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Subject:

RELION 2.0.1 tutorial discrepency with MotionCorr

From:

"Hoover , David (NIH/CIT) [E]" <[log in to unmask]>

Reply-To:

Hoover , David (NIH/CIT) [E]

Date:

Fri, 7 Oct 2016 09:57:42 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (66 lines)

What version of MotionCorr should be used with RELION 2.0.1?  I am following the tutorial and I'm getting the following errors:

 WARNING: there was an error executing: /usr/local/apps/RELION2.0/motioncorr_v2.1/bin/dosefgpu_driftcorr  -InMrc Micrographs/Falcon_2012_06_12-14_33_35_0_movie.mrcs -OutMrc MotionCorr/job002/Micrographs/Falcon_2012_06_12-14_33_35_0.mrc -OutStack 1 -Patch 1 1 -Gpu 0 >> MotionCorr/job002/Micrographs/Falcon_2012_06_12-14_33_35_0.out 2>> MotionCorr/job002/Micrographs/Falcon_2012_06_12-14_33_35_0.err

In the .out file,

$ cat MotionCorr/job002/Micrographs/Falcon_2012_06_12-16_55_40_0.out
Undefined option: Micrographs/Falcon_2012_06_12-16_55_40_0_movie.mrcs .Abort.
Error: Failed to read parameters. Abort!

I have v2.1 of MotionCorr.  The options -InMrc, -OutMrc, -OutStack, -Patch, don't exist:

$ /usr/local/apps/RELION2.0/motioncorr_v2.1/bin/dosefgpu_driftcorr
Dose Fractionation Tool:
Drift correction v2.1 (Nov 21, 2013)

    Input: InputStack.mrc [OPTION VALUE] ...
          *Note: If OPTION isn't specified, the default value will be used.

           OPTION     VALUE(Default)    Introduction
           -crx       0                 Image crop offset X
           -cry       0                 Image crop offset Y
           -cdx       0                 Image crop dimension X. 0: Use maximum size.
           -cdy       0                 Image crop dimension Y. 0: Use maximum size.
           -bin       1                 1 or 2. Bin stack before processing, only 1x and 2x binning
           -nst       0                 First frame (0-base) used in alignment.
           -ned       0                 Last frame (0-base) used in alignment. 0: Use maximum value.
           -nss       0                 First frame (0-base) used for final sum.
           -nes       0                 Last frame (0-base) used for final sum. 0: Use maximum value.
           -gpu       0                 GPU device ID.
           -bft       150               BFactor in pix^2.
           -pbx       96                Box dimension for searching CC peak.
           -fod       2                 Number of frame offset for frame comparision.
           -nps       0                 Radius of noise peak.
           -kit       1.0               Threshold of alignment error in pixel.
           -hgr       1                 1: Use gain reference in MRC header(MRC mode 5 only). 0: No.
           -fgr       FileName.mrc      Gain reference. Applied when specified.
           -fdr       FileName.mrc      Dark reference. Applied when specified.
           -srs       0                 1: Save uncorrected sum. 0: No.
           -ssr       0                 1: Save uncorrected stack. 0: No.
           -ssc       0                 1: Save corrected stack. 0: No.
           -scc       0                 1: Save CC Map. 0: No.
           -slg       1                 1: Save Log. 0: No.
           -atm       1                 1: Align to middle frame N/2+1. 0: No. <0: to |VALUE|.
           -dsp       1                 1: Save quick results. 0: No.
           -fsc       0                 1: Calculate FSC. 0: No.
           -frs       FileName.mrc      Uncorrected sum
           -frt       FileName.mrc      Uncorrected stack
           -fcs       FileName.mrc      Corrected sum
           -fct       FileName.mrc      Corrected stack
           -fcm       FileName.mrc      CC map
           -flg       FileName.txt      Log file

Additional Notes:
    1) MRC mode 5 was defined based on standard MRC format as following:
       a) A 32-bit-float Gain Reference is stored in the end of MRC extended header(Symmetry Data).
       b) Dark-subtracted frames is in format of unsigned 8-bit integer (unsigned char).
    2) If both -hgr and -fgr are enabled, -fgr will be disabled.

  Wrote by Xueming Li @ Yifan Cheng Lab, UCSF

Any hints would be helpful.

Cheers,
David Hoover
HPC @ NIH

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