February 23, 2012 ================= An additional parameter, dAst, was added to CARD 4 to restrain the amount of astigmatism in the CTF fit. This makes the fitting procedure more robust, especially in cases where the Thon rings are not easily visible. July 25, 2010 ============= ctffind3 (version 3.4 and higher) and ctftilt (version 1.5 and higher) can now make use of openMP. Use the _mp makefiles to compile, for example make -f Makefile_linux_mp This will produce executables ctffind3_mp.exe ctftilt_mp.exe To use more than one processor, you will need to set the environmental variable NCPUS. For example, when using the csh shell: setenv NCPUS 8 to use 8 processors. With 8 processors, ctffind3 runs about 6 times faster and ctftilt about 4 times faster. Software description ==================== This software is distributed under the GNU General Public License (GPL). If you use this software, please cite Mindell, J. A. & Grigorieff, N. (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347. C***************************************************************************** C C CTFFIND3 - determines defocus and astigmatism for images of C arbitrary size (MRC format). Astigmatic angle is measured form C x axis (same convetiones as in the MRC 2D image processing C programs). C C CARD 1: Input file name for image C CARD 2: Output file name to check result C CARD 3: CS[mm], HT[kV], AmpCnst, XMAG, DStep[um] C CARD 4: Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep[A], dAst[A] C C The output image file to check the result of the fitting C shows the filtered average power spectrum of the input C image in one half, and the fitted CTF (squared) in the C other half. The two halfs should agree very well for a C sucessfull fit. C C CS: Spherical aberration coefficient of the objective in mm C HT: Electron beam voltage in kV C AmpCnst: Amount of amplitude contrast (fraction). For ice C images 0.07, for negative stain about 0.15. C XMAG: Magnification of original image C DStep: Pixel size on scanner in microns C Box: Tile size. The program devides the image into square C tiles and calculates the average power spectrum. Tiles C with a significatly higher or lower variance are C excluded; these are parts of the image which are unlikely C to contain useful information (beam edge, film number C etc). IMPORTANT: Box must have even pixel dimensions. C ResMin: Low resolution end of data to be fitted. C ResMaX: High resolution end of data to be fitted. C dFMin: Starting defocus value for grid search in Angstrom. C Positive values represent an underfocus. The program C performs a systematic grid search of defocus values C and astigmatism before fitting a CTF to machine C precision. C dFMax: End defocus value for grid search in Angstrom. C FStep: Step width for grid search in Angstrom. C dAst: Expected amount of astigmatism in Angstrom. C C***************************************************************************** C example command file (UNIX): C C #!/bin/csh -x C # C # ctffind3 C # C time /public/image/bin/ctffind3.exe << eof C image.mrc C power.mrc C 2.6,200.0,0.07,60000.0,28.0 C 128,100.0,15.0,30000.0,90000.0,5000.0,500.0,100.0 C eof C # C***************************************************************************** C***************************************************************************** C C CTFTILT - determines defocus, astigmatism tilt axis and tilt angle C for images of arbitrary size (MRC format). Astigmatic angle is measured C from x axis (same conventions as in the MRC 2D image processing C programs). C C CARD 1: Input file name for image C CARD 2: Output file name to check result C CARD 3: CS[mm], HT[kV], AmpCnst, XMAG, DStep[um],PAve C CARD 4: Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep[A], dAst[A], TiltA[deg], TiltR[deg] C C The output image file to check the result of the fitting C shows the filtered average power spectrum of the input C image in one half, and the fitted CTF (squared) in the C other half. The two halves should agree very well for a C successful fit. C C CS: Spherical aberration coefficient of the objective in mm C HT: Electron beam voltage in kV C AmpCnst: Amount of amplitude contrast (fraction). For ice C images 0.07, for negative stain about 0.15. C XMAG: Magnification of original image C DStep: Pixel size on scanner in microns C PAve: Pixel averaging (PAve x PAve) for input image C Box: Tile size. The program divides the image into square C tiles and calculates the average power spectrum. Tiles C with a significantly higher or lower variance are C excluded; these are parts of the image which are unlikely C to contain useful information (beam edge, film number C etc). IMPORTANT: Box must have a even pixel dimensions. C ResMin: Low resolution end of data to be fitted. C ResMaX: High resolution end of data to be fitted. C dFMin: Starting defocus value for grid search in Angstrom. C Positive values represent an underfocus. The program C performs a systematic grid search of defocus values C and astigmatism before fitting a CTF to machine C precision. C dFMax: End defocus value for grid search in Angstrom. C FStep: Step width for grid search in Angstrom. C dAst: Expected amount of astigmatism in Angstrom. C TiltA: Expected tilt angle in degrees. C TiltR: Expected tilt angle uncertainty in degrees. C C***************************************************************************** C example command file (UNIX): C C #!/bin/csh -x C # C # ctftilt C # C time /public/image/bin/ctftilt.exe << eof C image.mrc C power.mrc C 2.6,200.0,0.07,60000.0,28.0,2 C 128,100.0,15.0,30000.0,90000.0,5000.0,500.0,100.0,0.0,5.0 C eof C # C*****************************************************************************