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.
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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:
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.
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
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.