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+
+
+
+The VARNA RNA Viewer
+
+
+The VARNA RNA Viewer
+Since Jalview
+2.7.1, VARNA has been
+integrated into Jalview for interactively viewing structures opened by
+selecting the "Structure→View
+Structure:" option in
+the sequence id pop-up menu (if
+you can't see this, then no RNA structure is associated with your
+sequence or alignment. In the pop-up menu all structures that
+are associated with this sequence and all sequences that are
+associated with the alignment are available.
+
+
Different structures
+
+ -
+ Alignment structures:
+ Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
+
+ - Consensus structure: the individual sequence folded into the consensus structure
+ - Trimed consensus structure: the individual sequence
+ folded into the the gap-free consensus structure. That means all
+ columns that contained gaps in the individual sequence were
+ removed. If this breaks a base-pair the pairing is removed also.
+ This can be considered as an approximation for the individual structure.
+
+
+ -
+ Individual structures:
+ this is a structure associated with the individual sequence and therefore not related to the alignment
+
+
+Controls
+
+- Rotate view - Left Click and drag
+- Zoom in - Press '+'
+- Zoom out - Press '-'
+- Choose a different structure - Left click on structure in the left hand panel
+- Highlighting bases - Move mouse over columns in the Jalview alignment panel
+
+
+Functionality provided by Jmol
+VARNA's own functions are accessed by right-clicking in the
+structure display area. That will open the VARNA pop-up menu,
+which provides access to a number of features like different draw algorithm, color highlighting or annotations.
+
+More Information
+VARNA is a very powerful RNA viewer on it's own. Only the
+essentials have been described here - the interested reader is
+referred to VARNA's own
+comprehensive online documentation.
+
+