NMRPipe is a processing program written by Frank Delaglio (delaglio@nih.gov) available from the NMRPipe web page. Given NMRPipe data noe150.pipe you convert it to UCSF format with:% pipe2ucsf noe150.pipe noe150.ucsf This creates the file noe150.ucsf. Only the real component is taken from the NMRPipe file. NewPipe is an outstanding YouTube client that lets you download Youtube videos with total privacy. The best part is that it lets you stream music in the background and do practically anything you can do with the official client.
Please do not hesitate to contact us with questions or requests for pulse sequences, tools, scripts, data and (spinevolution) input files that are used in our published work (even if not listed below). Below you will find a listing of some scripts and programs, typically designed to aid the analysis and processing of solid state NMR data. Please let us know if you find them useful, and especially if you encounter bugs or other issues. Note that much of our work and many of these resources rely on the freely available software packages listed further down.
Data and Materials
- Chemical shifts of huntingtin N-terminal fragments in the fibrillar form – BMRB Entry #25146
- Chemical shifts of cataract-related P23T gD crystallin as amorphous aggregates – BMRB Entry #27039
- Chemical shifts of huntingtin exon1 fibrils (44 Gln residues) – BMRB Entry # 27045
- Diagrams and information of homebuilt ultracentrifugal sample packing tools – available upon request
NMRPipe-related scripts
nmrPipe/nmrDraw configuration script
Some fairly trivial modifications to the nmrpipe initialization file allow nmrDraw/Pipe usage from a Bash shell. The modified file is available upon request.
Nmrpipe Sp
Adding/combining datasets
A convenient (?) gui for the adding together of identical datasets using the nmrPipe program addNMR: combiner.tcl
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Automated external referencing based on adamantane chemical shifts – available upon request
CCPNMR Analysis Macros
A few simple macros for the CCPNMR Analysis program: propagate assignments, make intermediate peak (from split peaks).
Analysis of oriented 2H NMR data
Nmrpipe Download
The following two programs were written for analyzing 2H NMR spectra of specifically deuterated peptides in macroscopically aligned membrane systems, while in the lab of Roger Koeppe II. Please contact me if these could be of interest to you. While being designed for helical WALP (or gramicidin) peptides systems, both programs largely rely on PDB structure files for input, so should/might be applicable to non-ideal or non-helical structural motifs.
- TrpFit – a program for matching tryptophan orientational constraints from the peptide backbone and indole geometry to deuterium NMR line shapes measured in aligned membrane systems.
- GALA – a program for determining peptide tilt angles from Ala-CD3 splittings measured in aligned membrane systems.
Below is an overview of various NMR-related programs, with some additional notes and links. Note the RSS links of various user groups, as these provide a convenient way to keep up with changes, news and useful questions and answers.
Sparky Assignment Software
Link: NMRFAM-Sparky (new!); UCSF Sparky Home Page (old)
User-groups, etc: New: Google Group ; Yahoo User Group (Ending 2019)
CCPNMR / Analysis Assignment Software
Link: CCPNMR SoftwareDownloads
User-groups, etc: mailing list, online documentation, ssnmr usage, ssnmr extensions
nmrPipe Processing Software
Link: NMRPipe Home Page
User-groups, etc: Yahoo User Group
Nmrpipe Sol
SPINEVOLUTION NMR Simulation Program
Link: SPINEVOLUTION Home Page
User-groups, etc: Google User-group
Data and Materials
- Chemical shifts of huntingtin N-terminal fragments in the fibrillar form – BMRB Entry #25146
- Chemical shifts of cataract-related P23T gD crystallin as amorphous aggregates – BMRB Entry #27039
- Chemical shifts of huntingtin exon1 fibrils (44 Gln residues) – BMRB Entry # 27045
- Diagrams and information of homebuilt ultracentrifugal sample packing tools – available upon request
NMRPipe-related scripts
nmrPipe/nmrDraw configuration script
Some fairly trivial modifications to the nmrpipe initialization file allow nmrDraw/Pipe usage from a Bash shell. The modified file is available upon request.
Nmrpipe Sp
Adding/combining datasets
A convenient (?) gui for the adding together of identical datasets using the nmrPipe program addNMR: combiner.tcl
Automated external referencing based on adamantane chemical shifts – available upon request
CCPNMR Analysis Macros
A few simple macros for the CCPNMR Analysis program: propagate assignments, make intermediate peak (from split peaks).
Analysis of oriented 2H NMR data
Nmrpipe Download
The following two programs were written for analyzing 2H NMR spectra of specifically deuterated peptides in macroscopically aligned membrane systems, while in the lab of Roger Koeppe II. Please contact me if these could be of interest to you. While being designed for helical WALP (or gramicidin) peptides systems, both programs largely rely on PDB structure files for input, so should/might be applicable to non-ideal or non-helical structural motifs.
- TrpFit – a program for matching tryptophan orientational constraints from the peptide backbone and indole geometry to deuterium NMR line shapes measured in aligned membrane systems.
- GALA – a program for determining peptide tilt angles from Ala-CD3 splittings measured in aligned membrane systems.
Below is an overview of various NMR-related programs, with some additional notes and links. Note the RSS links of various user groups, as these provide a convenient way to keep up with changes, news and useful questions and answers.
Sparky Assignment Software
Link: NMRFAM-Sparky (new!); UCSF Sparky Home Page (old)
User-groups, etc: New: Google Group ; Yahoo User Group (Ending 2019)
CCPNMR / Analysis Assignment Software
Link: CCPNMR SoftwareDownloads
User-groups, etc: mailing list, online documentation, ssnmr usage, ssnmr extensions
nmrPipe Processing Software
Link: NMRPipe Home Page
User-groups, etc: Yahoo User Group
Nmrpipe Sol
SPINEVOLUTION NMR Simulation Program
Link: SPINEVOLUTION Home Page
User-groups, etc: Google User-group
SIMMOL & SIMPSON
Link: SIMMOL/SIMPSON Home Page
User-groups, etc: Yahoo User Group
Other NMR-related software
Nmrdraw
- BMRB overview of residue-specific NMR chemical shifts
- Chemical shift analysis software (PLUQ) from the group of Mei Hong (MIT).
Other scientific scripts and downloads
- Scripts and notes to facilitate the transition from Mekentosj Papers v3 to other literature / referencing software (Applescript/Keyboard Maestro code). See also these discussions on the Zotero forum.
Download NMRPipe, including all 5 files.
Reference: F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeiferand A. Bax: NMRPipe: a multidimensional spectral processing system basedon UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995).
Make an experimental directory and move the files there. Thisrequires either the sudo command or login as the super user.
To move files into this new directory, go back to the directory youhave saved the files and then move the files.
Change permissions, and decompress the following files.
Install the necessary Ubuntu packages.
Install NMRPipe
Edit your ~/.bashrc file. (This assumes you're using a bash shell by default)
Add the following to your bash shell script:
Reload your new shell script.
- 20160415 - Removed the LIBGL_DRIVERS_PATH environment variable from the bashrc file. This variable introduces problems with the proper loading of OpenGL libraries on the system.
- 20150415 - Initial post
