Is there any great benefit to one version or the other?
> On Oct 7, 2016, at 12:33 PM, Sjors Scheres <[log in to unmask]> wrote:
>
> Hi David,
>
> There are 2 different programs with very similar names:
>
> 1) Motioncorr, developed by Xueming Li, apparentloy now has a version 2.1. This is also called driftcorr (and many other names), and is the program you refer to below. This is the standard MotionCorr to which RELION-1.4 wrapped, and RELION-2.0 also wraps.
>
> 2) Then there is Shawn Zheng and David Agard's new MotionCor2 program, which you can find here: http://msg.ucsf.edu/em/software/motioncor2.html
>
> RELION-2.0 wraps to both programs. To distinguish it has an additional question on the GUI: "Is this MOTIONCOR2"? Say NO if you use the program under 1). Say YES if you use 2)
>
> HTH,
> Sjors
>
>
> On 10/07/2016 05:26 PM, Hoover , David (NIH/CIT) [E] wrote:
>> 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
>
> --
> 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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