriate, contact the STEM group for advice.
  4. If the model seems reasonable but the size or height are not close to 1.0, move the mouse or arrow keys to get the best alignment (smallest dX & dY) and strike the <F9> key once. Note that the automatic particle selection is based on these parameters, so values close to 1.0 are more likely to get all the particles or filament segments of interest.
  5. Move the model with the arrow keys to try for a better alignment and strike <F9> again. Repeat until size and height parameters are both close to 1.0.
  6. Enter several manual or automatic mass measurements using this model (as in Tytorials 1 or 2). Strike the <o> key and select the appropriate row and column to view the fitting parameters. Above the main histogram on the right panel you will see a collection of small panels labeled: Bkg RMS, RMS, Sym RMS, Size and Height. Below each label is listed the current selection range for that parameter. Points are plotted for each particle. The x-axis in each case is massp and particles outside the selection criteria are plotted as red ( failed BkgRMS) or yellow (failed something else). Those satisfying all criteria are in green. The second row (Ml, etc.) are diagnostic of possible problems with the image. Ml & Mm should be directly correlated with Mp, while X, Y, and bkg should be uncorrelated.
  7. Note any “clumping” indicative of particle classes. At this point it may be useful to go back to the image to understand what is “wrong” with outliers. This can be done with the <i> mode described in tutorial 1 or the <o> mode in tutorial 2. For example, the yellow points in the RMS panel come from the side-view molecules which have a poorer fit to the model. To change the hurdle height (upper or lower) for any parameter, hold down the SpaceBar and move the mouse pointer to the panel of interest, hold down the left mouse button, drag the bar (note the change in value) and release the left mouse button. Move the mouse (with SpaceBar released) to clear the display and strike <o> to replot.
  8. Once satisfied with model parameters, you can edit the PCMmods.dat file to make your changes permanent. The model parameters for all used models are saved at the end of each *.smm results file and read in each time that image is opened. If the current parameters for a model are not the same as those used for previous measurements, a question will appear showing what is different asking if you wish to go back to your previous parameters. If you wish to make a fresh start with new model parameters, it is best to erase all the *.smm files using the File Manager to avoid repeated questions.


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Last Modified: June 12, 2009
Please forward all questions about this site to: Kathy Folkers

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