AGNuS/AutoProc

Introduction

Autoproc/AGNuS is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. AGNuS automatically generates NMRPipe scripts for processing multidimensional NMR experiments and provides functions for chemical referencing.  AGNuS calls information  for specific experiments and spectrometers stored in table files, which can be generated/modified by users with permission.  AGNuS is also capable of processing reduced dimensionality/GFT experiments. 

Please check SOP of AGNuS for addtional information and examples of processing 2D and 3D NMR experiments.

Processing a GFT Experiment

Here are some instructions for processing a GFT experiment:

Before run AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. These table file of the most used NMR experiments are availble from AGNus. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select *MULTI for GFT basic experiments process.

Example of pulse sequence table for GFT_43D_CABCAcoNHN

file_type : single_fid_table
name : GFT_43D_CBCACAcoNHN
nickname : HNcoCACB_GFT
synonym : GFT_43D_CBCACAcoNHN_MULTI
dimensions :  [
  nuclei : H
  offset_parameter : tof
  acquisition_mode : Complex
  ]
dimensions :  [
  nuclei : C
  offset_parameter : dof
  acquisition_mode : Complex
  ]
dimensions :  [
  nuclei : N
  offset_parameter : dof2
  acquisition_mode : Complex
  ]

processing_defaults : [
  name : "Sine Bell Default"
  dimensions :  [
    transformation : FT
    apodization : "SP -off 0.45 -end 0.98 -pow 2"
    first_point_correction : 0.5
    ]
  dimensions :  [
    transformation : FT
    apodization : "SP -off 0.45 -end 0.98 -pow 1"
    first_point_correction : 1.0
    ]
  dimensions :  [
    transformation : "FT -neg"
    apodization : "SP -off 0.45 -end 0.98 -pow 1"
    first_point_correction : 0.5
    ]
    xy_plane : 002
  ]

• To run AGNus, simply go to the directory only contains the Varian fid and procpar (parameter) file; type agnus and follow the instructions prompted by AGNus. Type agnus -help for help.
  1. Select *MULTI for GFT basic experiments process (optional, AGNus will go to the next step if non-GFT data if identified)
  2. Selecting the spectrometer
  3. Select the basic information about where files are located, name of conversion scripts, and names of converted files.
  4. Run the conversion script provided by AGNus to convert NMR data format to Pipe format. Modify the conversion script is necessary.
  5. Run the process scripts (3D and XY, XZ planes process scripts for 3D data) provided by AGNus. Modify the Buffalo.NMRPipe process parameters such as phase values if necessary.
     1. AGNus will lauch NMRDraw to let the user to check the process data and get the phase values.
     2. Use CTRL-C to quit AGNus after phasing the spectrum with NMRDraw
     3. Rerun AGNus and manually type in or correct the phase when come to the process scripts change step. Modify the base line parameter as well if necessary
     4. Run the final process after all parameters be carefully reviewed.
  6. Run the UCSF conversion and cleanup script if use SPARKY for NMR data analysis. Run SPSCAN to conver Buffalo.NMRPipe format data to XEASY format data if use XEASY.

-- GaohuaLiu - 31 May 2007

-- Updated by JimAramini - 11 Nov 2009