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LBEM-CH / focus

High Throughput Electron Microscopy Image Processing Software
http://www.focus-em.org
GNU General Public License v2.0
36 stars 14 forks source link

FFT file #192

Closed Eladbic closed 6 years ago

Eladbic commented 7 years ago

Hi All, I try to run the single particle mode and everything run ok but after process the files I don't get any FFT files and there are no error. I had problem with numpy so I disable the EMAN directory and it fix this issue.

Thanks,

rdrighetto commented 7 years ago

Dear Eladbic,

Thank you for your interest in FOCUS. Could you please explain in more detail what are you trying to accomplish? Which FFT files do you expect to have after processing in single-particle mode? It's not clear to me if you are talking about the "single-particle project" mode or about "single-particle processing of 2D crystals" mode.

Eladbic commented 7 years ago

Hi Ricardo,

Thanks you for your help. I am try to run FOCUS in single particle projcet mode workflow. From import new file to process the micrographes (motioncor, CTF, picking). The motioncor and gCTF work well and I get output but in the library tab I don't get any FFT image of the micrographes (bifore or after drift corr). Also if I try the iciness script I get this error:

ERROR: movie_aligned_Sum_fft.mrc does not exist.

I run the FOCUS version from SBgrid: /focus/1.1.0_nightly/bin/focus.

OS: CentOS 6

Thanks,

On Tue, Jun 13, 2017 at 3:55 AM, Ricardo Righetto notifications@github.com wrote:

Dear Eladbic,

Thank you for your interest in FOCUS. Could you please explain in more detail what are you trying to accomplish? Which FFT files do you expect to have after processing in single-particle mode? It's not clear to me if you are talking about the "single-particle project" mode or about "single-particle processing of 2D crystals" mode.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/C-CINA/focus/issues/192#issuecomment-308051749, or mute the thread https://github.com/notifications/unsubscribe-auth/AcBV5m_mK2MfXR6DGom1mOf8lvBdFShBks5sDk5-gaJpZM4N3esY .

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Elad Binshtein, Ph.D. Cryo EM specialist - staff scientist Center for Structure Biology (CSB) Vanderbilt University Nashville, TN Mobile: +1-615-481-4408 E-Mail: elad.binshtein@vanderbilt.edu eladbi@gmail.com

sthennin commented 7 years ago

Dear Elad, we use IMOD's "clip fft" to compute the Fourier transforms of the final 2D averaged images. Could it be that IMOD is not running correctly on your setup? When you look at the "Setting" button top right, does IMOD show up in the Software tab? As what does it show up there? (On my computer it is /usr/local/IMOD). Is that entry black or red?

What does the Output window show if you put the verbosity level to maximum (right edge of OUTPUT window)?

Henning.