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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