HIFI-NMR is our adaptive approach for rapid and automated collection of NMR data.  The software implementing the algorithms used in HIFI is available for Varian spectrometers on both SUN and LINUX platforms.  Also available is a complete data set demonstrating the capabilities of HIFI.

BACKGROUND

A Powerpoint presentation describing HIFI is available ( PPT / PDF )

 

This is the beta release of the HIFI package for fast automated backbone data collection.

At this point the experiments supported are the most sensitive and robust ones. These are the standard experiments:

hnco
hnca
hncoca
cbcaconh
hncacb
hncb (same sequence as hncacb but with longer ca->cb transfer as a result no ca in peak list)

As for all 3D -> 2D methods, HIFI will work for well-behaved small to medium size proteins. Please note that, similar to any other NMR experiment, HIFI requires some minimum signal strenght.

To evaluate whether HIFI will work for your protein or not, you can collect the 0 degree orthogonal planes (i.e. H1-C13 2D planes) for a reasonable amount of scans and time. If you are able to easily see most of the peaks in these 2D planes (don't worry about overlap, just peak intensity), then you can start the automated HIFI data collection. But, if you only see few peaks in the 2D-planes, then HIFI (and, most likely, any other fast method) will not work. For such a protein you may try running long 3D experiments (where signal gets accumulated over a long period of time) although, in the end, peaks may be missing from such spectra as well.

DOWNLOAD

Download the Sun package in a single (tar) file.

Download the Linux package in a single (tar) file.

INSTALLING HIFI

HIFI can be installed either in the main directory: /vnmr/
or in your local directory: <home directory>/vnmrsys/
where <home directory> is the path to your home directory where you want to install HIFI.


0) HIFI uses nmrPipe to process the orthogonal and tilted planes
   and, thus, you need to install nmrPipe on the spectrometer Sun (or
   Linux-Dell) first.
   nmrPipe is free and is very simple to install. Go to
   http://spin.niddk.nih.gov/bax/software/NMRPipe for more information
   or to download the program.
   Once you have installed nmrpipe, do NOT add any source commands into
   the .login or .cshrc files, as these may interfere with vnmr (vnmrJ).  
   As explained in more detail below, inside the hifi/com directory we also
   provide a "nmrpipe.csh" file that will be automatically sourced each
   time an orthogonal or tilted plane is processed.


1) EXTRACT THE HIFI FILES FROM THE TAR FILE TO THE PROPER DIRECTORY

cd /vnmr  
-or-  
cd <home directory>/vnmrsys        -if you are installing it locally
                     (replace <home directory> with the
                     actual path to your home directory

tar xvf <path>/hifi.tar        -where <path> is the location of the hifi.tar file
                 this will create a new directory "hifi" and distribute
                 files to the "psglib" "maclib" "parlib" "templates"
                 and "user_templates" directories

2) INSTALL THE MATLAB LIBRARIES
   the tilt prediction and peaklist generation programs are written using Matlab

cd hifi/com
unzip MCRInstaller.zip        -this will extract all the matlab libraries and
                 copy them into a subdirectory named "v72"

3) SET THE PATHS FOR THE HIFI SCRIPTS AND MACROS
   this is critical for HIFI to work at all, there are 5 files require to be
   modified

*** HIFI scripts in the "hifi/com" directory ***

    in the "hifi/com" directory, you need to set the proper path for two shell scripts:
        1- hifi.sh
            2- generate_peaklist.sh
    at the beginning of BOTH these files, set the "LIBDIR" variable to point to the
    correct location of the "hifi/com" directory, e.g.:

    LIBDIR='/vnmr/hifi/com'                -if installing hifi in the main
                             directory
    -or-
    LIBDIR='<home directory>/vnmrsys/hifi/com'    -example for local installation
                              in your vnmrsys directory
                             (replace <home directory> with the
                             actual path to your home directory)

*** nmrPipe source file also in the "hifi/com" directory ***

    in the same directory ("hifi/com"), set the correct nmrpipe path at the beginnig of
    the file:
        3- nmrpipe.csh
    for example, if nmrPipe is installed in "/export/data/nmrPipe", set the variable
    NMRBASE to point to this path:

    setenv NMRBASE         /export/data/nmrPipe

    as explained above this file is automatically sourced before each orthogonal or
    tilted plane is processed


*** HIFI macros in the "maclib" directory ***

    in the maclib directory set the proper hifi path in two macro files:
        4- mHIFI
        5- VNMR2PIPE
    at the beginning of each macro, edit the variable $HIFI_DIR to point to the
    correct location of the hifi scripts (hifi.sh and generate_peaklist.sh).
    For example:
        $HIFI_DIR='/vnmr/hifi/com'    -if installing HIFI in the main
                         directory
        -or-
        $HIFI_DIR='<home directory>/vnmrsys/hifi/com'    -for local installation in
                                 your vnmrsys directory
                                 (replace <home directory>
                                with the actual path to
                                your home directory)

4) COMPILE THE PULSE SEQUENCES WITH "psggen"

    ***    if you are installing HIFI in the /vnmr directory, then as vnmr1, give the
    following commands in a unix shell:

        > cd /vnmr/psglib
        > seqgen NEW*                -pulse sequences will be compiled
                             in the vnmr1 seqlib directory
                             (~/vnmrsys/seqlib) and need to be
                             moved to the common psglib directory
                             (/vnmr/seqlib)
        > mv ~/vnmrsys/seqlib/NEW* /vnmr/seqlib/.
        > rm -f ~/vnmrsys/psglib/NEW*        -delete the c files from the local
                             psglib directory

    NOTE: "~" in these commands corresponds to the vnmr1 home directory (since you are
          logged in as vnmr1)


    ***    if you are installing HIFI into your local directory, then login as yourself and
    give the following commands in a unix shell:

        > cd ~/vnmrsys/psglib
        > seqgen NEW*                -pulse sequences will be compiled
                             into your local seqlib directory

    NOTE: "~" in these commands corresponds to your  home directory (since you are logged
          in as yourself)

5) RUN ALL THE PREDICTION AND PEAK EXTRACTION PROGRAMS THE FIRST TIME BY EXECUTING
   THE "first_run.csh" SCRIPT

    *** the first time (and only the first time) that the tilt prediction and extraction
    programs are executed, new files are extracted and written to the disk
    *** in order to do this properly, we provide a script named "first_run.csh" that is
    located in:
        <path>/hifi/com/first_run/first_run.csh
    *** the "first_run.csh" script needs to be executed by the owner of the directory
    where hifi is being installed
    *** simply, in a unix shell window give the commands:
        > cd <path>/hifi/com/first_run
        > ./first_run.csh
    *** be patient , running this script may take a little while depending on how fast
    is the computer.
    *** note: once these new files have been extracted, they can not be moved to a different
    directory. If you wish to move these programs, you will have

MANUAL

After installing the HIFI package please look at the examples in the hifi/examples directory and the documentation in the hifi/man directory to learn how to set up the automated HIFI run.

 

EXAMPLE

Download HIFI-NMR Example files.

CITATION