Dear Eriks,

first of all thank you for the contsructive critic, which will help us to improve the manuscript.

Below you will find the answers to your comments:

Comment: My personal critique is that the proposed library statements in some cases are not easily readable or memorable, which may repel some potential users. For instance, the code for the HNCO experiment (Fig. 2) does make some sense whereas the 4D NOESY pulse program syntax (Fig. 4) hardly makes any sense. It starts with a mixTime statement which may include some pulses, but as the first statement in a NOESY experiment makes little sense.

Response: We agree that parts of the library syntax aren’t particularly readable and might obscure its functionality. Since the most straightforward method of using the library to implement a new pulse program is to copy and edit an existing one, we will improve their readability.

Improvements to the manuscript: We will add comments to the sequences describing the functionality of imports, most significantly the use of start.incl and end.incl modules to select 2D blocks in NOESY programs.

Comment: A couple lines down the sequence this is followed by DISTAL_MC1, DISTAL_MC2 and PROXIMAL_MC3. Again, these statements make little sense as such, but it is also difficult to see whether more user-friendly syntax can be invented.

Response: The MC macros appeared in the pulse program code due to the limitations of the programming language. The approach used in the original submission was a compromise between user-friendliness and customizability. Upon deeper reflection we have decided to separate the programming facilities for both scenarios. We will revise the text to use a user-friendly version and describe the customizable (expert) facilities in library documentation.

Improvements to the manuscript: We will amend the library code, so that those statements aren’t needed in standard pulse programs, and update the corresponding figure in the manuscript.

Comment: Finally, it is also not clear whether the Bruker TopSpin software can display such sequences for users to understand the experiments in detail.

Response: While the functionality of dps command in VNMR/VNMRJ was much better, TopSpin is also able to render a pictorial representation (using GUI or the spdisp command) of the pulse program based on the current value of the ZGOPTNS parameter. Unfortunately, the same cannot be said for the configuration of variants using ZGOPTNS as there is no default GUI facility for presenting possible options or indicating which are mutually exclusive. We will complete the implementation and describe the use of a GUI configurator utility for the setting of common ZGOPTNS options using radio buttons and drop-down menus.

Improvements to the manuscript: We will add a subsection presenting the use of a GUI to configure a NOESY pulse program.

Comment: Minor remarks:

1) Introduction, line 6 - “oft-used” should be spelled out properly.

2) Page 2, section 2 - “... function can evaluate to a 90 degree ...” perhaps would better read “function can translate into a 90 degree ...”. See other similar instances in the main text.

3) Page 14, line 1 - a reference is missing.

Response: A number of linguistic errors have unfortunately slipped through our initial proof-reading. We will carefully review the language used throughout the manuscript.

Improvements to the manuscript: We have corrected a number of language errors and added the missing reference to Schanda, P., Van Melckebeke, H., and Brutscher, B.:

Speeding Up Three-Dimensional Protein NMR Experiments to a Few Minutes, J. Am. Chem. Soc., 128, 9042–9043, https://doi.org/10.1021/ja062025p, 2006.

Dear Bernhardt,

We are grateful for your carrefull review givig us help to improve the quality of manuscript. Below you will find the answers to your comments.

Comment: Running a NMR experiment requires an appropriate pulse sequence as well as a related set of acquisition parameters (pulse lengths, pulse shapes, frequency offsets, delays, constants, …) . As I understand some of these parameters are predefined, but others need to be set by the user. How is this handled in practice?

Response: The experiments use a combination of automatically set (using prosol utilities) or calculated parameters. All user-set parameters are accessible from the appropriate TopSpin menu (accessed using the ased command) and are annotated with a description and a default value. In the version of the library accompanying the revised manuscript we will provide a TopSpin utility for setting default values of parameters defined within the library, which can be used to configure individual parameter sets or used to prepare a base parameter set that can then be copied and re-used for multiple experiments. Unfortunately, TopSpin parameter sets aren’t usually re-usable between different spectrometers.

Although the parameter sets can be relatively easily adjusted, they also pose a risk to the spectrometer if some of the adjustments are omitted and inappropriate parameter values or routing configuration is used. For this reason, we chose not to directly distribute parameter sets.

Improvements to the manuscript: We will mention the parameter-setting program in the text and point the users to a section of the library manual on setting up experiments using the library’s functionality.

Comment: Along the same lines, making these modules usable by a broad range of users requires a documentation of all available modules, what they are doing, what are the available options and how to implement them, as well as the relevant acquisition parameters that need to be adjusted. I could not find such a compiled description ?!

Response: We agree that the library requires separate documentation, especially since TopSpin’s pulse programming language and associated environment don’t have any built-in helper facilities like docstrings and syntax completion. Initially, we had problems with finding an appropriate format - especially one that would allow for easy modification as the library evolves. We have now made the choice to provide the documentation using Markdown, making it directly accessible from the libraries GitHub repository without the need to use external software and easy to update using a just a text editor.

Improvements to the manuscript: We will add documentation to the library repository provided in the “Data availability section”, with a short mention in manuscript text.

Comment: As also pointed out by Eriks Kupe, the examples given (HNCO and 4D NOESY) in the manuscript are certainly very compact in terms of lines of code, but difficult to understand as such. Again it would be useful to somehow add comments that make the pulse code more readable. I doubt that many potential users will dig deep into the modular elements code to understand what they are doing.

Response: We concur that parts of the initial codebase were too terse. Since the primary interaction users have with the library is through a pulse program, we will improve the readability of the included example experiments.

Improvements to the manuscript: In the library code, we will include comments that expand on the functionality of the imports used in the supplied pulse programs. We will update the Figures illustrating HNCO and NOESY sequences.

Comment: May be a useful addition to the manuscript would be to pick out 1 or 2 elements, and discuss in a separate section what spin manipulation they are performing, what options they provide and how they can be implemented, and what other parameters need to be taken care of when using this particular module.

Response: In the initial submission, we neglected to show how the concepts of general and specific modules are implemented. We will use a simple HSQC block (used standalone or as a part of a 3D or 4D NOESY experiment) as an example and explain how it is included in a pulse-program using high-level functionality and how it achieves the desired spin manipulation using low-level functionality of the library.

Improvements to the manuscript: We will add a section describing the functionality of the end.incl general module and the hsqc.pp specific module implementing a (non-sensitivity-enhanced) HSQC. The latter will cover the options for gradient selection, flipback, bipolar gradients and accommodation of shaped pulses.

Minor points:

The authors employ at several occasions the term “multiple spin echos” to refer to particular coherence transfer pulse sequence blocks. I suggest replacing this by more commonly used nomenclature ?!

Response: We used the term spin echo to describe a part (block) of a pulse program with 180 deg pulse flanked by delays and 90-degree pulses. We will change this to "evolution periods" and we will reconsider each use of this term in the text separately, to preserve clarity.

Comment: Page 14, line 242: I would replace “even at higher scan repetition rates” by “especially at higher scan repetition rates”. And the reference is missing.

Response: We have reworded this sentence fragment as suggested, as it originally carried the wrong emphasis. In our experience, BEST experiments were almost always more sensitive and the effect was more pronounced at higher scan repetition rates. We have added the missing reference to Schanda, P., Van Melckebeke, H., and Brutscher, B.: Speeding Up Three-Dimensional Protein NMR Experiments to a Few Minutes, J. Am. Chem.Soc., 128, 9042–9043, https://doi.org/10.1021/ja062025p, 2006.

Comment:

- Please avoid Bruker nomenclature in the main text, e.g. gsHSQC (page 2, line 54)

-There are quite some typos in the manuscript. Some examples are listed below:

Page 2, line 53: “it” instead of “in”

Page 2, line 59: “whole in” ?

Page 3, line 81: “allows has”

Page 4, line 93: “a named variables”

Page 4, line 109: “time a during pulse”

Page 4, line 112: “ for consciously during”

Page 8, line 194: “the sequence this block”

Response: We have removed the jargon terms and corrected a number of language errors. We will carefully proof-read the manuscript before submitting a revised version.

Dear Eriks,

We agree with the need to provide further technical documentation.

Together with a revised manuscript, we will provide a manual directly in the library repository describing both the programming facilities and the included pulse programs.