Stable admonitions

Input_peak_lists_for_4D-GraFID/peak_list_full_format_guide.md

@@ -11,8 +11,8 @@ layout: default
 
 ### Backbone assignments
 
->  ![Warning]
->  Differentiation between backbone and side chain peaks in the **3D** experiments is currently not supported by 4D-GraFID; please, remove any known sidechain peaks from the peak lists. 
+> **Warning:** Differentiation between backbone and side chain peaks in the **3D** experiments is currently not supported by 4D-GraFID; please, remove any known sidechain peaks from the peak lists.
+{: .admonition .warning}
 
 
 
@@ -28,8 +28,8 @@ layout: default
 
 ### Side chain assignments & structure
 
-> ![Info]
 > Coming soon to 4D-GraFID
+{: .admonition .info}
 
 | Name             | Example Bruker pulse sequence | Expected atoms                                     | Intensity            |
 | ---------------- | ----------------------------- | -------------------------------------------------- | -------------------- |
@@ -52,8 +52,8 @@ Non-paired experiments **will not be considered**
 
 ## User assignments reference
 
-> ![NOTE]
-> Currently *(as of 16. Feb 2026)*, only assignments of 15N-HSQC are considered. 
+> **Important:** Currently *(as of 16. Feb 2026)*, only assignments of 15N-HSQC are considered.
+{: .admonition .important}
 
 The assignment must match the format: `<1-letter RESTYPE><RESNUM><ATOM-w1>-<ATOM-w2>`.
 

SPARKY_and_POKY/Protein_NMR_workflow.md

@@ -33,16 +33,16 @@ layout: default
 - Integrate a confirmed single HN peak in 1D, then other peaks to determine their multiplicity (singlets, doublets, etc.).
 - Mark and identify as many HN peaks as possible using integrals from 1D and the overlaid 1D+2D TOCSY spectra.
 
-> ![NOTE]
-> Ignore peaks exactly below HA peaks around 4.8 ppm as correspond to water absorption - ignore them!
+> **Note:** Ignore peaks exactly below HA peaks around 4.8 ppm as correspond to water absorption - ignore them!
+{: .admonition .note}
 
 **Peak Assignments**
 - Assign as many H?-HN, H?-HA, H?-HB, etc., peaks as possible. Note that the first residue's HN does not appear in the spectrum; the second residue's HN is the most leftward.
 - Use the HA(i)-HN(i+1) NOEs to assign as many peaks as you can to atoms/residues. Sparky identifies the closest atom resonance when you try to add labels.
 - Use the HN(i)-HN(i+1) NOEs to assign as many peaks as you can to atoms/residues. Sparky identifies the closest atom resonance when you try to add labels.
 
->![NOTE]
-> Strong HN(i)-HN(i+1) NOEs are characteristic of alpha- and 3/10-helical structures (~2.8 A, ~2.6 A) and turn I (~2.6 A).
+> **Note:** Strong HN(i)-HN(i+1) NOEs are characteristic of alpha- and 3/10-helical structures (~2.8 A, ~2.6 A) and turn I (~2.6 A).
+{: .admonition .note}
 
 - Use the HB(i)-HN(i+1) NOEs to assign as many peaks as you can to atoms/residues. Sparky identifies the closest atom resonance when you try to add labels.
 - Use the rest of the NOEs to assign as many more atoms as you can. Sparky identifies the closest atom resonance when you try to add labels.

TOPSPIN/NUS_reconstruction/4D.md

@@ -24,33 +24,34 @@ Tested environment:
 * OS: AlmaLinux 9 (as an Oracle virtual machine)
 * 20 CPU cores, 120 GB of RAM.
 
-> [!WARNING]
-> Not everything is thoroughly tested yet
+> **Caution** Not everything is thoroughly tested yet
+{: .admonition .caution}
 
 # General workflow
 
 1. Copy the raw 4D spectrum in a new directory by executing `wrpa` command. This will make working with the 4D neat and safe.
-> ![NOTE]
-> NUS FIDs before reconstruction are not that heavy: the `ser` files are usually <1 Gb. 
+> **Note:** NUS FIDs before reconstruction are not that heavy: the `ser` files are usually <1 Gb.
+{: .admonition .note}
 2. Switch to the newly copied procedure; Open up the processing parameters (`edp` or the tab `PROCPAR`). 
 3. Adjust the size of the dimensions in the final spectrum with the parameter `SI`. **Always set it to a power of 2**. 
 For example, if `TD` values under `ACQUPARS` is `160`, then se `SI` to `256` or `512`.
-> [!IMPORTANT]
-> Always set the `SI` to the next or higher power of 2, never lower than the respective `TD` value! 
+> **Important:** Always set the `SI` to the next or higher power of 2, never lower than the respective `TD` value!
 > Otherwise TopSpin behaves weirdly, e.g. will leave indirect dimensions in time domain.
+{: .admonition .important}
+
 4. If there were recorded test 2D **planes** (or 3D cubes) with **this exact** 4D pulse program, check their processing parameters:
     * Phasing in the direct and indirect dimensions
     * Window functions (rarely changes from default)
     * Baseline correction parameters (rarely changes from default)
     * Linear Prediction (**LP**), if you use it.
-> [!TIP]
-> **NUS and LP should not be combined.** NUS simulates fitfully the whole FID, while LP simulates 
-> the FID decay that was truncated out. As such, NUS reconstruction substitutes LP and LP must not be applied to any 
+> **Tip:** **NUS and LP should not be combined.** NUS simulates fitfully the whole FID, while LP simulates
+> the FID decay that was truncated out. As such, NUS reconstruction substitutes LP and LP must not be applied to any
 > spectrum (4D, 3D) recorded with NUS.
-> If recorderd without NUS, Using LP can enhance resolution, especially if the time domain (TD) values are small or if your 
-> FIDs are truncated. In TopSpin, you can use LP for improving resolution in particular dimensions during the Fourier 
-> Transform process by specifying the `ME_mod` and `NCOEF` parameters for those dimensions. Note that it may cause 
+> If recorderd without NUS, Using LP can enhance resolution, especially if the time domain (TD) values are small or if your
+> FIDs are truncated. In TopSpin, you can use LP for improving resolution in particular dimensions during the Fourier
+> Transform process by specifying the `ME_mod` and `NCOEF` parameters for those dimensions. Note that it may cause
 > additional wiggles.
+{: .admonition .tip}
 
 ![processing_parameters_window_top](../../Non_Uniform_Sampling/images/processing_parameters_1.png)
 ![processing_parameters_window_bottom](../../Non_Uniform_Sampling/images/processing_parameters_2.png)
@@ -61,14 +62,15 @@ For example, if `TD` values under `ACQUPARS` is `160`, then se `SI` to `256` or
 7. Note down the signal region in the direct dimension. It can be extracted either from the test planes or the 2D experiments (HSQC, TOCSY, etc). 
     * Go to the 2D experiment. Zoom in such that the signal-free regions are trimmed as much as possible. Issue the `.ftf2region STSR` command, it will prompt to  `Save display region to Parameters STSR\SI`.
     * Issue the `STSR` command. Note down the values for the direct dimension. Same with `STSI`
-> [!TIP]
-> Those values may be obtained manually: in the 1D or 2D spectrum, note the "col Index" (`16` on the screenshot). Save 
-it into `STSR`. Move the coursor to the right and calculate the width of the dimension in points, save that number into `STSI`.   
+> **Tip:** Those values may be obtained manually: in the 1D or 2D spectrum, note the "col Index" (`16` on the screenshot). Save
+> it into `STSR`. Move the coursor to the right and calculate the width of the dimension in points, save that number into `STSI`.
+{: .admonition .tip}
 
 ![coursor_position](../../Non_Uniform_Sampling/images/coursor_position.png)
 
-> [!IMPORTANT]
-> If you copy the FT region from the planes, make sure the spectrum windows (SW) of the 4D and the test planes are the same. If they are not, the signal regions have to be adjusted manually. 
+> **Important:** If you copy the FT region from the planes, make sure the spectrum windows (SW) of the 4D and the test planes are the same. If they are not, the signal regions have to be adjusted manually.
+{: .admonition .important}
+
 8. Go to the `NUS` section. Set the NUS mode to `cs`. Set the phasing of the indirect dimensions to the same values as in the `Phase` section (i.e. `PH0` and `PH1`). 
 9. For the CS reconstructions in Topspin, it’s a good idea to increase the number of iterations. Since 4D spectra have 
 a high dynamic range, weaker peaks are typically reconstructed in later iterations. The default setting of 
@@ -82,8 +84,8 @@ likely unnecessary.
 * `ftnd` will run the NUS reconstruction, followed by FT all directions, with the Window Multiplication (WM) and 
 baseline correction as specified in the PROCPARS. `0` stands for "all dimensions",  `nusthreads 16` allocates 16 CPU 
 cores for the process (Topspin's limit). 
-> ![NOTE]
-> Whereas NUS reconstruction is parallelized, FT stage uses only a single thread, therefore takes multiple hours.
+> **Note:** Whereas NUS reconstruction is parallelized, FT stage uses only a single thread, therefore takes multiple hours.
+{: .admonition .note}
 11. *Optionally*: adjust baseline correction parameters and apply the automatic baseline correction to the whole reconstructed 4D spectrum.
     - I am not sure whether baseline correction only in F4 or in all F1-F4 would be better - if better than without baseline correction.
 Topspin offers the command `absnd` but you have to execute it for each dimension individually, which is tedious as the 
@@ -207,9 +209,6 @@ Axis order:
 |---|---|---|---|
 |HN|N|C|Hc|
 
-<!---
-@Katja: THIS IS NOT NECESSARY FOR TOPSPIN; IS IT? Instead, THE PHASING SHOULD TAKE CARE OF IT?
-<------->
 ### Processing steps
 
 1. **Correct 1-Point Delay in 13C:**
@@ -320,8 +319,8 @@ Axis order:
    |MddF180|      |true|true|false|
    |MdPHASE|      |90|90|-45|
 
-> ![NOTE]
-> This specific phasing in the indirect dimension takes care of the 1-point delay incorporated into the pulse program in ¹³C channel. 
+> **Note:** This specific phasing in the indirect dimension takes care of the 1-point delay incorporated into the pulse program in ¹³C channel. 
+{: .admonition .note}
 
 Optionally increase the number of iterations with `Mdd_CsNITER 600`.
 
@@ -361,25 +360,4 @@ The following parameters are automatically set:
 
 - Petr Padrta, 14.6.2024
 - Thomas Evangelidis
-- Ekaterina Burakova
-
-
-<!--- 
-
-## Simple alerts
-> ![NOTE]
-> This is a note.
-
-> [!TIP]
-> This is a tip. (Supported since 14 Nov 2023)
-
-> [!IMPORTANT]
-> Crutial information comes here.
-
-> [!CAUTION]
-> Negative potential consequences of an action. (Supported since 14 Nov 2023)
-
-> [!WARNING]
-> Critical content comes here.
-
-<---->
+- Ekaterina Burakova

TOPSPIN/Topspin_Installation.md

@@ -6,8 +6,8 @@ layout: default
 # Topspin installation on Linux 
 
 Here we consider just Debian-based systems. 
-> ![NOTE]
-> Bruker officially supports only RHEL-based Linux, such as AlmaLinux. 
+>  **Note:** Bruker officially supports only RHEL-based Linux, such as AlmaLinux. 
+{: .admonition .note}
 
 1. Log in to your Bruker account, find the latest release of Topspin and download it. The file will have `.sh` extension. 
 2. Meanwhile, go to the [Wibu.com](https://www.wibu.com/support/user/user-software.html) 
@@ -33,5 +33,5 @@ sudo chmod 777 -R /opt/topspin-4.4.0/
 
 9. Your installation is complete!
 
-> ![NOTE]
-> Sometimes Topspin can not start because of the error "Failed to connect to a data server". To us, the reasons are yet unknown, but perhaps they have something to di with the network and firewall configuration. If this happens, simply turn *off* your internet connection while starting TopSpin. Turn it back on once the GUI is loaded. 
+> **Note:** Sometimes Topspin can not start because of the error "Failed to connect to a data server". To us, the reasons are yet unknown, but perhaps they have something to di with the network and firewall configuration. If this happens, simply turn *off* your internet connection while starting TopSpin. Turn it back on once the GUI is loaded. 
+{: .admonition .note}

assets/css/style.scss

@@ -116,3 +116,44 @@
   display: block;
   margin: 0 auto;
 }
+
+.admonition {
+  margin: 1rem 0;
+  padding: 0.85rem 1rem;
+  border-left: 4px solid #3c78d8;
+  background: #f7f9ff;
+  border-radius: 6px;
+}
+
+.admonition > :first-child {
+  margin-top: 0;
+}
+
+.admonition > :last-child {
+  margin-bottom: 0;
+}
+
+.admonition.note {
+  border-left-color: #2f80ed;
+  background: #f3f8ff;
+}
+
+.admonition.tip {
+  border-left-color: #2f9e44;
+  background: #f3fbf6;
+}
+
+.admonition.warning {
+  border-left-color: #f59f00;
+  background: #fff8e6;
+}
+
+.admonition.caution {
+  border-left-color: #e03131;
+  background: #fff4f4;
+}
+
+.admonition.important {
+  border-left-color: #6f42c1;
+  background: #f7f2ff;
+}