Hello,
I’ve noticed a few common ‘annoyances’ that everyone tends to deal with when processing nmr data in one way or another and I thought I’d offer a few solutions:
1) Getting started with nmrPipe/nmrDraw: Converting data in Topspin
Learning nmrPipe can be a hassle, especially if you’re not horribly familiar with writing code or using the terminal. Fortunately, a Bruker applications engineer has been working on a macro to help with that. If you are using TopSpin 3.5pl7, then you already have it. If not, just copy the attached file to the directory:
/opt/topspin3.XXX/exp/stan/nmr/au/user
Then while you’re in TopSpin, after processing the 2D or 3D to your liking, simply type ‘convert2pipe’ and it will ask a few questions regarding referencing and then create the necessary scripts to copy your TopSpin processing into nmrPipe format, and even run them and open nmrDraw for you. From there, you can then modify the script using a text editor as you see fit.
2) Getting started with nmrPipe/nmrDraw: Bypassing complicated scripts
If you have one of the latest versions of nmrPipe installed, then it mysteriously came with a few new scripts that make processing arguably easier, including NUS processing:
basicFT1.com
basicFT2.com
basicFT3.com
basicFT4.com
In principle, after running the ‘bruker’ script to create fid.com and test.fid, you can simply type ‘basicFT2.com’ and you’ll get your processed data using a set of default options. Type ‘basicFT2.com -help’ to learn some of the options. I think minimally, you’ll actually need something like this:
basicFT2.com -yFTARG auto -xP0 12.3 -xP1 0.0 -yP0 90 -yP1 180
This will include the phasing that you need to do. You can modify everything the same way you do with an nmrPipe script, but this way it’s just a single command.
3) Dealing with nmrDraw’s ridiculous window sizes
If you have a large monitor, or multiple monitors, then you know that when you open nmrDraw it likes to engulf your entire screen. To prevent this, I recommend creating an alias for nmrDraw and passing a few extra options when opening your data. First, go to your home directory and open the hidden file called .cshrc. Literally anywhere in that file copy this line:
alias nmrDraw ‘nmrDraw \!* -nlev 15 -plev 15 -Ws 1280 960 &’
Now, when you open up your data, it will be in a smaller, more reasonable window size and with 15 contour levels instead of 10.
That’s all for now. If you have any particularly annoying things you have to do all the time when processing data, let me know and I may have a solution to make it easier for you. I’ve seen pretty much everything! You might say “I have a script for that” 🙂
Enjoy the new tricks!
Alex