Hi Sjors,
Thank you so much!!
Best wishes.
Wenjuan
> On 8 Oct 2016, at 10:15, Sjors Scheres <[log in to unmask]> wrote:
>
> Hi Wenjuan,
> The august-version of MotionCor2 does write out the movies, so in
> principle you could put those back into per-particle movie-refinement and
> polishing in relion. I think the movies written out are not dose-weighted,
> but polishing would do that for you.
> HTH,
> Sjors
>
>
>> Hi Axel,
>> How do you find that the patch size is automatically increased if there
>> is not enough signal to hit the accuracy threshold? I didn’t know that
>> and I did with 10 10 patches, which took quite a long time to
>> finish…Besides, MotionCor2 cannot give us the motioncorred movies,
>> which should be used for movie correction and particle polishing, right?
>> It means that we cannot do movie correction and particle polishing after
>> using MotionCor2?
>>
>> Many thanks.
>> Wenjuan
>>
>>
>>
>>> On 7 Oct 2016, at 23:21, Axel Brilot <[log in to unmask]> wrote:
>>>
>>> The patch size is automatically increased if there is not enough signal
>>> to hit the accuracy threshold.
>>> We have had good results here with 5 5 patches.
>>>
>>> HTH
>>>
>>> Axel
>>>
>>> On Fri, Oct 7, 2016 at 3:19 PM, Reza Khayat <[log in to unmask]
>>> <mailto:[log in to unmask]>> wrote:
>>> Any suggestions on what patch sizes to try?
>>>
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>>
>>> ________________________________________
>>> From: Collaborative Computational Project in Electron cryo-Microscopy
>>> <[log in to unmask] <mailto:[log in to unmask]>> on behalf of Sjors
>>> Scheres <[log in to unmask] <mailto:[log in to unmask]>>
>>> Sent: Friday, October 7, 2016 5:33 PM
>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>> Subject: Re: [ccpem] RELION 2.0.1 tutorial discrepency with MotionCorr
>>>
>>> We also have had great results with Motioncor2. We haven't tried yet to
>>> do
>>> polishing after Motioncor2, but did compare unblur+polishing versus only
>>> motioncor2 on the 2.2A betagal data set from Sriram (EMPIAR-10061).
>>> Unblur+polishing gave a few resolution shells more information (2.2 vs
>>> 2.3A), but does come at an important computational costs compared to
>>> only
>>> doing motioncor2. Therefore, at LMB, I'm now recommending people to
>>> first
>>> do MotionCor2 (with patches and dose-weighting) and then do all your
>>> classifications etc. Then, at the very end, if you did get your
>>> almost-final high-resolution map, and do want to see whether you can
>>> squeeze out a bit more information, do try polishing as well. As many
>>> data
>>> sets never go to very high resolution and it thus wouldn't be worth to
>>> do
>>> polishing anyway, this should save quite a bit of computational
>>> resources
>>> (CPU time and disk space).
>>> HTH,
>>> Sjors
>>>
>>> PS: one note of warning: in order to get the dose-weighting correct you
>>> need to know the correct dose per frame. This sounds logical, but many
>>> errors are being made with this. Especially with non-counting detectors.
>>>
>>>
>>>> Motioncorr2 can also do dose weighting and it allows motion correction
>>> of
>>>> patches (not only whole frame).
>>>> In our hands motioncorr2 seems to always perform as good or better
>>> than
>>>> driftcorr.
>>>> This also means that using motioncorr2 we do not get any benefit
>>> anymore
>>>> of doing particle-polishing at the end of the relion process (Using K2
>>>> camera and ribosomes) and therefore skip this step.
>>>>
>>>> Cheers
>>>> Marcus
>>>>
>>>>
>>>> Marcus Fislage, PhD
>>>>
>>>> Howard Hughes Medical Institute (HHMI)
>>>> Columbia University
>>>> Department of Biochemistry and Biophysics
>>>> Lab of Joachim Frank
>>>> New York, NY
>>>>
>>>> email address: [log in to unmask]
>>> <mailto:[log in to unmask]>
>>>> Phone: 212.305.9524 <tel:212.305.9524>
>>>> Fax: 212.305.9500 <tel:212.305.9500>
>>>>
>>>>
>>>> ________________________________________
>>>> From: Collaborative Computational Project in Electron cryo-Microscopy
>>>> [[log in to unmask] <mailto:[log in to unmask]>] on behalf of
>>> Hoover , David (NIH/CIT) [E]
>>>> [[log in to unmask] <mailto:[log in to unmask]>]
>>>> Sent: Friday, October 07, 2016 12:47 PM
>>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>>> Subject: Re: [ccpem] RELION 2.0.1 tutorial discrepency with MotionCorr
>>>>
>>>> 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]
>>> <mailto:[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
>>> <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
>>> <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] <mailto:[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
>>> <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
>>> <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 <tel:%2B44%20%280%291223%20267061>
>>>>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>> <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 <tel:%2B44%20%280%291223%20267061>
>>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>> <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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