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CorrectCoordinates
When you extract your particles some of them are lost because they are too near to the border of the micrograph. The python script CorrectBorderForMark allows you to correct your coordinate file .pos. It moves the coordinates that are too near to the border and generates a new coordinate file in which no particles will be eliminated.
CorrectBorderForMark 80 micrograph.raw.inf micrograph.raw.Common.pos micrograph.raw.Common_corrected.pos
where 80is the box size, micrograph.raw.infis the .raw.inf file,micrograph.raw.Common.posin the input .pos file and micrograph.raw.Common_corrected.pos is the output .pos file.
If you have used the xmipp_preprocess_A.csh and xmipp_preprocess_B.csh scripts you will have a file system in which each micrograph is in a separate folder with its .pos file. In this case you can do the coordinate correction in a automatic way with the shell script CorrectAllCoordinates
-- Main.RafaelNunezRamirez - 05 Jan 2007