search

StochasticAnalytics / emClarity

GNU Lesser General Public License v3.0
41 stars 6 forks source link

Import Relion style coordinate #77

Open inter1965 opened 5 years ago

inter1965 commented 5 years ago

Given the following star as an example, we need to import this relion style coordinate into emClarity project (feed BH_geometryInitialize). To be more specific, I guess:

  1. we need to use fileds in the star file (_rlnMicrographName, _rlnCoordinateX, _rlnCoordinateY, _rlnCoordinateZ) to generate a surrounding box first, and then mimic emClarity's XX_recon.coords and XX_1_recon.txt.
  2. convert each individual subtomo's coordinate (by adding oX/oY/oZ ?) according to the newly generated emClarity's XX_recon.coords and write emClarity's XX_M_binX.mod.

Thanks in advance

data_

loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnCoordinateZ #4
_rlnImageName #5
_rlnCtfImage #6
_rlnAngleRot #7
_rlnAngleTilt #8
_rlnAnglePsi #9
_rlnLogLikeliContribution #10
_rlnGroupNumber #11
_rlnOriginX #12
_rlnOriginY #13
_rlnOriginZ #14
_rlnClassNumber #15
_rlnNormCorrection #16
_rlnRandomSubset #17
_rlnMaxValueProbDistribution #18
_rlnNrOfSignificantSamples #19
fixedStacks/p102.st 2276.65 1846.63 388.959 subtomos/p102/p102_1000943.mrc wedges/p102_wedge.mrc 21.498249 109.010099 -45.62028 935349.7 1 -2.02151 2.490987 -2.94651 1 1.0 1 0.131404 13
fixedStacks/p102.st 2110.99 1996.05 335.161 subtomos/p102/p102_1000399.mrc wedges/p102_wedge.mrc -22.3352 112.810418 -59.42557 935311.9 1 -1.02151 -1.02151 -0.50901 1 1.0 1 0.104216 33
fixedStacks/p102.st 2130.11 1972.38 353.381 subtomos/p102/p102_1000611.mrc wedges/p102_wedge.mrc 4.546142 114.170952 -49.62758 935298.0 1 -0.02151 0.490987 -2.45901 1 1.0 1 0.070705 32
fixedStacks/p102.st 2341.19 1813.65 333.221 subtomos/p102/p102_1000266.mrc wedges/p102_wedge.mrc -33.59716 107.663235 -48.31802 935277.1 1 -3.50901 0.978487 -0.99651 1 1.0 2 0.055007 70