Dear Qiu-Xing,

Ctffind4 implements heuristics to try to "boost" high-frequency rings so 
that they may be seen more easily in the diagnostic image and in the 1D 
plots. The problem with those heuristics is that they create 
artefactural features when the fitted CTF and the experimental 
amplitudes do not agree anymore (i.e. at high frequencies). You are 
pointing out such artefacts in your attachment. Be assured though that 
these weird features are only occuring in the diagnostic image and there 
is no such heuristic being used when doing the actual fitting.

Alexis

On 03/08/2015 06:59 PM, Qiu-Xing Jiang wrote:
> Dear all,
> We switched to CTFfind4 recently. It worked well. Meanwhile, as showed in
> the enclosed png file (pixel 1.05 A), we noticed that  there is a circular
> mask to ~2.92 angstrom, and beyond that resolution, there were evenly
> spaced rings in the background. It does not affect the accuracy of the
> fitting. I am curious to know whether anyone in this group noticed the
> same and/or tried to get rid of the background. Thanks.
>
> Qiu-Xing
>
>
> On 3/1/15, 4:10 AM, "Sjors Scheres" <[log in to unmask]> wrote:
>
>> Hi Jian,
>> Sometimes jobs die due to glitches in the system. You may then miss your
>> star file. The program has an option --only_make_star that you can use in
>> this cases: it will only generate the star file, without having to re-run
>> the whole job.
>> HTH,
>> S
>>
>>> Hi Sjors,
>>> I met a problem recently when I deal with movie data. I followed manual.
>>> After ran the CTF estimation, it didn't generate the xxxx_ctf.star file.
>>> However, I can find all ctf files in the Micrographs folder with for
>>> each
>>> mrc files, for example, ctffind3.com, and ctffind3.log. I used ctffind4
>>> to
>>> do the ctf correction.
>>> Is there a way or command to generate the ctf_star file from the results
>>> in Micrographs folder? Why did it happen? How to correct it?
>>> The command line I used is shown below
>>> /opt/relion/1.3/bin/relion_run_ctffind_mpi --i all_AVG.star --o
>>> all_AVG_ctf.star --ctfWin -1 --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 122058
>>> --DStep 14 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000
>>> --FStep 500 --dAst 0 --ctffind3_exe /opt/ctffind/4.0.8/bin/ctffind
>>> --omp-num-threads 1 --old-school-input"
>>> Thanks a lot.
>>> You have a wonderful weekend.
>>> Sincerely yours,
>>> Jian
>>>
>>
>> --
>> 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
>
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