FYI: in relion-1.4 the default for ResMin will be 30A, not 200A. :-)
HTH,
S
> 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]>
>>
>> ********************************************************************
>>
>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
|
