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Subject:

Re: CTF star file

From:

Qiu-Xing Jiang <[log in to unmask]>

Reply-To:

Qiu-Xing Jiang <[log in to unmask]>

Date:

Sun, 8 Mar 2015 22:59:18 +0000

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (66 lines) , Screen Shot 2015-03-08 at 4.45.21 PM.png (66 lines)

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


________________________________

UT Southwestern


Medical Center



The future of medicine, today.


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