unmasked consensus map after focused refinement

[Madeline Rollins]

Hi,

Here is the output from e2version.py

EMAN 2.99.53 ( GITHUB: 2023-10-08 20:44 - commit: 38bec8c533d1c871ae00aac59be7028532e49b9e )

Your EMAN2 is running on: Linux-4.18.0-305.57.1.el8_4.x86_64-x86_64-with-glibc2.28 4.18.0-305.57.1.el8_4.x86_64

I am trying to run a focused refinement job for the domain of interest for my particle. I made a customized mask for the domain and then used the 3D particle information and 2D alignment information from my previous whole particle refinement to run the focused refinement job:

e2spt_refine_new.py --ptcls=spt_06/aliptcls3d_02.lst --ref=spt_06/threed_03.hdf --loadali2d=spt_06/aliptcls2d_03.lst --loadali3d --goldcontinue --sym=c1 --iters=p,p,t –keep=0.95 --localrefine --mask=masks/domain_mask.mrc --parallel=thread:24:/scratch/beagle3/mgrollins --threads=24 --startres=15 --m3dthread

At the end of the run, my project folder has the unmasked/unfiltered half maps for the last completed iteration, but not an unmasked/unfiltered consensus map. Is there a way to generate an unmasked/unfiltered consensus map from the two half maps?

All the best,

Madeline

[Muyuan Chen]

I typically just copy the threed_raw_even/odd.hdf files in the spt_xx folder to a new iteration number (spt_xx/threed_10_even.hdf), then run a e2refine_postprocess.py on that with the desired masking etc. If you just want an unfiltered version, simply add the even/odd files together. 

Muyuan

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[Madeline Rollins]

Thanks so much. I have two follow-up questions:

I typically just copy the threed_raw_even/odd.hdf files in the spt_xx folder to a new iteration number (spt_xx/threed_10_even.hdf), then run a e2refine_postprocess.py on that with the desired masking etc.

If I want to tophat filter the map based on local resolution (--tophat=local) but I didn't specify this in the original spt_xx run, can I do this when running e2refine_postprocess.py? I just tried it, and I get an "Error running: e2fsc_real_local.py" message. However, I don't get any error messages if I specify --tophat=localwiener or leave the default wiener filtering. 

If you just want an unfiltered version, simply add the even/odd files together.

You mean the three_raw_even/odd.hdf files, right? Not the threed_even/odd_unmasked.hdf files?

Madeline

[Muyuan Chen]

You rerun the e2refine_postprocess.py command with --tophat local. You can find the last command by "grep refine_postprocess .eman2log.txt", and change the parameters from there. Make sure to back up. Running the same command on the same file twice will cause problems because it overwrites. 

Yes raw_even is unfiltered and even_unmasked is filtered.

Muyuan

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