'''Q: How do I go about doing CTF correction in EMAN1''' '''A:''' Much of this is described in the 4 step tutorial interface, but the description here is more up to date. CTF correction in EMAN1, is, unfortunately, a somewhat time-consuming process. This has been massively simplified in EMAN2, but as EMAN2 still remains 'experimental' you may wish to stick with EMAN1 for a while longer for serious refinement work. It is a VERY good idea to make sure you are using a current snapshot version of EMAN1, rather than 1.8. There are 3 steps for optimally performing CTF correction in EMAN1: 1. Determine a [[EMAN1/FAQ/StructureFactor|1-D Structure Factor]] from 3-5 of your images * Use images over a reasonable range of defocuses * Don't forget to pick a good amplitude contrast (10-20% works best for cryo data) 1. Use fitctf to fit all of your particle stacks automatically * use the same %AC you used above * guess at a B-factor based on the fitting above. For a high-end 300 keV instrument this may be as low as 50-100. For a typical 200 FEG scope it will be in the 150-200 range, and for older/LAB6 scopes it may be as high as ~1000. Note that these are 2 different conventions for B-factor, EMAN1 B-factors are multiplied by 4 to compare with the MRC convention. * run this program once for each stack of particles (one stack per frame). The particles should be unmasked and unfiltered ! * fitctf sf= apix= V= Cs= acfix= Bhint= 1. Go back and [[FAQ_EMAN_USING_23|manually]] check your results * Run 'ctfit *.tnf' This will open the results of the automatic fitting. * If you need to correct any of the fit values (you very well may): * select the image in the upper right list in the control panel * make necessary adjustments * press the 'set' button below the lower right list in the control panel, this will save your parameters to disk * Do NOT use the 'phase flip' menu item when working this way, since you loaded '.tnf' files instead of the original particle stacks, it will not work right. * Instead, after correcting all of the CTF parameters and 'set'ing them, exit ctfit, and use 'applyctf' to flip the phases and store the parameters: * applyctf will get the CTF parameters from the memories you set in ctfit (ctfparm.txt file) * applyctf image1.hed image1.fix.hed setparm flipphase * applyctf image2.hed image2.fix.hed setparm flipphase * ... Now you can continue with processing. Typically: mkdir refine cd refine lstcat.py start.hed ../*.fix.hed lstfast.py start.hed cp start.hed start.img (make threed.0a.mrc) refine ... Note that the above commands create a start.hed/img file which is not really in imagic format. Rather it's a text file linking to the *fix.hed particles you created, so it's very important that you not rename or remove those files. EMAN1 will treat these text files as if they were real image files.