Update the documentation to Docusaurus 3.0

website/docs/examples/binding.md

@@ -32,7 +32,7 @@ step, the major purpose is to obtain residue-specific parameters.
 
 Further analysis of the fitting results can be carried out with the aid of
 additional functions in ChemEx (refer to
-[`Plotting best-fit parameters`](user_guide/additional_modules.md#plotting-best-fit-parameters)
+[`Plotting best-fit parameters`](user_guide/additional_modules.mdx#plotting-best-fit-parameters)
 subsection). During the whole fitting process K<sub>d</sub> is fixed to the
 value obtained from ITC experiments, more details about this example can be
 found in the reference.[^1]

website/docs/experiments/cest/cest_13c.md

@@ -17,32 +17,32 @@ CEST block. This keeps the spin system purely in-phase throughout, and is
 calculated using the (3n)×(3n), single-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 ## References
 
-- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713
-  (2014)
-- G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774
-  (2014)
-- P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159
-  (2013)
-- D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289
-  (2013)
-- G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012)
-- E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**,
-  187-199 (2015)
+-   P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713
+    (2014)
+-   G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774
+    (2014)
+-   P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159
+    (2013)
+-   D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289
+    (2013)
+-   G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012)
+-   E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**,
+    187-199 (2015)
 
 ## Example
 
-- An example for studying side-chain methyl groups in selectively ¹³C-labeled
-  sample is available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/).
-- An example for studying
-  [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
-  available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/).
+-   An example for studying side-chain methyl groups in selectively ¹³C-labeled
+    sample is available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/).
+-   An example for studying
+    [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
+    available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/).
 
 ## Sample configuration file
 

website/docs/experiments/cest/cest_15n.md

@@ -17,22 +17,22 @@ CEST block. This keeps the spin system purely in-phase throughout, and is
 calculated using the (3n)×(3n), single-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 ## Reference
 
-- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**,
-  8148-8161 (2012)
+-   P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**,
+    8148-8161 (2012)
 
 ## Examples
 
-- An example for studying ¹⁵N-labeled sample is available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/).
-- An example for studying
-  [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
-  available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/).
+-   An example for studying ¹⁵N-labeled sample is available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/).
+-   An example for studying
+    [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
+    available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/).
 
 ## Sample configuration file
 

website/docs/experiments/cest/cest_15n_cw.md

@@ -16,14 +16,14 @@ Analyzes chemical exchange in the presence of ¹H CW decoupling during the CEST
 block. Magnetization evolution is calculated using the (15n)×(15n), two-spin
 matrix, where n is the number of states:
 
-    {        Ix(a),   Iy(a),   Iz(a),   Sx(a), IxSx(a), IySx(a), IzSx(a),
+    \{        Ix(a),   Iy(a),   Iz(a),   Sx(a), IxSx(a), IySx(a), IzSx(a),
       Sy(a), IxSy(a), IySy(a), IzSy(a), Sz(a), IxSz(a), IySz(a), IzSz(a),
              Ix(b),   Iy(b),   Iz(b),   Sx(b), IxSx(b), IySx(b), IzSx(b),
-      Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... }
+      Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012)
+-   G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012)
 
 ## Example
 

website/docs/experiments/cest/cest_15n_tr.md

@@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**,
-  8820-8825 (2014)
+-   D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**,
+    8820-8825 (2014)
 
 ## Example
 

website/docs/experiments/cest/cest_1hn_ap.md

@@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci.
-  USA_ **113**, E2794-E2801 (2016)
+-   A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci.
+    USA_ **113**, E2794-E2801 (2016)
 
 ## Example
 

website/docs/experiments/cest/cest_1hn_ip_ap.md

@@ -16,15 +16,15 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## References
 
-- T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125
-  (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
+-   T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125
+    (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
 
 ## Example
 

website/docs/experiments/cest/cest_ch3_1h_ip_ap.md

@@ -16,8 +16,8 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 :::note
 
@@ -27,8 +27,8 @@ The same module works for both ¹³CH₃- and ¹³CHD₂-labeled methyl groups.
 
 ## References
 
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_13c_ip.md

@@ -17,18 +17,18 @@ during the CPMG block. This keeps the spin system purely in-phase throughout,
 and is calculated using the (3n)×(3n), single-spin matrix, where n is the number
 of states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 The CW decoupling on ¹H is assumed to be strong enough (> 15 kHz) such that
 perfect ¹H decoupling can be achieved. In the case of CHD2 experiment, CW
 decoupling on 2H should be applied properly.
 
 ## References
 
-- D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am.
-  Chem. Soc._ **130**, 2667-2675 (2008)
-- E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016)
+-   D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am.
+    Chem. Soc._ **130**, 2667-2675 (2008)
+-   E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_13co_ap.md

@@ -17,8 +17,8 @@ magnetization throughout the CPMG block. This results in lower intrinsic
 relaxation rates and therefore better sensitivity. The calculations use a
 (6n)×(6n), two-spin matrix, where n is the number of states:
 
-    { COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a),
-      COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... }
+    \{ COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a),
+      COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... \}
 
 Because of the length of the shaped pulses used during the CPMG blocks,
 off-resonance effects are taken into account only for the 90-degree pulses that
@@ -29,7 +29,7 @@ the "refocusing" flag, with such option ncyc_cp should be set as even.
 
 # Reference:
 
-- Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008)
+-   Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_15n_ip.md

@@ -17,16 +17,16 @@ during the CPMG block. This keeps the spin system purely in-phase throughout,
 and is calculated using the (3n)×(3n), single-spin matrix, where n is the number
 of states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 The CW decoupling on ¹H is assumed to be strong enough (> 15 kHz) such that
 perfect ¹H decoupling can be achieved.
 
 ## Reference
 
-- D.F. Hansen, P. Vallurupalli, and L.E. Kay. **J. Phys. Chem. B** **112**,
-  5898-5904 (2008)
+-   D.F. Hansen, P. Vallurupalli, and L.E. Kay. **J. Phys. Chem. B** **112**,
+    5898-5904 (2008)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_15n_ip_0013.md

@@ -17,17 +17,17 @@ during the CPMG block. This keeps the spin system purely in-phase throughout,
 and is calculated using the (3n)×(3n), single-spin matrix, where n is the number
 of states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 This version is modified such that CPMG pulses are applied with [0013] phase
 cycle as shown in Daiwen's paper. The CW decoupling on ¹H is assumed to be
 strong enough (> 15 kHz) such that perfect ¹H decoupling can be achieved.
 
 ## Reference
 
-- B. Jiang, B. Yu, X. Zhang, M. Liu, and D. Yang. _J. Magn. Reson._ **257**, 1-7
-  (2015)
+-   B. Jiang, B. Yu, X. Zhang, M. Liu, and D. Yang. _J. Magn. Reson._ **257**, 1-7
+    (2015)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_15n_tr.md

@@ -18,22 +18,22 @@ exchange dynamics. Resulting magnetization intensity after the CPMG block is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a),
-      Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... }
+    \{ Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a),
+      Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... \}
 
 ## Reference
 
-- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc.
-  Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007)
+-   P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc.
+    Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007)
 
 ## Examples
 
-- An example use of the module is given
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_15N_TR/).
-- An example use of the module in the context of
-  [RDC measurement of a protein minor, short-lived state](../../examples/trosy_cpmg_rdc.md)
-  can be found
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/N15_NH_RDC/).
+-   An example use of the module is given
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_15N_TR/).
+-   An example use of the module in the context of
+    [RDC measurement of a protein minor, short-lived state](../../examples/trosy_cpmg_rdc.md)
+    can be found
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/N15_NH_RDC/).
 
 ## Sample configuration file
 

website/docs/experiments/cpmg/cpmg_15n_tr_0013.md

@@ -18,17 +18,17 @@ exchange dynamics. Resulting magnetization intensity after the CPMG block is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a),
-      Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... }
+    \{ Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a),
+      Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... \}
 
 This version is modified such that CPMG pulses are applied with [0013] phase
 cycle as used in ¹⁵N pure in-phase experiments.
 
 ## References
 
-- Jiang, Yu, Zhang, Liu, and Yang. J Magn Reson **257**, 1-7 (2015)
-- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc.
-  Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007)
+-   Jiang, Yu, Zhang, Liu, and Yang. J Magn Reson **257**, 1-7 (2015)
+-   P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc.
+    Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_1hn_ap.md

@@ -17,14 +17,14 @@ magnetization throughout the CPMG block. This results in lower intrinsic
 relaxation rates and therefore better sensitivity. The calculations use a
 (6n)×(6n), two-spin matrix, where n is the number of states:
 
-    { Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a),
-      Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... }
+    \{ Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a),
+      Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... \}
 
 ## Reference
 
 Adapted from:
 
-- Ishima, and Torshia. _J. Biomol. NMR_ **25**, 243-248 (2003)
+-   Ishima, and Torshia. _J. Biomol. NMR_ **25**, 243-248 (2003)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_1hn_ap_0013.md

@@ -17,15 +17,15 @@ magnetization throughout the CPMG block. This results in lower intrinsic
 relaxation rates and therefore better sensitivity. The calculations use the
 (6n)×(6n), two-spin matrix, where n is the number of states:
 
-    { Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a),
-      Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... }
+    \{ Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a),
+      Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... \}
 
 This version is modified such that CPMG pulses are applied with [0013] phase
 cycle to help better overcome off-resonance effects.
 
 ## Reference
 
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **73**, 641-650 (2019)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **73**, 641-650 (2019)
 
 ## Example
 

website/docs/experiments/cpmg/cpmg_ch3_13c_h2c.md

@@ -19,13 +19,13 @@ even ncyc should be recorded. Resulting magnetization intensity after the CPMG
 block is calculated using the (6n)×(6n), two-spin matrix, where n is the number
 of states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- P. Lundström, P. Vallurupalli, T.M. Religa, F.W. Dahlquist, and L.E. Kay. _J.
-  Biomol. NMR_ **38**, 79-88 (2007)
+-   P. Lundström, P. Vallurupalli, T.M. Religa, F.W. Dahlquist, and L.E. Kay. _J.
+    Biomol. NMR_ **38**, 79-88 (2007)
 
 ## Example