[log in to unmask]" type="cite">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]> 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]
------------------------------------------------------------------------
Alexis Rohou
Research Specialist
Grigorieff Lab
http://grigoriefflab.janelia.org
Tel. +1 571 209 4000 x3485
--
********************************************************************
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]
********************************************************************