dose weighting in RELION 5

[DrJesseHansen]

hi Biochemfan,

I am sorry for posting this here, I'm not sure how else to contact you.

I am wondering if it's possible to include a dose weighting scheme for subtomo averaging in RELION 5? I see during import I can specify the dose per tilt, but nowhere else can I edit this. I am processing hybrid cryo-ET SPA data where there's an initial zero tilt image with high dose then a tilt series with normal dose distribution. Is there a way to tell this info to RELION?

thanks

Jesse

This is a template for reporting bugs. Please fill in as much information as you can.

Describe your problem

Please write a clear description of what the problem is. Data processing questions should be posted to the CCPEM mailing list, not here. DO NOT cross post a same question to multiple issues and/or many mailing lists (CCPEM, 3DEM, etc).

Environment:

• OS: [e.g. Ubuntu 16.04 LTS]
• MPI runtime: [e.g. OpenMPI 2.0.1]
• RELION version [e.g. RELION-3.1-devel-commit-6ba935 (please see the title bar of the GUI)]
• Memory: [e.g. 128 GB]
• GPU: [e.g. GTX 1080Ti]

Dataset:

• Box size: [e.g. 256 px]
• Pixel size: [e.g. 0.9 Å/px]
• Number of particles: [e.g. 150,000]
• Description: [e.g. A tetrameric protein of about 400 kDa in total]

Job options:

• Type of job: [e.g. Refine3D]
• Number of MPI processes: [e.g. 4]
• Number of threads: [e.g. 6]
• Full command (see note.txt in the job directory):

  `which relion_refine_mpi` --o Refine3D/job019/run --auto_refine --split_random_halves --i CtfRefine/job018/particles_ctf_refine.star --ref PostProcess/job001/postprocess.mrc --firstiter_cc --ini_high 12 --dont_combine_weights_via_disc --scratch_dir /ssd --pool 3 --pad 2  --ctf --ctf_corrected_ref --particle_diameter 142 --flatten_solvent --zero_mask --solvent_mask Result-by-Rado/run_class001_mask_th0.01_ns3_ngs7_box400.mrc --solvent_correct_fsc  --oversampling 1 --healpix_order 3 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym O --low_resol_join_halves 40 --norm --scale  --j 8 --gpu "" --keep_scratch --pipeline_control Refine3D/job019/

Error message:

Please cite the full error message as the example below.

A line in the STAR file contains fewer columns than the number of labels. Expected = 3 Found = 2
Error in line: 0 0.0
in: /prog/relion-devel-lmb/src/metadata_table.cpp, line 966
=== Backtrace  ===
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x42e981]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MetaDataTable12readStarLoopERSt14basic_ifstreamIcSt11char_traitsIcEEPSt6vectorI8EMDLabelSaIS6_EESsb+0xedd) [0x4361ad]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MetaDataTable8readStarERSt14basic_ifstreamIcSt11char_traitsIcEERKSsPSt6vectorI8EMDLabelSaIS8_EESsb+0x580) [0x436f10]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN10Micrograph4readE8FileNameb+0x5a3) [0x454bb3]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN10MicrographC2E8FileNameS0_d+0x2e3) [0x4568b3]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN17MicrographHandler14isMoviePresentERK13MetaDataTableb+0x180) [0x568280]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN17MicrographHandler17cullMissingMoviesERKSt6vectorI13MetaDataTableSaIS1_EEi+0xe6) [0x568dc6]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(_ZN13MotionRefiner4initEv+0x56f) [0x49e1ff]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi(main+0x31) [0x42a5e1]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b7ac026e495]
/prog/relion-devel-lmb/bin/relion_motion_refine_mpi() [0x42b3cf]
==================

[biochem-fan]

Does --pre_exposure do what you want?

I am not involved in the STA aspect of RELION at all; I do not know if subsequent processing respects this metadata.

[EuanPyle]

There is a way to implement hybrid dose tilt schemes but you'll have to do some things manually. But it's not too complicated if you can write a simple python script.

After running Import, use a program to edit star files (I like https://github.com/teamtomo/starfile) to read the star files in Import/jobXYZ/tilt_series/, read the column rlnMicrographPreExposure, and adjust the values depending on what dose you used for each. i.e. the first image should be 0, if you used a dose of 10 when collecting the first image then the second should be 10, then if you used a dose of 3 for the rest, the third should be 13, fourth 16, etc.

Overwrite the existing star files containing the new rlnMicrographPreExposure values. That should work.