Question about 2D particles extract in WarpTools

47 views
Skip to first unread message

yuanyuan zeng

unread,
Sep 9, 2026, 9:48:15 PMSep 9
to Warp
Hello all.I have a question about WarpTools.I have generated a high resolution structure through WarpTools/M with 3D subtomogram .Now.I want to try WarpTools with 2D particles extract along with relion5.0.I use the last iteration results of M's particls.star as input of WarpTool 2D particles extraction, but the result of average.mrcs in each tilt is strange,and the results of relion5.0 refinment are almost noise in the first few iterations,and the resolution is too low ,about 17A, the map is also strange.I wonder what is wrong during the processing? Sincerely thank you for helping me! I 'd like to give you my 3D and 2D star files below: 
3D:

data_

loop_
_wrpCoordinateX1 #1
_wrpCoordinateY1 #2
_wrpCoordinateZ1 #3
_wrpAngleRot1 #4
_wrpAngleTilt1 #5
_wrpAnglePsi1 #6
_wrpRandomSubset #7
_wrpSourceName #8
_wrpSourceHash #9
  3484.70337  3789.01782  1472.34229    27.51451   68.81159   104.26852  2  TS_0034.tomostar  244FCRH0LradusfEil5B4V9UQlk

2D:

data_general

_rlnTomoSubTomosAre2DStacks   1




data_optics

loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
_rlnSphericalAberration #3
_rlnVoltage #4
_rlnTomoTiltSeriesPixelSize #5
_rlnCtfDataAreCtfPremultiplied #6
_rlnImageDimensionality #7
_rlnTomoSubtomogramBinning #8
_rlnImagePixelSize #9
_rlnImageSize #10
_rlnAmplitudeContrast #11
   1   opticsGroup1  2.394  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   2   opticsGroup2  2.705  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   3   opticsGroup3  2.324  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   4   opticsGroup4  2.751  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   5   opticsGroup5  2.678  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   6   opticsGroup6  4.356  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   7   opticsGroup7  2.976  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   8   opticsGroup8  2.844  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
   9   opticsGroup9  3.341  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  10  opticsGroup10  2.950  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  11  opticsGroup11  3.761  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  12  opticsGroup12  2.390  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  13  opticsGroup13  2.972  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  14  opticsGroup14  3.104  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  15  opticsGroup15  1.911  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  16  opticsGroup16  1.307  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  17  opticsGroup17  1.144  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  18  opticsGroup18  0.713  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  19  opticsGroup19  1.180  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  20  opticsGroup20  3.512  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  21  opticsGroup21  2.110  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  22  opticsGroup22  1.165  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  23  opticsGroup23  1.672  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  24  opticsGroup24  2.480  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  25  opticsGroup25  2.056  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  26  opticsGroup26  2.298  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  27  opticsGroup27  2.695  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  28  opticsGroup28  1.746  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  29  opticsGroup29  2.040  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  30  opticsGroup30  2.108  300.000  0.75500  1  2  2.00000  1.51000  216  0.070
  31  opticsGroup31  2.765  300.000  0.75500  1  2  2.00000  1.51000  216  0.070




data_particles

loop_
_rlnTomoName #1
_rlnTomoParticleId #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnCoordinateZ #5
_rlnAngleRot #6
_rlnAngleTilt #7
_rlnAnglePsi #8
_rlnTomoParticleName #9
_rlnOpticsGroup #10
_rlnImageName #11
_rlnOriginXAngst #12
_rlnOriginYAngst #13
_rlnOriginZAngst #14
_rlnTomoVisibleFrames #15
_rlnRandomSubset #16
  TS_0034.tomostar     1  2307.750  2509.283   975.061    27.515   68.812   104.269     TS_0034/1   1  /ssd/zsy5/particleseries/TS_0034/TS_0034_1.51A_000001.mrcs  0.0  0.0  0.0  [1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1]  2
Reply all
Reply to author
Forward
0 new messages