Biopack

From NMR Wiki

Biopack is a Varian, Inc. collection of pulse sequences and calibration macros for Protein, DNA and RNA NMR experiments, which is based on user contributions.

Once Biopack is calibrated, experiments are to be set up by simply typing name of the pulse sequence into the command line. For example, to run HNCO type ghn_co, then follow with setting up basic parameters specific to your sample (pw, nt, spectral widths, RF carrier frequencies, numbers of increments) and you should be ready to run the experiment.

Installation

• log in as vnmr1
• download loadbiopack.tar.Z (BioPack installer, password required)
• place downloaded file into /vnmr/userlib/maclib directory
• download BioPack.tgz (BioPack distribution, password required)
• place file into /vnmr/userlib/psglib
• in unix shell type:

cd /vnmr/userlib
./extract maclib/loadbiopack

This will install the BioPack installer macro

• start vnmr software
• in vnmr command line type: loadbiopack
• a console window will open - you will have to answer some questions (most likely all 'yes')
• after that's done click in vnmr 'Main Menu'->'Setup'->'Activate Biopack'->'Create new probefile'

Users other then vnmr1 must type BPrmlocalfiles after update of files in vnmr1 account.

Biopack calibration

Biopack calibration optimizes parameters to pulse sequences and stores them in the vnmrsys/parlib directory of the current user - if calibration is run in the regular user account. Calibration will also update current probe file (value of probe parameter). Probe file is located in the vnmrsys/probes directory. Biopack calibration assumes that you have ¹⁵N,¹³C labelled sample in 90:10 H₂O:D₂O

In vnmr

In vnmr biopack is calibrated by following "Main menu"->"Setup"->"Proteins"->"Calibrate". At this stage there will be options