Downloads

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. 

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

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.

External NMR Software Packages

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 Software   Downloads

User-groups, etc:  mailing list, online documentation, ssnmr usage, ssnmr extensions

nmrPipe Processing Software

Link: NMRPipe Home Page

User-groups, etc: Yahoo User Group 

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

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.