Particle Localization and Identification

PyTom: Localize Macromolecules by template matching

Overview

Features in a tomogram that resemble a structural 'template' can be localized in an automated fashion using 'template matching'. In this approach a 3D template is correlated with a given tomogram. In this procedure the different possible rotations and translations are sampled exhaustively using the algorithm described in Förster et al, Meth. Enzymol. 483:215-43 (2010).

Tutorial files

You will find sample localization scripts in the tutorial repository in the RibosFromLysate/localization directory. It contains symbolic file-links to the tomogram, reference and mask + a submit example. The referenced tomogram must be reconstructed first because it is too big for download! Please note that the submit file starting the localization is specifically designed for our cluster. You will find a more generic openmpi command in the following paragraphs. Scripts for determining potential macromolecules (extract.sh) and to fit a Gaussian into the score histogram get an estimate of the number of macromolecules (plotFit.sh) are available,too. Do not hesitate to modify the scripts after you processed them at least once. You can always fall back to the original script by typing

git checkout -- TheFileYouChanged

Detect putative particles using localization.py

The script bin/localization.py allows computing the constrained local correlation of a tomogram and a reference in a local area described by a mask. The script supports MPI, which allows running the script on large computer clusters. Here is a call of the script:

mpirun --hostfile "pathToYourHostfile" -c "numberOfCPUs" pytom localization.py job.xml 2 2 2

The last 2 2 2 specify that the tomogram will be split into 2 parts along x,y,z dimension. => 8 subcubes are distributed during localization and merged when finished.This splitting of the volume does not change the results. However, please keep in mind that splitting a tomogram along either one dimension resulting in a volume size smaller than the reference size will fail! All parameters that influence the result are specified in the XML file job.xml . In detail, the XML file specifies: