hi,
you are not using MotionCor2, you are are using motioncorr (dosef) 2.1.
So say NO in the files "Is this MOTIONCOR2?"
MotionCor2: http://msg.ucsf.edu/em/software/index.html
cheers,
wolfgang
On 10/07/2016 03:57 PM, Hoover , David (NIH/CIT) [E] wrote:
> 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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