mrcdisp filename to view image can also view histogram of densities fftrans filename.img filename.fft calculate fft mrcdisp filename.fft display fft prnimg filename to obtain postscript output for printing ghostview prnimg.ps to preview postscript output lp prnimg.ps to send output to printer label filename.img to select smaller area from image - For correcting xtal distortions in image histo filename.img to obtain histogram of image label filename.img to reduce image size by factor of 2 fftrans filename.red filename.fft to calculate Fourier transform mrcdisp filename.fft to display fft and obtain lattice parameters a*,b* joba (image id, dimension, print flag set within script) to find actual positions of unit cells in image ccua to apply corrections to original image fftrans corimage transform corrected image wcbox to obtain ampl and phases and evaluate success of unbending jobb 2nd round of unbending if necessary ccub 2nd round of unbending fftrans corimage wcbox to obtain ampl. and phases from transform ctfapply img.cnt -> ctfk.aph and plot82.plt to apply correction for ctf to phases and ampl. origtilt < origmerg.cnt -> merged.aph to determine right phase origins and merge images avrgamphs < avrgamphs.cnt -> avrg ampl and phase file to create single data set of averaged data avrgphases < avrgphases.cnt -> avrg phase file for only phases remove first line from output of avrgamphs or avrgphases makemtz to make mtz file for next step fourcalc_aph Fourier synthesis and contour map generated