• EMAN2
• Programs
• e2RCTboxer

Picking untilted/tilted particle pairs in EMAN2

The selection of untilted/tilted particles paris from pairs of micrographs is a crtical step in Randon Conical Tilt (RCT) reconstructions and validation via tilt pairs http://www.ncbi.nlm.nih.gov/pubmed/14568533. The program e2RCTboxer.py implements this in EMAN, and is based on e2boxer.py, having a similar look and feel. To run the program type:

e2RCTboxer.py <untilted micrograph> <tilted micrograph> options

Where options are:

• --boxsize, the starting boxsize for particle selection

• --slow, which enables realtime update of particle position in the particles widget upon particle drtagging in the mainwindow (I reccoemend not using this)

Using e2RCTboxer.py

Upon lanuching e2RCTboxer.py you will see four windows appear. Two main windows containing the ultilted and tilted micrographs, a particles image window, which will contain the selected particles, and a contol GUI. In the control GUI, main tab, there are two boxing tools, listed in a combobox, a manual tool and a pairpicker tool. The manual picker allow the user to pick untilted/tilted particle pairs by alternatly picking between the two boxes. For example, a untilted particle is selected, then a tilted particle, then a untilted, etc. When a particle is selected a number is list in the upperleft hand corner of the box. This number will be the same in both the untilted and tilted micrograph windows allowing the user to easily find pairs. In additon the untilted and tilted particle pairs are drawn to the particle image list box, with the number listed in the lower left hand corner, and the type of particle(untilted or tilted) list just above it. When a user deletes a particle the particle pair partner is also deleted in both the mainwindows and the particle list box.

To enhance ease of use, the user can move to the Pair Picker mode, where once a minimum of three particle pairs are selected, a particle pair partner is picked once either the tilted or untilted paricle is picked. To implement this, the program solves the linear transformation between the untilted and tilted micrograph. From this the computed tilt angle between the untilted and tilted micrograph, the tilt axis and the gamma angle are computed. For more information see: http://www.ncbi.nlm.nih.gov/pubmed/19374019 and http://www.ncbi.nlm.nih.gov/pubmed/3058896.

Describe EMAN2/Programs/e2RCTboxer here.