Done with structure viewer documentation. Updated some images.

yeastrc · Oct 29, 2015 · e1d70de · e1d70de
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diff --git a/docs/images/project-overview-explore-data.png b/docs/images/project-overview-explore-data.png
diff --git a/docs/images/project-overview-public-access.png b/docs/images/project-overview-public-access.png
diff --git a/docs/images/project-overview-researchers1.png b/docs/images/project-overview-researchers1.png
diff --git a/docs/using/project.rst b/docs/using/project.rst
@@ -15,8 +15,8 @@ help on all of the sections.
 
 Project Information
 =========================
-Project owners may edit the title or abstract by clicking the pencil icon next to the
-respective item. Logged-in users may add notes to the project by clicking "[+Note]".
+Project members may edit the title or abstract by clicking the pencil icon next to the
+respective item. Project members may add notes to the project by clicking "[+Note]".
 Notes may be edited or deleted by clicking on the associated pencil or delete (X) icons.
 The title, abstract, and notes are visible to public users (if public access is enabled,
 see below).

diff --git a/docs/using/spectrum-viewer.rst b/docs/using/spectrum-viewer.rst
@@ -1,4 +1,22 @@
-==================
-Spectrum Viewer
-==================
-
+==================
+Spectrum Viewer
+==================
+
+ProXL uses a version of the `Lorikeet spectrum viewer <https://github.com/UWPR/Lorikeet>`_ that has been modified to support crosslinked
+and looplinked spectra. Lorikeet was a pure-HTML and Javascript viewer that requires no 3rd party plugins to use.  Although no installation
+is required, the source code of the customized version of Lorikeet may be found here. Some knowledge of interpreting tandem mass spectra
+is assumed in this document.
+
+Unlinked Spectra
+---------------------------------
+This is the view of unlinked spectra, that is PSMs that are not looplinked or crosslinked:
+
+
+
+Crosslinked Spectra
+---------------------------------
+
+Looplinked Spectra
+---------------------------------
+
+
diff --git a/docs/using/structure.rst b/docs/using/structure.rst
@@ -467,6 +467,60 @@ comparison of results between searches.
 
 Render mode
 -------------------------
+Provides access to different rendering modes for the structure, itself. The options are:
+
+Cartoon (default)
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Provides a helix, strand coil cartoon view of the structure.
+
+Smooth Line
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Draws the structure as a smoothed line tracing consecutive alpha carbons..
+
+Trace
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Draws the structure as straight lines connecting consecutive alpha carbons.
+
+Lines
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Draws the struture at atomic resolution using lines for bonds.
+
+Points
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Draws the structure as point cloud of all atoms.
+
 
 Filter Data
-============================
+============================
+The data presented in the viewer may be filtered using the form at the top of the page and clicking "Update From Database". The
+filtering options are:
+
+PSM Q-value cutoff
+--------------------
+Only links with at least one peptide that have at least one peptide spectrum match (PSM) with a q-value <= to this cutoff will be shown.
+Additionally, when viewing PSMs for peptides, only PSMs with with a q-value <= to this cutoff will be shown.
+
+Peptide Q-value cutoff
+-----------------------
+Only links with at least one peptide with a peptide-level q-value <= to this cutoff will be shown. If the pipeline used to
+generate the search results does not generate peptide-level q-values, this field has no effect.
+
+Exclude xlinks with
+--------------------
+Links that exclusively have peptides with any of the checked attributes will not be shown. The attributes are:
+
+	* no unique peptides - If the link (crosslink, looplink, or monolink) was exclusively identified by peptides that also map to othe proteins
+	* only one PSM - If a given link was identified by a single PSM
+	* only one peptide - If a given link was identifed by a single peptide, where a peptide is the combination of sequence, linked positions, and modifications
+
+Exclude proteins with
+----------------------
+This option limits which proteins will appear in the pull-down menu for mapping proteins to PDB chains.
+Proteins that contain any of the checked options will not appear. For example, checking 'No links' prevents
+proteins that do not contain crosslinks, looplinks, or monolinks from appearing. This will also prevent any
+links involving excluded proteins from being drawn on the structure.
+
+Exclude organisms
+--------------------
+This options limits which proteins will appear in the pull-down menu for mapping proteins to PDB chains. No proteins from any of the checked organisms will appear.
+This will also prevent any links involving excluded proteins from being drawn on the structure.