This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
pipeline:subtract:projsubtract [2021/02/01 15:47] shaikh created |
pipeline:subtract:projsubtract [2021/10/11 17:17] shaikh |
||
---|---|---|---|
Line 20: | Line 20: | ||
sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE): | sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE): | ||
- | \\ __1. Average and low-pass filter a map for segmentation __ | + | \\ __1. [[avgfilt|Average and low-pass filter a map for segmentation]] __ |
\\ __2. Locate regions to be subtracted __ | \\ __2. Locate regions to be subtracted __ | ||
- | \\ __3. Mask a soft mask of the region to be excluded __ | + | \\ __3. [[sp_mask|Mask a soft mask of the region to be excluded]] __ |
- | \\ __4. Compute re-projections of map to be subtracted, and subtract them from the original images __: | + | \\ __4. [[projsubtract|Compute re-projections of map to be subtracted, and subtract them from the original images]] __: |
mpirun -np 16 sp_signalsubtract.py projsubtract --origparts=particle_stack --map2subtract=map_to_subtract --projparams=projection_parameters --outdir=output_subtraction_directory --nmontage=number_of_examples --inmem --saveprojs | mpirun -np 16 sp_signalsubtract.py projsubtract --origparts=particle_stack --map2subtract=map_to_subtract --projparams=projection_parameters --outdir=output_subtraction_directory --nmontage=number_of_examples --inmem --saveprojs | ||
Line 36: | Line 36: | ||
By the default, the intermediate projections will be deleted after subtraction. To save them, use the " | By the default, the intermediate projections will be deleted after subtraction. To save them, use the " | ||
- | \\ __5. Compute reconstruction of density remaining after signal-subtraction __: | + | \\ __5. [[pipeline: |
sp_meridien.py bdb: | sp_meridien.py bdb: | ||
Line 44: | Line 44: | ||
Note: If the " | Note: If the " | ||
- | \\ __6. Center map of the remaining density __ | + | [{{ : |
+ | |||
+ | \\ __6. [[centershift|Center map of the remaining density]] __ | ||
\\ | \\ | ||
===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; %%--%%origparts : Original particle stack before signal subtraction. (default | + | ; %%--%%origparts : Original particle stack before signal subtraction. (default |
- | ; %%--%%map2subtract : Map whose projections will be subtracted from the original images. (default | + | ; %%--%%map2subtract : Map whose projections will be subtracted from the original images. (default |
- | ; %%--%%projparams : Angles and shifts, from Meridien. (default | + | ; %%--%%projparams : Angles and shifts, from Meridien. (default |
; %%--%%outdir : Directory where outputs will be written. (default required string) | ; %%--%%outdir : Directory where outputs will be written. (default required string) | ||
| | ||
Line 77: | Line 79: | ||
\\ | \\ | ||
==== Reference ==== | ==== Reference ==== | ||
+ | Bai XC, Yan C, Yang G, Lu P, Ma D, Sun L, Zhou R, Scheres SHW, Shi Y. (2015) "An atomic structure of human γ-secretase." | ||
\\ | \\ | ||
Line 85: | Line 88: | ||
Tapu Shaikh | Tapu Shaikh | ||
+ | Based on a protocol developed by Zhong Huang and Pawel Penczek | ||
\\ | \\ | ||
==== Keywords ==== | ==== Keywords ==== |