Using Falcon Hack

Chen Xu

$BrandeisEM: ~/emdoc/articles-xml/Flacon-Hack/article.xml 1 2014-03-10 01:38:24 xuchen Exp$

Now, Falcon II fast readout (Falcon Hack) is in place and running happily, we need a brief document describing how to use this new system.

Using the system includes a few parts. 1) How to start and stop the capturing. 2) How to monitor captured file being generated. 3) How to view the newly captured MRC stack files. 4) How to align the stacks at background, automatically. 5) for tomography users, how to stack the aligned mrc output according to the order in SerialEM's mdoc file. I will try to cover these.

You can also get pdf version of this document here.

Table of Contents
1 Start and Stop Falcon Frame Capturing
2 How to Monitor Capturing Process
3 Align the Stacks at Background
4 View Flacon Stack File
5 Restacking Aligned Falcon Frames for Tomography

1 Start and Stop Falcon Frame Capturing

  1. From Tecnai F30 computer, login to as capture using a SSH client. On Tf30, you can use "putty".

  2. Start capturing program with a Suffix.

[capture@localhost ~]$ start_capture XC-Sample1
    User account: [capture] capture
    Saving data to directory /mnt/SSD_RAID/captured/2014-03-10_capture_XC-Sample1
    capture: no process killed
    24147: old priority 0, new priority -20 

    This command will kill any exsiting capture job and start a new one. It also creates a new direcotry /mnt/SSD_RAID/captured/2014-03-10_capture_XC-Sample1 for your captured frames from now on.