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:
[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



--

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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]

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