NCMI-CryoEM Baylor College of Medicine

Goal

Automated Fitting of Constrast Transfer Function Parameters

Authors

Wen Jiang @ Baylor College of Medicine
Chao Yang @ Lawrence Berkeley National Laboratory

Reference

Yang C, Jiang W, Chen D-H, Adiga U, Ng EG, Chiu W.
Estimating contrast transfer function and associated parameters by constrained non-linear optimization.
Journal of Microscopy (2009) vol. 233 (3) pp. 391-403.

Features

1. Fit structural factors by simutaneous fitting of multiple micrographs
2. Fit astigmatism and drift
3. Automated batch mode fitting, no need of initial seeding
4. Fast (seconds)
5. Robust. Defocus and background are VERY reliable
6. Compatible with GUI program ctfit program in EMAN
7. Cross platform: Linux, Windows and any platform that EMAN and Matlab run

Method

We use the constrained nonlinear multi-variable optimization function fmincon in Matlab as the core technique. The Contrast Transfer Function (CTF) of electron microscope is modeled as in the EMAN software.

Software dependency

Software	Version	Comments	Cost
Matlab	any	Version 6.5 and 7.0 are tested.Other versions might also work	Commercial
Matlab Optimization Toolbox	any	To provide fmincon function	Commercial
Python	2.3 and above	must have optparse module	Free Open Source
pymat	CVS version. v1.1.90 does not work (at least not on Mandrake 9.0) Here is the one I am using: pymat-python2.3-matlab6.5-linux.tar.gz, pymat-python2.3-matlab7-linux32.so, pymat-python2.3-matlab6.5-win32.pyd, pymat-python2.3-matlab7-win32.pyd	provides Python module to control Matlab engine to install the one I provide: untar the file pymat-python2.3.tar.gz, mv the new directory pymat to a directory in the $PYTHONPATH values, or create the PYTHONPATH variable to contain the pymat directory make sure to include the following files from your Matlab installation into your run time library search path (i.e. LD_LIBRARY_PATH). $MATLAB refers to the root directory of your Matlab installation. $MATLAB/extern/lib/glnx86/libeng.so $MATLAB/extern/lib/glnx86/libmat.so $MATLAB/extern/lib/glnx86/libmx.so $MATLAB/extern/lib/glnx86/libut.so $MATLAB/sys/os/glnx86/libstdc++-libc6.1-2.so.3
Numeric Python	any	required by pymat. most linux distributions have it but might not install it by default
EMAN	>2004-4-4 release	must have Python wrapping built

Usage

Just type fitctf.py and it will display the usage documentation as the following:

usage:
fitctf.py
<*.img>|<*.hdf>|<*.tnf> [options]

options:

--version            
show program's version number and exit

  -h,
--help           
show this help message and exit

  --sf=<structural factor file>

the structural factor curve file. use constant

structural factors if this file is not given

  --fitsf=<structural factor file>

fit the structural factor curve from the images and

save to the file

  --apix=<Angstrom/pixel>

[Required] the sampling of the image, in unit of

Angstrom/pixel

--cs=<Cs>            
[Required] the microscope's spherical abberation, in

unit of mm

  --voltage=<voltage>   [Required] the
microscope's accelerating voltage, in

unit of kV

  --min_s=<minimal spatial freq>

the minimal spatial frequency to include in fitting, in

unit of 1/Angstrom. default to 0.01

  --max_s=<maximal spatial freq>

the maximal spatial frequency to include in fitting, in

unit of 1/Angstrom. default to 1.0

  --min_defocus=<minimal defocus>

the closest focus to consider, in unit of micrometer

and positive for underdefocus. default to 0

  --max_defocus=<maximal defocus>

the largest focus to consider, in unit of micrometer

and positive for underdefocus. default to 4

  --max_bfactor=<maximal B-factor>

the largest B-factor to consider, in unit of

Angstrom^2. default to 1000

  --min_ac=<minimal amplitude contrast>

the smallest amplitude contrast to consider, in range

[0-1]. default to 0

  --max_ac=<maximal amplitude contrast>

the largest amplitude contrast to consider, in range

[0-1]. default to 0.2

  --oversample=<n>      oversample
<n> times the power spectrum so there is

enough sampling points to fit for small particles. only

used when inputs are individual particle images.

default to 1 to disable

  --gridbox=<box size>  if perform grid boxing first
for a large micrograph/ccd

image. default to 0 to disable

  --anisotropy_bins=<number of angular bins>

the number of angular bins (>8) to fit astigmatism and

drift. default to 0 to disable astigmatism/drift

fitting

  --ctfparm=<output parameter file>

the output filename for the fitting results to save.

default to ctfparm.txt

  --astigmatism         to
fit astigmatism. must also set anisotropy_bins>=8 to

activate. disabled by default

--drift              
to fit drift. must also set anisotropy_bins>=8 to

activate. disabled by default

  --pause=<seconds>     to pause the
fitting for the specified number of

seconds after each micrograph, -1 will stop and wait

for keyboard return to continue. default to 0 to

disable pausing

--show_fit           
to show the fitting plot during the fitting process.

disabled by default

--keep_pwr           
to keep the power spectrum files (*.pwr). disabled by

default

  --useoldmfile        
won't write new Matlab .m scripts and use exisiting

scripts. disabled by default to output new scripts

Download

Python executable + examples, 11.4MiB (requires EMAN and MATLAB)

FitCTF Fitting Contrast Transfer Function