- Use RNAView for secondary structure - if selected, the - pyRNA RNAView service (https://github.com/fjossinet/PyRNA) - will be called to derive secondary structure information for RNA - chains. -
Add secondary structure annotation to alignment - if
selected, Jmol's
implementation DSSP will be used to add annotation to polypeptide
@@ -228,7 +223,7 @@
the backbone atoms in the PDB file will be extracted as annotation
lines shown on the alignment.
Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.
- Default structure viewer - choose Jmol, CHIMERA, CHIMERAX or PYMOL for + Default structure viewer - choose Jmol, CHIMERA, CHIMERAX or PYMOL for viewing 3D structures.
Path to Chimera/X/Pymol program - Optional, as Jalview will search
@@ -236,6 +231,13 @@
installed the chosen viewer in a non-standard location, you can specify it
here, by entering the full path to its executable.
For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also double-click this field to open a file chooser dialog.
+ Sequence <-> Structure Mapping Method - This setting controls whether + Jalview attempts to retrieve mappings between Uniprot protein + sequences and 3D structures in the PDBe with SIFTS, or constructs a + mapping by conservative alignment between the sequences and chains + in the 3D structure data using the Needleman and Wunsch algorithm. + SIFTS is enabled by default. +
PDB Fields shown in Search and Structure Summaries - ticks in this table indicate fields shown by default when browsing results of a free text search via the PDB sequence fetcher, or 3D structures