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Dear Ali, In Dieter's case, the problem was solved by setting the minimum resolution for fitting to 30A (it was set to 200A by default by Relion, but 30A is the default ctffind4 suggests). Ctffind4 should not accept 200A as a minimum resolution - I will look into fixing this for a future release. Could you re-try your test micrograph with minimum resolution of 30A with ctffind4? In general, I would encourage any ctffind users to let me know when ctffind4 fails where ctffind3 worked. Thanks, Alexis On 01/20/2015 12:55 PM, Ali Khan wrote: > We had the same thing occur to us. ctffind4 failed and ctffind3 > worked. We can send you our data set if you like as well. > > Cheers, > Ali Khan > > On Tue, Jan 20, 2015 at 8:20 AM, Alexis Rohou <[log in to unmask] > <mailto:[log in to unmask]>> wrote: > > Dear Dieter, > > It seems in this case ctffind4 failed where ctffind3 succeeded. > > So far, the only times ctffind3 performed better than ctffind4 was > when dealing with digitized film micrographs - is this the case > here? If not (i.e. if this is a ccd/cmos/direct-detector dataset), > would you mind sending me the micrograph so I can debug ctffind4? > > Many thanks > Alexis > > > > On 01/20/2015 05:40 AM, Dieter Blaas wrote: > > Hi Sjors and all, > > I re-run an old dataset now following the protocol for > relion-1.3 (using autopicking and the new ctffind4) and > noticed that the defocus values output by the two versions of > ctffind were quite different (see example of one micrograph > below): > > ctffind4: > # Columns: #1 - micrograph number; #2 - defocus 1; #3 - > defocus 2; #4 - azimuth of astigmatism; #5 - cross > correlation; #6 - spacing (in Angstroms) up to which CTF rings > were > detected > 1.000000 30174.35 30167.60 838.7715 > 0.2366101E-01 18.90870 > > ctffind3: > DFMID1 DFMID2 ANGAST CC > > 20262.43 20335.00 58.02 0.19150 Final Values > > In addition, whereas the observed and estimated > quarter-Thon-rings coincided very well in ctffind3 they did > not so in ctffind4 and the final resolution obtained from the > same dataset was by about 4 A less. > > what might be wrong? > > Thanks, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: [log in to unmask] > <mailto:[log in to unmask]> > ------------------------------------------------------------------------ > > > > -- > Alexis Rohou > > Research Specialist > Grigorieff Lab > http://grigoriefflab.janelia.org > Tel. +1 571 209 4000 x3485 <tel:%2B1%20571%20209%204000%20x3485> > > > > > -- > > ******************************************************************** > > Ali K. Khan > > M.D.-Ph.D. Candidate > > Medical Scientist Training Program > > Department of Molecular Physiology and Biological Physics > > University of Virginia School of Medicine and > > Graduate School of Arts and Sciences > > Sheridan G. Synder Translational Research Building, Rm 320 > > 480 Ray C. Hunt Drive > > Charlottesville, VA 22908 > > Phone: 434-243-2520 > > Email:[log in to unmask] <mailto:[log in to unmask]> > > ******************************************************************** >