e2spt_tempmatch.py

[thorsten...@googlemail.com]

Hi,

I would like to run template matching on a tomogram (MRC format). I've downloaded a PDB and calculated a map with 

e2pdb2mrc.py PDB.pdb1 PDB.mrc --apix 10 --res 20 --center --box 16

If I change vthr to 3 I get quite some particles. However, if I set it to 0.3, I get less particles. How can that be?

Additionally, does the reference and the tomogram require any specific scaling? Do they both need to be normalized? Or is that done internally?

Best,

Thorsten

[thorsten...@googlemail.com]

After checking the code I saw that its normalized by edgemean. However, the problem with getting less particles with lower threshold still confuses me.

[Muyuan Chen]

It looks for isolated density blobs in the cross correlation map. At lower threshold, some nearby blobs connects to each other, leading to fewer peaks being identified. 

Muyuan

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