Hello,<\/p>\n
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:<\/p>\n
1) Getting started with nmrPipe\/nmrDraw: Converting data in Topspin<\/p>\n
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:<\/p>\n
\/opt\/topspin3.XXX\/exp\/stan\/nmr\/au\/user<\/p>\n
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.<\/p>\n
2) Getting started with nmrPipe\/nmrDraw: Bypassing complicated scripts<\/p>\n
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:<\/p>\n
basicFT1.com
\nbasicFT2.com
\nbasicFT3.com
\nbasicFT4.com<\/p>\n
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:<\/p>\n
basicFT2.com -yFTARG auto -xP0 12.3 -xP1 0.0 -yP0 90 -yP1 180<\/p>\n
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.<\/p>\n
3) Dealing with nmrDraw’s ridiculous window sizes<\/p>\n
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:<\/p>\n
alias nmrDraw ‘nmrDraw\u00a0 \\!* -nlev 15 -plev 15 -Ws 1280 960 &’<\/p>\n
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.<\/p>\n
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” \ud83d\ude42<\/p>\n
Enjoy the new tricks!<\/p>\n
Alex<\/p>\n","protected":false},"excerpt":{"rendered":"
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<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-1350","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p7sxod-lM","jetpack-related-posts":[{"id":1208,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2016\/12\/09\/postdoctoral-positions-available\/","url_meta":{"origin":1350,"position":0},"title":"Postdoctoral positions available","author":"Mark Foster","date":"December 9, 2016","format":false,"excerpt":"Postdoctoral Positions in NMR Structural Biology, Columbus Ohio. Two NIH-funded postdoctoral positions are available immediately (starting January 2017) for NMR studies of protein-protein and protein-nucleic acid interactions. Funded projects involve characterizing interactions between eukaryotic transcription factors and their host and viral binding partners, development of small molecule inhibitors of the\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1922,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2023\/10\/23\/fosterlab-spins-gateway-nmr\/","url_meta":{"origin":1350,"position":1},"title":"FosterLab Spins Gateway NMR","author":"Mark Foster","date":"October 23, 2023","format":false,"excerpt":"Antonia, Joe and Rodrigo shared their research at the Gateway NMR meeting at Notre Dame Oct 20-21. Thanks Jeff Peng and Evguenii Kovrigin for hosting!!","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2023\/10\/image-1.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":1789,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2022\/02\/26\/phase-sensitive-nd-data-processing-tips-from-frank-delaglio\/","url_meta":{"origin":1350,"position":2},"title":"Phase-Sensitive nD data Processing Tips from Frank Delaglio","author":"Mark Foster","date":"February 26, 2022","format":false,"excerpt":"(Quoted from Frank Delaglio's NMRPipe Yahoo group, since migrated to nmrpipe@groups.io) Greetings, Dear Pipers, In the various phase-sensitive multidimensional experiments, the real and imaginary parts of the indirect dimensions are generated via separate measurements. Ideally, these are cos(t) for the real part, and -sin(t) for the imaginary part. Sometimes, ether\u2026","rel":"","context":"In \"delaglio\"","block_context":{"text":"delaglio","link":"https:\/\/research.cbc.osu.edu\/foster.281\/tag\/delaglio\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1052,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2016\/05\/28\/janie-frandsen-awarded-cmbp-fellowship\/","url_meta":{"origin":1350,"position":3},"title":"Janie Frandsen Awarded CMBP Fellowship","author":"Mark Foster","date":"May 28, 2016","format":false,"excerpt":"Foster Lab collaborator and honorary member, Janie Frandsen (Henkin Lab, and OSBP), has been awarded a prestigious fellowship from the CMBP training program. Congratulations Janie! Janie is using NMR and structure probing methods to understand mechanisms of translational regulation by non-canonical T-box RNAs.","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/media.licdn.com\/media\/p\/4\/005\/061\/26f\/33b972f.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":1914,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2023\/09\/29\/whats-that-in-the-background-soon-1-2-ghz-will-be-live-osu\/","url_meta":{"origin":1350,"position":4},"title":"What’s that in the background?!! 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In addition, we study how TRAP binding to the trp leader RNA\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/posts\/1350","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/comments?post=1350"}],"version-history":[{"count":1,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/posts\/1350\/revisions"}],"predecessor-version":[{"id":1351,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/posts\/1350\/revisions\/1351"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/media?parent=1350"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/categories?post=1350"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/tags?post=1350"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}