Ahhh! This is confusing, I didn't even know there was a version 2.1 of
motiocorr1.....
Yes, Wolfgang is correct: I mean David Agard's MotionCor2. If you use
Motioncorr1, then say No to that question on the GUI.
S
On 10/07/2016 03:12 PM, Wolfgang Lugmayr wrote:
> 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
>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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