The jump return indicated by the name in this pulse is no longer used

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1 HNHA_jr This pulse sequence correlates the HN proton with the HA proton of the same residue. The pulse sequence we use is from Lewis Kay's lab and is referred to as hnha_jr_800_c_enhanced_v2. The original reference is Kuboniwa et al J. Biomolecular NMR 4, 871 (1994) and Vuister and Bax JACS 115, 7772 (1993). The jump return indicated by the name in this pulse is no longer used 1H carrier: 4.7 ppm 13C 15N carrier: 119 ppm (center of amide NH) The water flipback pulse in this sequence occurs prior to a 90 pulse rather than after it. Therefore use t2pul_lek_sel4 rather than t2pul_lek_sel3 to calibrate the flipback pulse. First set phse_sl=5 and tpwrsl=14 and array pw_sl around 1500 to find optimum pw_sl. Then find optimum phase_sl by arraying from 0 to 10 with pw_sl set to value found above. Optimal value is around 5. Set parameters in hnha to these values. For 13C labeled samples there is a C_180 option (is his an option or is always active?) to decouple 13C. This uses an on resonance chirp adiabatic pulse. From the shapelib dir run apod_chirp The 20 indicates 20% truncation. The output is called Apod_Chirp.RF. Rename as chirp_80k.rf. A composite pulse is used for short d2, but this switches to adiabatic at longer d2. Original pulse sequence used a triax gradient. ( pfgon='yyy'). The lock may decrease and it may be possible to bring back by touching up the shims. The reason for the loss in lock level is not known. Check with Varian. Or change all 'x' gradient pulses to the 'z' axis. (This is what we did.) Optimize gzlvl6 for best water suppression and signal/noise ratio. This experiment should be run with shifting and folding of the data. It is unfolded in nmrpipe using the CS command with rs 2.0 ppm -neg -sw. The -neg option gives the proper phase of the unfolded peaks when they are unfolded. Standard parameter settings for 800 sw=10000, sw1=6000, sw2=2500 (adjust sw2 to get all of N15 dimension for your protein) dof=58 ppm, dof2=118 ppm dm2=nnny, dmm2=cccp, dseq2=waltz16, dpwr2=45 (was 56), dmf2=5494 fscuba=n, fsat=n, f1180=y, f2180=n, H180_flg=n dm=nnnn HNHA Analysis Use nmrview HNHA analysis menu First create a peak list by picking both the diagonal and crosspeak of a given residue.

2 First create a peak list by picking both the diagonal and crosspeak of a given residue. If overlap of diagonal is very bad you may want to consider skipping that pair. Names should be something like HN-HN-N and HN-HA_N for the pair (and of course there is the res # also). Save peaklist to disk from Assign-Peaks panel (should always save peaklists). Choose this peaklist name in dialog box. D2 dimension is the 2nd (indirect) H dimension. epsilon = BigT+tauxh (about 10 msec) rmsd = 0 (don't need this) correction factor = 9 compensates for different relaxation properties of diagonal and crosspeak then name output file. Use hnha2tbl perl script to convert into format for CNS/Xplor VNMR Processing Use nmrpipe for final processing, but VNMR is good for examining data left shift F1 frequency by remove H2O with ssfilter (300 to 500) lp1 = -180, rp1 = 90 and adjust rp1 as necessary F1F3 processing Press Tcl buttons for setting LP in t1 and t2 make sure # complex points is set correctly (=> 2*ni) enter window function in command line gaussian / gausshift / pi3ssbsq / etc. do backward LP in F1 BPsetlp1(ni*2,ni,3) make sure # complex points is set correctly (=> 2*ni) transform 1st F1F3 plane enter dc2d('f1') in command line to remove baseline offsets F2F3 processing peaks will look out of phase (and cannot be phased correctly) because sesitivity enhancement. Nonetheless, the peaks should be obvious if experiment is working. 3D processing use nmrpipe (see below) NMRPipe Processing Scripts Varian data input (fid.com) - note Rance-Kay option > more fid.com var2pipe -in./fid \ -xn yn 128 -zn 64 \ -xt 768 -yt 64 -zt 32 \ -xmode Complex -ymode Complex -zmode Rance-Kay \ -xsw ysw zsw \ -xobs yobs zobs \ -xcar ycar zcar \ -xlab D1_H1 -ylab D2_H1 -zlab D3_N15 \ -ndim 3 -aq2d States \

3 -ndim 3 -aq2d States \ -out./data/test%03d.fid -verb -ov sleep 5 f1f3 dimension processing % cat ftxy # nmrpipe -in data/test001.fid \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -auto \ nmrpipe -fn PS -p0-62 -p1 0 -di \ nmrpipe -fn LP \ nmrpipe -fn SP -off end 1.0 -pow 2 -c 1.0 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT -auto -verb \ nmrpipe -fn PS -p p di \ nmrpipe -fn CS -rs 2.0ppm -neg -sw \ nmrpipe -out f1f3.dat -ov f2f3 dimension processing % cat ftxz xyz2pipe -in./data/test%03d.fid -z -ri2c -first 1 -last 1 \ nmrpipe -fn TP -hyper \ pipe2xyz -out./data/xz%03d.fid -x -ov # Transform x dimension nmrpipe -in./data/xz001.fid \ # nmrpipe -fn SOL -fl 16 \ nmrpipe -fn SP -off end pow 2.0 -c 0.5 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn PS -p0-62 -p1 0 -di \ # Transform z dimension \ # nmrpipe -fn LP -before -pred 3\ nmrpipe -fn LP \ nmrpipe -fn SP -off end pow 2.0 -c 1.0 \ nmrpipe -fn ZF -size 128 \ nmrpipe -fn FT -auto -verb \ nmrpipe -fn PS -p0 0 -p1 0 -di \ nmrpipe -out f2f3.dat -ov rm./data/xz*.fid bugs 184%

4 linear 3D transform (no LP) Linear transform may be adequate with hbha since few signals in 2nd dimension. So ou can probably safely add LP statements. Otherwise, use convoluted scheme below. % cat ft3df # Fast FT without LP # X dimension \ xyz2pipe -in data/test%03d.fid -x -verb \ # nmrpipe -fn SOL -fl 16 \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn PS -p0-62 -p di \ # Y dimension \ # nmrpipe -fn LP \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -auto \ nmrpipe -fn FT \ nmrpipe -fn PS -p0-90 -p di \ nmrpipe -fn CS -rs 2.0ppm -sw -neg \ # nmrpipe -fn BASE -nw 3 -nl 0% 5% 95% 100% \ pipe2xyz -out ft/test%03d.ft3 -x # Z dimension \ xyz2pipe -in ft/test%03d.ft3 -z -verb \ # nmrpipe -fn LP \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -size 64 \ nmrpipe -fn FT \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # # nmrpipe -fn BASE -nw 3 -nl 0% 5% 95% 100% \ # nmrpipe -fn REV \ pipe2xyz -out ft/test%03d.ft3 -z -inplace 3D transform (convoluted with LP) % cat ft3d # Final FT with LP in Z and Y # Transform x dimension xyz2pipe -in data/test%03d.fid -x -verb \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -size 1024 \ nmrpipe -fn PS -p0-62 -p di \ pipe2xyz -out ft/test%03d.ft3 -x -ov # Transform z dimension xyz2pipe -in ft/test%03d.ft3 -z -verb \ nmrpipe -fn SP -off end pow 1 -c 1.0 \

5 nmrpipe -fn SP -off end pow 1 -c 1.0 \ nmrpipe -fn ZF -zf 1 \ nmrpipe -fn PS -p0 0 -p1 0 -di \ # pipe2xyz -out ft/test%03d.ft3 -z -inplace # Transform y dimension xyz2pipe -in ft/test%03d.ft3 -y -verb \ # nmrpipe -fn LP -before -pred 2 \ nmrpipe -fn LP -fb \ nmrpipe -fn SP -off end pow 2 -c 1.0 \ nmrpipe -fn ZF -size 256 \ nmrpipe -fn PS -p0-90 -p di \ nmrpipe -fn CS -rs 2.0ppm -sw -neg \ # nmrpipe -fn BASE -nw 3 -nl 0% 5% 95% 100% \ pipe2xyz -out ft/test%03d.ft3 -y -inplace # Un/Re transform z dimension xyz2pipe -in ft/test%03d.ft3 -z -verb \ nmrpipe -fn HT -auto \ nmrpipe -fn PS -inv -hdr \ nmrpipe -fn FT -inv \ nmrpipe -fn ZF -inv \ nmrpipe -fn SP -inv -hdr \ # nmrpipe -fn LP -before -pred 2 \ nmrpipe -fn LP -fb \ nmrpipe -fn SP -off 0.4 -end pow 2 -c 1.0 \ nmrpipe -fn ZF -size 64 \ nmrpipe -fn PS -hdr -di \ pipe2xyz -out ft/test%03d.ft3 -z -inplace # Output nmview format xyz2pipe -in ft/test%03d.ft3 -x -verb \ pipe2xyz -nv -ov -out data3d.nv Biotechnology Graduate Program Chemistry Biology Materials Science url: The University of Alabama in Huntsville, Huntsville, AL site updated: 07 January 2002 (jws)

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