Please, be more direct.
What version of MotionCorr is the correct version?
The webpage at http://cryoem.ucsf.edu/software/driftcorr.html only shows v2.1. What other versions are available and from where?
David Hoover
HPC @ NIH
> On Oct 7, 2016, at 10:26 AM, Sjors Scheres <[log in to unmask]> wrote:
>
> 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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