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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