From e90149b7ac3995cd6c525b87a8a6700cd2971a37 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 27 Aug 2024 11:00:57 -0700 Subject: [PATCH] Fix typo --- rnapolii/modeling/.template.deposition.ipynb | 2 +- rnapolii/modeling/deposition-colab.ipynb | 2 +- rnapolii/modeling/deposition.ipynb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/rnapolii/modeling/.template.deposition.ipynb b/rnapolii/modeling/.template.deposition.ipynb index d005760..443d546 100644 --- a/rnapolii/modeling/.template.deposition.ipynb +++ b/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):" ] }, { diff --git a/rnapolii/modeling/deposition-colab.ipynb b/rnapolii/modeling/deposition-colab.ipynb index d81f7d1..f7f1ce7 100644 --- a/rnapolii/modeling/deposition-colab.ipynb +++ b/rnapolii/modeling/deposition-colab.ipynb @@ -674,7 +674,7 @@ "## Cross-linker type\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):" ] }, { diff --git a/rnapolii/modeling/deposition.ipynb b/rnapolii/modeling/deposition.ipynb index f6e082f..0b1a686 100644 --- a/rnapolii/modeling/deposition.ipynb +++ b/rnapolii/modeling/deposition.ipynb @@ -646,7 +646,7 @@ "## Cross-linker type\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):" ] }, {