ctfphaseflip(1) ctfphaseflip(1) NAME ctfphaseflip - correct tilt series for microscope CTF by phase flipping SYNOPSIS ctfphaseflip options DESCRIPTION This program will correct the CTF of an input tilt series by simple phase flipping. The user can select a subset of projection views of the input tilt series to correct and can specify a defocus value for each selected view through a text defocus file. The output file of ctfplotter is usually used as the defocus file. Ctfphaseflip corrects each view strip by strip. A strip is defined as an image region whose defocus difference is less than a user specified value, but the width is also limited to 256 pixels. It can be run in a parallel mode similiar to the Tilt program by setting the TotalViews option. The script Splitcorrection can be used to prepare command files for running the program in parallel. A sample command file for running the program with "subm" can be found in the IMOD/com directory (ctfcorrection.com). Options Ctfphaseflip uses the PIP package for input (see the manual page for pip). Options can be specified either as command line arguments (with the -) or one per line in a command file (without the -): -input OR -InputStack File name Input stack that will be corrected -output OR -OutputFileName File name Name of output file for the corrected views -angleFn OR -AngleFile File name File containing tilt angles for the input stack. Each line of this file is the tilt angle for a view of the input stack. The angles are listed in order starting from view 1. -invert OR -InvertTiltAngles Invert the sign of the tilt angles to compensate for a left- handed coordinate system in the microscope. When the sign of the tilt angles and the value of the tilt axis rotation angle are such that reconstructions are generated with inverted hand- edness, then this option is needed for a proper correction. -defFn OR -DefocusFile File name File with list of tilt angle ranges and defocus values in nanometers, such as was output by ctfplotter. Each line should have a starting and ending view number (numbered from 1), a starting and ending tilt angle, and a defocus value. Defocus is in nanometers, with positive values for underfocus. The pro- gram will assign that defocus value to the midpoint of the range of views. For a view at a given tilt angle, it will find the defocus either by interpolating between two surrounding midpoint angles, if there are such angles, or by taking the nearest defo- cus value, if the angle is beyond the range of the available midpoint angles. To correct a tilt series with a single value of defocus, supply a file with a single line containing "20 20 0. 0. defocus_value". -defTol OR -DefocusTol Integer Defocus tolerance in nanometers that limits the width of the strips. An image region with defocus difference less than this tolerance is considered to have constant defocus and can be cor- rected as one strip. The strip width is either the width of this region or 256 pixels, whichever is smaller; but strips will also be constrained to be at least 128 pixels wide. Each strip is corrected based on the defocus at the center of the strip. -iWidth OR -InterpolationWidth Integer The distance in pixels between the center lines of two consecu- tive strips. A pixel inside the region between those two center lines resides in both strips. As the two strips are corrected separately, that pixel will have 2 corrected values. The final value for that pixel is a linear interpolation of the 2 cor- rected values. -pixelSize OR -PixelSize Floating point Image pixel size in nanometers -volt OR -Voltage Integer Microscope voltage in kV -cs OR -SphericalAberration Floating point Microscope spherical aberration in millimeters -ampContrast OR -AmplitudeContrast Floating point The fraction of amplitude contrast. For Cryo-EM, it should be between 0.07 and 0.14. The value should be the same as was used when detecting the defocus. -views OR -StartingEndingViews Two integers The starting view and the ending view to correct in this run of the program, numbered from 1. This is an optional field. The default is to correct all views in the input stack. -totalViews OR -TotalViews Two integers The starting view and the ending view that need to be corrected in all parallel runs of the program. This field is only needed when doing parallel runs with direct writing to a single output file. The program is run initially with a StartingEndingViews entry of -1,-1 to set up the output file. Then it is run with actual starting and ending views for each parallel run, and each run writes to the existing output file. -boundary OR -BoundaryInfoFile File name Name of file with information about boundaries between chunks and files in which to write lines at the boundaries, when multi- ple runs are writing in parallel to an output file. -aAngle OR -AxisAngle Floating point This option is not supported. The tilt axis has to be vertical, i.e., to be coincident with the Y axis. Usually this means the input stack has to be the aligned stack. -param OR -Parameter Parameter file Read parameter entries from this file. -StandardInput Read parameter entries from standard input AUTHOR Quanren Xiong SEE ALSO ctfplotter BUGS Prior to IMOD 4.0.29, Ctfplotter had a bug in which the view numbers written to the defocus file were numbered from 0, not 1. When Ctf- phaseflip reads in the defocus file, it will do its best to detect this situation and adjust all the view numbers up by 1. If it does detect an inconsistency between view numbers and angular ranges, it will issue a warning. In general, the difference in CTF correction from having view numbers off by 1 was insignificant. Email bug reports to mast at colorado dot edu. BL3DEMC 4.3.7 ctfphaseflip(1)