From 1efd6f3318fa1dfd356dee0aa865b7c9e52aa756 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@minium.com.au>
Date: Mon, 28 Dec 2020 11:07:19 +1100
Subject: [PATCH] update install and selection

---
 doc/source/installation.rst | 17 +++++++++++++++++
 doc/source/selections.rst   | 18 ++++++++++++++----
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/doc/source/installation.rst b/doc/source/installation.rst
index 93624a7ce..7a0f3f4a6 100644
--- a/doc/source/installation.rst
+++ b/doc/source/installation.rst
@@ -55,6 +55,14 @@ To install the tests:
 
     conda install -c conda-forge MDAnalysisTests
 
+If you intend to use MDAnalysis in JupyterLab, you will have to install
+an extra package for the progress bar in analysis classes:
+
+.. code-block:: bash
+
+    conda install -c conda-forge nodejs
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager
+
 pip
 =====
 The following command will install or upgrade the latest stable version of MDAnalysis via ``pip``, with core dependencies. This means that some packages required by specific analysis modules will not be installed.
@@ -75,6 +83,15 @@ To install/upgrade tests:
 
     pip install --upgrade MDAnalysisTests
 
+If you intend to use MDAnalysis in JupyterLab, you will have to install
+an extra package for the progress bar in analysis classes:
+
+.. code-block:: bash
+
+    pip install nodejs
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager
+
+
 Development versions
 ====================
 To install development versions of MDAnalysis, you can compile it from source. In order to install from source, you will need ``numpy`` and ``cython``. See :ref:`create-virtual-environment` for instructions on how to create a full development environment.
diff --git a/doc/source/selections.rst b/doc/source/selections.rst
index 236704ba5..d984e6836 100644
--- a/doc/source/selections.rst
+++ b/doc/source/selections.rst
@@ -69,10 +69,15 @@ selection parser. The following applies to all selections:
 
 
 * String selections such as names and residue names can be 
-  matched with Unix shell-style wildcards. Using ``*`` 
-  in a string matches any number of any characters; ``?`` 
-  matches any single character; ``[seq]`` matches any character in *seq*; 
-  and ``[!seq]`` matches any character not in *seq*. For example, 
+  matched with Unix shell-style wildcards. These rules include:
+
+    * Using ``*``  in a string matches any number of any characters
+    * ``?`` matches any single character
+    * ``[seq]`` matches any character in *seq*;
+    * ``[!seq]`` matches any character not in *seq*
+    * ``[!?]`` selects empty strings
+  
+  For example, 
   the string ``GL*`` selects all strings that start with "GL", 
   such as "GLU", "GLY", "GLX29", "GLN". ``GL[YN]`` will select all "GLY" and 
   "GLN" strings. Any number of patterns can be included in the search.
@@ -141,6 +146,11 @@ altloc *alternative-location*
     e.g. :code:`resid 4 and resname ALA and altloc B` selects only the atoms of ALA-4
     that have an altloc B record.
 
+icode *icode*
+    a selector for atoms where insertion codes are available. This can be combined
+    with residue numbers using the ``resid`` selector above.
+    e.g. :code:`icode [!?]` selects atoms *without* insertion codes.
+
 moltype *molecule-type*
     select by the ``moltype`` :ref:`topology attribute <topology-attributes>`, e.g. ``moltype Protein_A``. At the moment, only the TPR format defines the ``moltype``.