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
