Changing Model Parameters

Since model customization may not be straightforward, J. Wall will be happy to provide a PCMmods.dat file with starting models suitable for your situation. These can be fine-tuned as described below. Each model has associated a name and a set of selection parameters (upper and lower limits for each fitting parameter). Model information is stored in a file named PCMmods.dat. One way to "tune up" a model is to start with one which is similar to your structure and edit the PCMmods.dat file with Notepad (double click on the file name in Windows Explorer). Each line recognized by PCMass begins with a key word: MODEL, BALL, HELIX, SELL, SELH or NAME. Other lines are ignored so comments can be interspersed. Follow the instructions at the beginning of the file. Make a copy of the original before editing in case something goes wrong.

Implementing Edited PCMods.dat

Close the edited PCMods.dat file and initialize all models to file values by striking the <M> key. Compare the model to your particles by re-selecting it and placing the mouse cursor over a "good" or "bad" particle. The image pixels should appear zoomed with its Mp below and its Ml (mass using local background) on the following line. The RMS difference between image and model pixels is displayed below the zoomed image and the next line shows the brms from ring or rectangle surrounding the particle. The arrow keys step the image one pixel at a time. Adjust integration radius with tT/yY and the particle angle with zZ/xX and observe the change in RMS and difference image. For 3-D models, Qq/Ww tilts about the X axis and Aa/Ss rotates about the Z axis. Note that pressing the left mouse button or the key will save the current parameters (for the particle pointed to by the mouse) in the *.smm results file.

Tuning Existing Models

A quick way to optimize a model is to select a model with the desired symmetry and degree of complexity (number of balls), choose a "good" particle in the field of view and place the mouse cursor on it. Check the size and ht parameters and the quality of fit. If the rms is greater that 0.1 and the absolute values of DX & DY are less than 1.0, the fitting routine probably "locked" onto your particle. Vary the radius of integration (t/y) so the particle you have chosen is fully inside. Note the values of SZ and HT to the right of the difference image. If they are not both close to one, strike F9 (the F keys are along the top edge of the keyboard) several times to scale the entire model so that SZ and HT are both close to 1.0 after fitting. Then strike F4, F5, F6, F7 and F8 to adjust ball sizes and positions individually. Each F key adjusts the parameter it controls +/- one or two small increments for each ball in the model (up to 24 balls). The RMS value for the starting position is shown in the center of the 5 columns displayed, with RMS values for increments of that parameter displayed to the left and right. Any improved RMS values are highlighted. The one increment making the greatest improvement in RMS is retained. When no further improvement is obtained by striking any of F4-F8, the process is complete. Note that this may not be the optimum model obtainable with this number of parameters because the small +/- increments may become stuck in a local minimum, rather than the global minimum. If the appearance of the difference image suggests that a better model is possible, strike <M> to revert to the default definitions of all the models in the PCMmods.dat file and try again using a different sequence of increments. When you are satisfied, note the final parameters and put them into PCMmods.dat with Notepad. For an unknown structure it is useful to try several different models for the same type of particle.

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