navya19j
commented
4 months ago I am facing this error too
Closed Amy1809 closed 4 months ago
navya19j
commented
4 months ago I am facing this error too
Amy1809
commented
4 months ago I am facing this error too
Hi Navya, I solved this problem. In the motion correction stage, at the 'Motion' panel, you need to input a 'gain.mrc' file as the blank for Relion to do the blanking.
After I input the gain.mrc file, the motion_corrected_tilt_series.star file has the '_rlnTomoMicrographNameEvn' and 'Odd' files showing up.
I hope this helps.
navya19j
commented
4 months ago Oh wow, where did you get the gain.mrc from?
Amy1809
commented
4 months ago Oh wow, where did you get the gain.mrc from?
In the data I pulled out, there is a file called 'processing', in this file, I get the 'gain.mrc' file.
navya19j
commented
4 months ago Thanks! I tested with that but I still don't see the two columns in my corrected_tilt_series.star. Did you change anything else too?
Amy1809
commented
4 months ago I only changed that bit. Is your file ending in '.mrc' or '.eer'? Here are my parameters setting: EER fractionation: 32 (this is according to the tutorial where if you are not using the .EER file, just leave it in 32) write output in float16?: Yes Save images for denoising?: Yes save sum of power spectra?: Yes sum power spectra every n frames: 4 Bfactor: 150 number of patches X,Y: 1, 1 group frames: 1 binning factor: 1 gain-reference image: gain.mrc (you need to browse to get the correct file in the correct path) gain rotation: no gatin flip: no defect file: I leave this one empty use RELION's own implementation?: yes
I hope this helps.
navya19j
commented
4 months ago Hi, it's .mrc and I supplied the gain reference image but I still end up with the same error. I am using AreTomo alignment, are you using that as well?
Amy1809
commented
4 months ago Hi, it's .mrc and I supplied the gain reference image but I still end up with the same error. I am using AreTomo alignment, are you using that as well?
Hi, yes I use AreTomo. I suppose you may want to check if there is anything wrong in your previous steps...? I am doing the denoise, so I have also set the "save the images for denoise?" in the motion correction step as "Yes".
navya19j
commented
4 months ago I was able to fix it, Thank you!
Amy1809
commented
4 months ago I was able to fix it, Thank you!
Happy to hear that! May I ask how did you fix that?
Describe your problem I am following the Relion pipeline starting from import - motion correction - CTF estimation. I have passed the tilt series alignment stage using AreTomo in Relion and now want to reconstruct tomograms. Here is my full command:
which relion_tomo_reconstruct_tomogram--t AlignTiltSeries/job028/aligned_tilt_series.star --o Tomograms/job033/ --w 4200 --h 4200 --d 300 --binned_angpix 10 --fourier --ctf_intact_first_peak --do_proj --centre_proj 0 --thickness_proj 10 --tiltangle_offset -2 --only_do_unfinished --j 1 --pipeline_control Tomograms/job033/ERROR: tomogramTable for Position_1 does not contain a rlnTomoMicrographNameEven labelHere is my input file from the tilt series alignment 'Aligned_tilt_series.star':
I can see that I am missing the _rlnTomoMicrographNameEven label, but this lable is not generated from my previous .star file during the motion correction and CTF estimation stage. I have looked at other people's file and know that Relion is looking for file similar to 'MotionCorr/job002/frames/ts_00105_45_0_EVN.mrc', however, in my process, this file is not generated. Many appreciation on any suggestions or advice of how it may go wrong.