AutoStructure

Getting Started

Staring a Calculation

The user can start a calculation from either the graphical user face or the command line. 

1. Launching a calculation from the GUI.

• Under the Autostructure pull-down on the main page, choosing Start -> Calc opens the dialogue box below. 

• Launching calculations from the GUI uses is generally slow since only the processors on your own machine are used.  To speed up the calculations use the command line on a cluster.

2.  Launching a calculation from the command line.

• Login in the a cluster.  At CABM we use AutoStructure version 2.2.1 on hummer.
• A simple command line run can be started as follows:

/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v

• Running the autostructure command gives the following options (like those avaliable in the GUI):

 AutoStructure/RPF Version 2.2.1 Copyright(C) 2007
     Center for Advanced Biotechnology and Medicine (CABM)
     Rutgers University

     Options:
         -c control_file      Required
         -o output_dir        Required
         -d                   For debug
         -h                   Help
         -m                   Exclude PCT-filter of Cycle1 for symmetry analysis
         -n                   Exclude CSI-based secondary structure analysis
         -i structure_file    inital fold for bootstrapping
         -j                   Include J-coupling constant data for angle constraint analysis (HYPER)
         -k float_number      Calibration coefficient
         -N                   Include NOE assignments in HYPER caluclation (under development)
         -q structure_file    AutoQF-Calculate the F and DP scores of the input structure_file (IUPAC naming)
         -r path              Restore from a prior outout_dir
         -R                   Include rotamer constraints in HYPER calculation (under development)
         -v                   Calculate the M score and average shifts

References

-- JimAramini - 07 Nov 2009