This wiki is deprecated!
This wiki is deprecated. Please check out the new MemXTerminator Wiki.
DEPRECATED
Micrograph Membrane Subtraction¶
1 Basic Idea¶
After the previous step of removing membrane signals from all particles, you can put these membrane-subtracted particles back into the original micrographs to obtain new micrographs with the membrane signals removed. These micrographs can be used for subsequent processing, like re-picking the membrane proteins in them.
-
For each particle \(F_{RI}(x,y)\), we have a particle with membrane signals removed, \(F_{SRI}(x,y)\);
-
Based on the positional information of particles provided by
cryoSPARC
, we can replace the original particle \(F_{MI}(x,y)\) in the micrograph with \(F_{SRI}(x,y)\) to obtain a micrograph with membrane signals removed; -
Of course, during the replacement process, considerations should be given to ensuring that \(F_{SRI}(x,y)\) is at the same scale as the original \(F_{RI}(x,y)\) and to how to deal with overlapping areas.
2 Specific Steps¶
2.1 Open Micrograph Membrane Subtraction Interface¶
First, open the MemXTerminator main program, select the Radonfit
mode, then choose Micrograph Membrane Subtraction
, and enter the Micrograph Membrane Subtraction interface:
2.2 Parameter Explanation¶
The Micrograph Membrane Subtraction interface is as follows:
In the interface, you need to enter the following file path:
Particles selected starfile
: Choose the star file that saves all particles information, usuallyparticles_selected.star
;
In the interface, you can set the following parameters:
-
Cpus
: You can set multiple CPUs for computation. Default is 15. However, if your GPU memory is limited, it is advised not to set too many CPUs to avoid memory issues; -
Batch size
: You can set how many micrographs are processed in parallel. Default is 30, twice the number of CPUs. It is recommended to set it as a multiple of the CPU number. If your GPU memory is limited, it is advised not to set a large Batch size.
After setting the appropriate parameters, click Launch
to begin the membrane signal removal from the micrograph.
How to resume from a breakpoint
Like particle membrane subtraction, if the job is interrupted for some reason, please don't worry. You can continue to do the micrograph membrane subtraction because every time you begin to do it, the software will read the run_data_mms.log
file, which records the micrographs that have been processed. The software will automatically skip the processed micrographs and continue to process the remaining micrographs.
3 Results¶
You will find a subtracted
folder next to your folder containing the original micrographs, like this:
Sxxx/
├── motioncorrected/
├── subtracted/
In the subtracted
folder, you will find all the .mrc
files of the micrographs with membrane signals removed. You can proceed with further processing using cryoSPARC
.
Note
The orginal micrographs don't have to be in the motioncorrected
folder. The software will take the second folder in the directory as the original micrographs folder. For exmaple, in the particles_selected.star
file, the rlnMicrographName
column contains the path like Jxxx/import/xxxmicrograph.mrc
. Then the software will take the import
folder as the original micrographs folder and create a subtracted
folder next to it.