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
|
