Bypassing to the 'direct' use of emClarity's template matching pipeline

[kexinliu0001]

hi,

i am doing the template matching pipeline.

i have done the ts alignment and reconstruction, is it ok to just use the reconstructed bin8 tomograms <ts_191.st_10.88Apx.mrc> to do template matching?
it seems that emClarity need to read <aliStacks/ts_191.st_10.88Apx_ali1.fixed>, can i bypass it?

[kexinliu0001]

as the related scrip is header = getHeader(MRCImage(stack,0)); in BH_multi_loadOrBuild, can i create a blank stack file just with the header information in the aliStacks folder?

[bHimes]

That might work, but if it does, it will only get you through the template matching stage. If you wanted to go on to subtomo alignment/classification, you would run into more problems, but maybe they would be worth you trying to sort out if your TM results are useful enough

(emClarity is meant to be an end to end pipeline. It is far too hard, given my time and resources, to try to ensure interoperability with other software)