Chris Waudby's pulse program library

• These sequences have been uploaded for my own convenience in synchronising work across multiple spectrometers. Some experiments remain under development. Use at your own risk!
• Please acknowledge the use of sequences from this library.
• With thanks to John Kirkpatrick on whose work many sequences are based.
• Contact: [email protected]

Table of Contents

• git quickstart
• syntax highlighting in vim
• my shell settings
• pulse programs

git quickstart

Creating a local clone of the pp repository

git clone https://github.com/chriswaudby/pp.git
# move `pp` directory to required location
# then within `pp`, configure git:
git config user.name "Chris Waudby"
git config user.email "[email protected]"
git config color.ui true
git config color.status auto
git config color.branch auto
git config core.editor vim
git config merge.tool vimdiff
git config --list

Updating local repo

git pull

This will fetch and merge remote changes.

Making changes

Based on http://rogerdudler.github.io/git-guide/

0. Check current repo status:

git status

1. Add new files to the index:

git add <filename>
git add *

2. Commit changes:

git commit -m "Commit message"

Now file is committed in local repo but not in remote.

3. Push changes to remote:

git push origin master

Here origin refers to the remote repo (from which we originally cloned the repository) and master is the branch to which changes should be pushed.

Bruker syntax highlighting in vim

• Copy contents of syntax-highlighting folding into ~/.vim
• Pulse programs will be automatically detected by the presence of #include <Avance.incl>
• Alteratively, in vim: set syntax=bruker

My shell settings

.bashrc

# history searching
bind '"\e[A": history-search-backward'
bind '"\e[B": history-search-forward'

# append history (in case of multiple sessions)
shopt -s histappend

# nice prompt
export PS1="\[\033[38;5;15m\][\[$(tput sgr0)\]\[\033[38;5;11m\]\u@\h\[$(tput sgr0)\]\[\033[38;5;15m\] \[$(tput sgr0)\]\[\033[38;5;13m\]\W\[$(tput sgr0)\]\[\033[38;5;15m\]]\\$ \[$(tput sgr0)\]"

# add utils to path
export PATH=$PATH:~/pp/util

# set aliases
alias vi=vim
alias ls='ls --color'

.cshrc

set savehist = (5000 merge )
set filec
set nobeep
set autolist=true

bindkey -k up history-search-backward # Use up and down arrow to search
bindkey -k down history-search-forward

# enable colouring for ls
setenv CLICOLOR

# custom prompt
set prompt="%B%{\033[36m%}[%c2]%b % "

# add utils to path
set path =($path ~/pp/util )

Installing nmrPipe

mkdir NMRPipe
cd NMRPipe/
wget https://www.ibbr.umd.edu/nmrpipe/install.com
wget https://www.ibbr.umd.edu/nmrpipe/binval.com
wget https://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ
wget https://www.ibbr.umd.edu/nmrpipe/s.tZ
chmod +x *.com
./install.com

Pulse programs

Checkmarks indicate a tested sequence.

• Calibration
• 1Ds
• 1H experiments
• 1H,15N correlation experiments
• 1H,13C correlation experiments
• Assignment
• Diffusion
• Relaxation and dynamics
• Miscellaneous

Calibration

• zg490.cw - 1H 90 calibration
• zgfd.cw - 1H water flip-down
• zgfb.cw - 1H water flip-back
• calib_15n.cw - 15N high-power 90 calibration
• calib_13c.cw - 13C high-power 90 calibration
• calib_1h_nut.cw - 1H calibration (2d array of pulse lengths)
• zg2h.cw - 2H 1D/calibration

1Ds

• zgesgp.cw - 1H 1D (excitation sculpting)
• zgpr.cw - 1H 1D (presaturation)
• zg_doublesolventsuppression.cw - 1H 1D (2x solvent flipdowns)
• cpmgpr1d - 1H CPMG with presat (TS3.5pl5 library)
• zgpg30 - 13C 1D (two-level cpd during d1 and acquisition, TS3.5pl5 library)

1H experiments

• project.cw - PROJECT (T2 relaxation via perfect echo)
• stddiffesgp.cw - STD (saturation transfer difference)
• wlogsy.cw - WaterLOGSY

1H,15N correlation experiments

• hsqcetfpf3gpsi2.cw - 1H,15N sensitivity-improved HSQC
• hsqcfpf3gpphwg.cw - 1H,15N HSQC (NB try this instead of fhsqc)
• fhsqcf3gpph.cw - 1H,15N FHSQC
• sfhmqcf3gpph.cw - 1H,15N SOFAST-HMQC
• trosyetf3gpsi.cw - 1H,15N TROSY
• sfhmqcf3gpphpr1d.cw - 15N filtered/edited 1D SOFAST with presaturation
• sfhmqcf3gpph.nuws.cw - 1H,15N SOFAST-HMQC with NUWS
• hetsofast.cw - based on IBS-HETSOFAST
• hzdqcf3.cw
• sfhzdqcf3.cw

1H,13C correlation experiments

• hmqcgpphpr.cw - 1H,13C HMQC
• hmqcgpphpr_2.cw - 1H,13C HMQC with purge element
• hmqcgpphpr_2_wet.cw - with WET solvent suppression
• hsqcctetgpsp.cw - 1H,13C constant-time HSQC
• hisqcetgpsp.cw - 1H,13C non-CT refocused (in-phase) HSQC
• hisqcctetgpsp.cw 1H,13C constant-time refocused (in-phase) HSQC
• sfhmqcf2gpph.nuws.cw - 1H,13C SOFAST-HMQC with NUWS
• sfhmqcf2et.nuws.cw - 1H,13C gradient-selected SOFAST-HMQC

Diffusion

• stebpgp1s.cw - 1H/19F STE (no solvent suppression)
• stebpgp1s19.cw - 1H STE (watergate)
• stebpgp1spr.cw - 1H STE (presaturation)
• stebpgp1spr_13c.cw - 1H STE (presat) with 13C decoupling during acquisition
• stebpgp1s19xn.4.cw - 15N XSTE
• sordid_pureZ.2pt.cw - 15N SORDID
• stebpgp1sprxc_dec.3.cw - 13C XSTE

Assignment

• b_hncogp3d.2 - BEST-HNCO (TS3.5pl6 library)
• b_hncacogp3d - BEST-HNCACO (TS3.5pl6 library)
• b_hncocacbgp3d.2 - BEST-HNCOCACB (TS3.5pl6 library)
• b_hncacbgp3d.2 - BEST-HNCACB (TS3.5pl6 library)
• ccconhgp3d.2 - CCCONH TOCSY (TS3.5pl6 library)
• hcchcogp3d - HC(C)H COSY (TS3.5pl6 library)
• hbhaconhgp3d.cw - HBHACONH
• hccconhgpwg3d2.cw - H(CCCO)NH TOCSY
• hcchdigp3d.cw - HC(C)H TOCSY
• hmcmcgcbca.linear.2h.cw - Cali assignment for linearised methyl backbones
• hmcmcgcbcaco.linear.2h.cw - CO assignment for linearised methyl backbones

Relaxation and dynamics

• 15N
• methyl
• CPMG relaxation dispersion
• CEST
• EXSY

15N relaxation

• T1N15_tr.cw - 15N T1 (TROSY)
• T1rhoN15_tr.cw - 15N T1rho (TROSY)
• T1rhoN15_tr_calib.cw
• N15HetNoe_tr.cw - 15N heteronuclear NOE (TROSY)
• hsqcfpf3gpphwg_T2.cw - amide 1H T2 measurement (for PREs)
• tract.cw - TRACT
• fab_nnh_tr_noSE.cw - N/HN CCR (symmetric reconversion method)
• best_trosy_ccr.cw - formerly v.7

methyl

• hmqcgpphpr_1HT2.cw - methyl 1H relaxation (L2 line, Tugarinov 2006)
• hmqcgpphpr_1HT2.1.cw - methyl 1H relaxation (all lines)
• hmqcgpphpr_1HT2.2.cw - methyl 1H relaxation (L1+L3 lines, Tugarinov 2006)
• hmqcgpphpr_1HT2.3.cw - methyl 1H relaxation (L1-L3 lines, Tugarinov 2006)
• hmqcgpphpr_HHHH.cw - HH/HH CCR (2Q or 3Q) for methyl order parameters (Tugarinov 2007, Sun 2011)
• hmqcgpphpr_HHHC.cw - HH/HC CCR for methyl order parameters
• hsqcphpr_1Hcoupled.cw - 1H,13C HSQC (F1-coupled)
• hsqcphpr_1Hcoupled.2.cw - 1H,13C HSQC (F1-coupled) with multiplet selection
• hsqcphpr_1Hcoupled.3.cw - 1H,13C HSQC (F1-coupled) with multiplet selection (pseudo-3D)
• 13C_T1.cw - 13C T1
• 13C_NOE.cw - 13C NOE
• hsqcphpr_1Hcoupled_T1p.cw - 13C T1p (with multiplet editing)
• adaptive_hsqcphpr.2d.cw
• adaptive_hsqcphpr.cw

CPMG relaxation dispersion

• hsqcrexfpf3gpsi_TS32.cw - 15N SQ CW-CPMG
• ch3_mq_cpmg.cw - 13C MQ CPMG for 13CH3 methyls (thanks to Vitali Tugarinov)
• CHD2_1H_CPMG.cw - 1H SQ CPMG for 13CHD2 methyls
• C13_CHD2_METmethylCPMG.cw - 13C SQ CPMG for 13CHD2 methyls (thanks to Goran Carlstrom, Lund)
• TQ_CPMG.cw - 1H 3Q CPMG for methyls

CEST

• cest_15N.cw - 15N CEST
• cest_15N_B1cal.cw - B1 calibration for 15N CEST
• 13Cm_CEST.cw - 13C methyl CEST
• 13Cm_CEST_B1cal.cw - B1 calibration for 13C methyl CEST
• cest_zz_H.cw - 1HN CEST (zz saturation)
• cest_zz_H_B1cal.cw
• cest_zz_H_B1cal.1d.cw
• cest_1H_zzstart.cw - 1HN CEST
• cest_13Cali.cw - 13Cali CEST (constant time t1 evolution)
• cest_13Cali_nonCT.cw - 13Cali CEST (non-constant time)
• cest_13Cali_B1cal.cw
• cest_1HA.cw - 1HA CEST
• cest_caconh.cw - 13CA CEST
• sfhmqcf3gpph_1H_cest.cw - crude 1H CEST

EXSY

• hsqc_Nz_exsy.cw - 15N EXSY

Misc

• zgesgp.kinetics.cw - 1H 1D for real-time measurements
• sfhmqcf3gpph.3d.cw - 1H,15N SOFAST-HMQC for real-time measurements
• 19F_CEST.cw - 19F CEST (pseudo-2D)
• 19F_xQ.cw - 19F DD/DD CCR measurements (pseudo-2D)
• 19F_T2.cw - 19F hahn-echo
• hsqcphpr_19Fcoupled.cw - 13C-19F HSQC
• imaging_zgesgp.cw - 1D CSI