Fix typo

rnapolii/modeling/.template.deposition.ipynb

@@ -681,7 +681,7 @@
     "## Cross-linker type {#xltype}\n",
     "\n",
     "For cross-linking experiments, the mmCIF file contains a description of the cross-linking reagent used. This information is not in the CSV file. It can be provided in the Python script with the `linker` argument to passed to the PMI ``~IMP::pmi::restraints::crosslinking::CrossLinkingMassSpectrometryRestraint``, but if this argument was missing (or incorrect) we can correct it here. By checking the publications for the cross-link datasets from [Al Burlingame's lab](https://www.mcponline.org/content/13/2/420.long) and\n",
-    "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717)), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the ``ihm.cross_linkers`` module (for less common linkers we can create an ``ihm.ChemDescriptor`` object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](@ref ihm.restraint.CrossLinkRestraint) in the [list of all restraints](@ref ihm.System.restraints):"
+    "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the ``ihm.cross_linkers`` module (for less common linkers we can create an ``ihm.ChemDescriptor`` object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](@ref ihm.restraint.CrossLinkRestraint) in the [list of all restraints](@ref ihm.System.restraints):"
    ]
   },
   {

rnapolii/modeling/deposition-colab.ipynb

@@ -674,7 +674,7 @@
         "## Cross-linker type<a id=\"xltype\"></a>\n",
         "\n",
         "For cross-linking experiments, the mmCIF file contains a description of the cross-linking reagent used. This information is not in the CSV file. It can be provided in the Python script with the `linker` argument to passed to the PMI [CrossLinkingMassSpectrometryRestraint](https://integrativemodeling.org/2.21.0/doc/ref/classIMP_1_1pmi_1_1restraints_1_1crosslinking_1_1CrossLinkingMassSpectrometryRestraint.html), but if this argument was missing (or incorrect) we can correct it here. By checking the publications for the cross-link datasets from [Al Burlingame's lab](https://www.mcponline.org/content/13/2/420.long) and\n",
-        "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717)), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the [ihm.cross_linkers](https://python-ihm.readthedocs.io/en/latest/cross_linkers.html#module-ihm.cross_linkers) module (for less common linkers we can create an [ihm.ChemDescriptor](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor) object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](https://python-ihm.readthedocs.io/en/latest/restraint.html#ihm.restraint.CrossLinkRestraint) in the [list of all restraints](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.System.restraints):"
+        "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the [ihm.cross_linkers](https://python-ihm.readthedocs.io/en/latest/cross_linkers.html#module-ihm.cross_linkers) module (for less common linkers we can create an [ihm.ChemDescriptor](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor) object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](https://python-ihm.readthedocs.io/en/latest/restraint.html#ihm.restraint.CrossLinkRestraint) in the [list of all restraints](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.System.restraints):"
       ]
     },
     {

rnapolii/modeling/deposition.ipynb

@@ -646,7 +646,7 @@
         "## Cross-linker type<a id=\"xltype\"></a>\n",
         "\n",
         "For cross-linking experiments, the mmCIF file contains a description of the cross-linking reagent used. This information is not in the CSV file. It can be provided in the Python script with the `linker` argument to passed to the PMI [CrossLinkingMassSpectrometryRestraint](https://integrativemodeling.org/2.21.0/doc/ref/classIMP_1_1pmi_1_1restraints_1_1crosslinking_1_1CrossLinkingMassSpectrometryRestraint.html), but if this argument was missing (or incorrect) we can correct it here. By checking the publications for the cross-link datasets from [Al Burlingame's lab](https://www.mcponline.org/content/13/2/420.long) and\n",
-        "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717)), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the [ihm.cross_linkers](https://python-ihm.readthedocs.io/en/latest/cross_linkers.html#module-ihm.cross_linkers) module (for less common linkers we can create an [ihm.ChemDescriptor](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor) object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](https://python-ihm.readthedocs.io/en/latest/restraint.html#ihm.restraint.CrossLinkRestraint) in the [list of all restraints](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.System.restraints):"
+        "[Juri Rappsilber's lab](http://emboj.embopress.org/content/29/4/717), we can determine that the [DSS](https://en.wikipedia.org/wiki/Disuccinimidyl_suberate) and [BS3](https://en.wikipedia.org/wiki/Bissulfosuccinimidyl_suberate) cross-linkers were used, respectively. These are common enough cross-linkers that python-ihm already includes definitions for them in the [ihm.cross_linkers](https://python-ihm.readthedocs.io/en/latest/cross_linkers.html#module-ihm.cross_linkers) module (for less common linkers we can create an [ihm.ChemDescriptor](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor) object from scratch to describe its chemistry). Then we just set the linker type for each [cross-linking restraint](https://python-ihm.readthedocs.io/en/latest/restraint.html#ihm.restraint.CrossLinkRestraint) in the [list of all restraints](https://python-ihm.readthedocs.io/en/latest/main.html#ihm.System.restraints):"
       ]
     },
     {