ConvertXmdfileToRelionPosFile

Convert XMD File to RELION Pos File

After 2D classification in Xmipp3 you could be interested in perform all the image processing in RELION using just these particles. Using this script you will get a Pos file for each plate from the xmd file obtained after the classification

Usage:

extract_coordinates_xmipp3ToRelion.bash images.xmd

The xmd file must have the following format:

# XMIPP_STAR_1 * 
# 
data_noname
loop_
 _image
 _micrograph
 _xcoor
 _ycoor
 _enabled
 _ctfModel
 _itemId
 _zScore
 _zScoreShape1
 _zScoreShape2
 _zScoreSNR1
 _zScoreSNR2
 _zScoreHistogram
 _imageOriginal
 _ref
 _flip
 _shiftX
 _shiftY
 _anglePsi
000063@Images/Extracted/run_001/extra/Falcon_2014_08_12-00_47_02.stk ./placas/Falcon_2014_08_12-00_47_02.mrc       1058       1459          1 Micrographs/Screen/run_001/extra/Falcon_2014_08_12-00_47_02/xmipp_ctf.ctfparam     128420     0.149747     0.149747     0.149747     0.033838     0.100681     0.112148 000003@Images/Preprocessed/run_001/images.stk        188 1     0.916507    -1.287166   -17.777778 
000078@Images/Extracted/run_001/extra/Falcon_2014_08_12-08_16_27.stk ./placas/Falcon_2014_08_12-08_16_27.mrc        787       3204          1 Micrographs/Screen/run_001/extra/Falcon_2014_08_12-08_16_27/xmipp_ctf.ctfparam     283667     0.158083     0.158083     0.158083     0.010800     0.124427     0.066915 000006@Images/Preprocessed/run_001/images.stk         19 0    -0.518930     6.971051     4.444444 
000131@Images/Extracted/run_001/extra/Falcon_2014_08_11-21_06_26.stk ./placas/Falcon_2014_08_11-21_06_26.mrc       2738       1932          1 Micrographs/Screen/run_001/extra/Falcon_2014_08_11-21_06_26/xmipp_ctf.ctfparam      75093     0.196583     0.139679     0.139679     0.196583     0.145624     0.133675 000015@Images/Preprocessed/run_001/images.stk        157 1     1.121070    -5.026890  -111.111111 
.........

The script ExtractCoordinatesXmipp3ToRelion generates a Pos file for each plate in the xmd file. When finished copy the new pos files (identified as manual) in the Relion directory where the plates are. Relion will read automatically the position of the selected particles.

-- Main.RafaelNunezRamirez - 2014-09-19