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NucAcidNMR

Pulse sequence development for Nucleic Acid NMR experiments

Objectives

  1. To build a thorough library of nucleic acid pulse sequences
  2. To optimize all sequences for quick and easy setup by any user

Conventions

The library will be divided into two categories, initially. The collected directory will contain pulse sequences found from any NMR lab. These can be both Varian/Agilent or Bruker sequences. The optimized directory will contain those sequences that have been optimized for Bruker spectrometers and made to conform to the following conventions:

  • Bruker pulse, power, and delay naming conventions with the appropriate choice of prosol relations
  • Compatible with latest patch levels of Topspin 3.2 and above (roughly Avance II and later)
  • Internal calculations must be field independent
  • All necessary non-conventional pulses, decoupling, etc must be provided
  • No additional 'include' files may be used
  • Avoid spaces and dashes in any file/directory naming, only use underscore ( _ )
  • All sequences should be well documented
    • Header - references, class/type info, initialled/dated change list, any special setup instructions
    • Safety checks - after "1 ze" and before the experiment starts, check validity of crucial parameters
    • Sequence - comment blocks of code (Hx -> HyCz, INEPT, CS Encode, etc.)
    • Footer - all parameters listed (ie. ;p10 : describe), any special processing instructions

Organization within these directories is still to be determined. In general, pulse sequences should be 90% complete with a simple 'getprosol' command. Whenever this isn't possible, python or au macros should be provided.

Example Code

;na_example
;avance-version (16/01/01)             ; I believe this is year/month/day ... not sure if important
;Example experiment code to highlight several conventions
;
;$CLASS=HighRes
;$DIM=2D
;$TYPE=NucleicAcids
;$SUBTYPE=Assignment
;$SUBTYPEB=Backbone
;$COMMENT=Class, Dim, Type, Subtype should be specified for easy experiment selection
;
; == SETUP ==
; While not a real experiment, please describe briefly any special instructions here
;
; == CHANGELIST ==
; Written by ALH, 15 Sept 2016
; -- 16 Sept 2016 / ALH - Added safety check

prosol relations=<triple_na>

#include <Avance.incl>
#include <Grad.incl>
#include <Delay.incl>

;### Pulses ###
"p2=p1*2"
"p4=p3*2"
"p22=p21*2"

;### Delays ###
"d11=30m"
"d12=20u"
"d13=2u"

;### Misc ###
aqseq 312
"acqt0=-p1*2/3.1415"		; set acqt0 for optimal phasing in direct dim
;baseopt_echo			; use if sequence ends with echo

/*******************************/
/* BEGIN ACTUAL PULSE SEQUENCE */
/*******************************/

1 ze
/***** PARAMETER CHECK *****/

  if "d1 < 0.5" {
    2u
    print "error: D1 too short"
    goto HaltAcqu
  }

/***** START EXPERIMENT *****/
2 d11
  d1

  ...
  < experiment code >
  ...

/***** ACQUISITION *****/

  go=2 ...
  d11 do:f# ...
  d11 mc ...
  d11 BLKGRAD
  
HaltAcqu, d11
exit

ph0=0			; Ideally, ph0 through ph3 should be X, Y, -X, -Y
ph1=1
ph2=2
ph3=3

ph4=0 2 2 0		; First phase cycle
ph31=0 0 2 2

;###################
;    Definitions
;-------------------

; ... Powers ...
;pl0    : 1H - No power
;pl1    : 1H - High power level
;pl2    : 13C - High power level
;pl3    : 15N - High power level
;pl14   : 13C - CPD low-power decoupling level

; ... Pulses ...
;p1     : 1H - hard 90 degree @ PL1 (used to find 1H shape powers)
;p2     : 1H - hard 180 degree @ PL1
;p3     : 13C - hard 90 degree @ PL2 
;p4     : 13C - hard 180 degree @ PL2
;p21    : 15N - hard 90 degree @ PL3
;p22    : 15N - hard 180 degree @ PL3
;p16    : Gradient  [1 ms]

; ... Shapes ...
;sp1    : 1H - H2O selective pulse
;spnam1 : Sinc1.1000

; ... Decoupling ...
;cpd2   : 13C - Decoupling according to sequence defined by cpdprg2
;pcpd2  : 13C - 90 degree pulse for decoupling sequence
;cpdprg2: 13C - garp4.p61 @ PL14

; ... Delays ...
;d0     : Incremented delay (2D)
;d1     : Interscan recovery delay
;d11    : Disk I/O delay [30ms]
;d12    : Short delay    [10us]
;d13    : Shorter delay  [2us]
;d16    : Gradient recovery delay  [200us]

; ... Constants ...
;cnst4  : J(CH) ~ 200 Hz

;  ... Miscellaneous ...
;ds     : >= 16
;ns     : 2*n
;inf1   : t1 increment
;zgoptns: 'LABEL_CN'

;FnMODE : States-TPPI in F1

; ... Gradients ...
;for z-only gradients:
;gpz1: 11%
;gpz2:  7%

;use gradient files:   
;gpnam1: SMSQ10.100
;gpnam2: SMSQ10.100


	;preprocessor-flags-start
;LABEL_CN: for C-13 and N-15 labeled samples start experiment with
;        option -DLABEL_CN (eda: ZGOPTNS)
	;preprocessor-flags-end

;Processing

;PHC0(F1): 90
;PHC1(F1): -180
;FCOR(F1): 1

Setup

In a desired directory (Mac/Linux) with 'git' installed, run:

git clone git@github.com:viochemist/NucAcidNMR.git

Set your name and e-mail with:

git config --global user.name = "My Name"
git config --global user.email = name@something.com

Once installed, collect any updates by running:

git pull

To contribute, run ssh-keygen and/or send me your .ssh/id_rsa.pub so that I can generate a key. Then, after you make changes to your local versions, run:

git add <changed files>
git commit -m "Message about changes"
git push

Always be sure to pull and merge before pushing any changes. This is a very basic workflow for now. Once the library has reached some sort of stable level, a master and development branch will be formed. For now, I'm just "hunting and gathering".