Identifying the 3D particles associated with the 2D particles

[Reza Khayat]

Hi,

I have identified a set of 2D particles, from aliptcls2d_XX.lst file, whose associated 3D particles I would like to identify. I'd like run additional refinement on these 3D, and associated 2D, particles. Are there tools available for doing this? 

Best wishes,
Reza

[Steve Ludtke]

By "identified" what do you mean?  Do you have a .lst file containing only the 2-D particles you wish to use, or a list of particle numbers, or something else?  Did you identify only a single 2-D particle for each 3-D particle, or do you have multilple 2-D particles for each.  The necessary metadata exists to do what you want, but the practical approach will depend on what you have.

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[Reza Khayat]

I have a list of 2D particles (a subset of the aliptcls2d_XX.lst). The file contains all tilts for each 3D particle. It's a one:one correspondence. 

[Steve Ludtke]

Hi Reza,

Sorry for the delay. Busy day.

I'm not 100% sure it's necessary to extract a 3-D substack, it might already only use 3-D particles which are referenced in the 2-D particles?  I'm not positive. Muyuan would have to answer. If you want to be careful, you'd need a little python script to extract the corresponding 3-D particles and remap the 2-D particles:

# This program will extract the 3-D particles corresponding to a subset of 2-D particles in SPT

# it will also generate a new 2-D file with renumbered 3-D references

# usage program.py <2d substack lst> <3d stack lst> <new 2d out> <new 3d out>

from EMAN3 import *

import sys,os

try: os.unlink(sys.argv[3])

except: pass

try: os.unlink(sys.argv[4])

except: pass

in2d=LSXFile(sys.argv[1])

in3d=LSXFile(sys.argv[2])

out2d=LSXFile(sys.argv[3])

out3d=LSXFile(sys.argv[4])

pt3did={int(x[2]["ptcl3d_id"]) for x in in2d}

pt3dlst=sorted(list(pt3did))

map=dict()

for i,j in enumerate(pt3dlst):

out3d[i]=in3d[j]

map[j]=i

for num,fsp,meta in in2d:

meta["ptcl3d_id"]=map[meta["ptcl3d_id"]]

out2d[-1]=num,fsp,meta

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[Reza Khayat]

Hi Steve,

Thanks so much, this works great!

Best wishes,
Reza