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could anyone suggest pulse sequences that are available in Varian's BioPack that can be readily run in reduced-dimensionality mode - with joint incrementation of several dimensions?

Can standard experiments be set up in RD mode by setting a special increment schedule?

asked Dec 09 '09 at 09:23

Magnethead's gravatar image


updated Dec 09 '09 at 14:03

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There are many sequences in BioPack that use reduced-dimensionality (RD). These are called "Projection Reconstruction" experiments. Eriks Kupce has modified 3D sequences for protein backbone assignment as well as some hsqc-based sequences. They all use "pra" as a variable specifying a projection angle. This angle (if 0<pra>90) will cause co-evolution of t1 and t2 to produce a 2D spectrum in which both F1 and F2 information is present in the 2D spectrum. A set of 4D->2D and 4D->3D experiments from the Duke group are also available.

You could "grep" for pra in BioPack's psglib, or just use the MainMenu "Experiments" drop-down menu in VnmrJ and select either "Protein Triple-Resonance" or "Protein HSQC Experiments". You'll see sub-menu options for Projection-Reconstruction (or, TILT) experiments. Selecting an experiment runs the setup macro. You can then go to the "PulseSequence" page in the Acquire folder and there you'll find an entry box for the "pra" parameter. If pra=0 you do the normal 2D/3D experiment as selected by ni/ni2/sw1/sw2/phase/phase2 so you use the same sequence for normal and RD experiments.

3D sequences using the "pra" parameter have a special "Projection Reconstruction" page in the Acquire folder. This permits you to queue up multiple experiments using different pulse sequences and have a single panel allowing you to specify experiments, the number of transients for each experiment, the number of increments for each and the option for automatic angle (pra) selection where different angles are automatically selected until all resonances are identified.

Re the question "Can standard experiments be set up in RD mode by setting a special increment schedule?". I assume here that you want to do "linear sampling". It is possible to modify a sequence to set each evolution time from an external table. This is done for the NLS (non-linear sampling) experiments. You can do this on a sequence by using the "Sampling" page in the Acquire folder and selecting either the Orekhov or Kozminski method. These operations cause the sequence to be modified (and re-nameed) to use an external table of evolution times. I would think that the new NLS sequence could be used with a different (user-generated) table and do an RD experiment. Of course, you could just copy the approach that Eriks used to modify a 3D sequence. See ghn_co.c, for example.

For more information, consult the BioPack manual in BioPack.dir/docs or use the MainMenu "Help" menu and select the appropriate sub-section of the manual to be displayed in a browser.

-George Gray NMR Applications Varian, Inc.


answered Dec 10 '09 at 13:28

georgeg's gravatar image


Yep. Thanks a lot! I get a list of 32 files this way. All in BioPack. - Magnethead (Dec 10 '09 at 15:12)

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