"Structure" Preferences tab added in Jalview 2.8.2
Process secondary structure from PDB - if selected, then structure information -read from PDB will be processed to derive secondary structure annotation. -
Use RNAView for secondary structure - if selected, the RNAView service will be -automatically called to derive secondary structure information. -
Add secondary structure annotation to alignment - if selected, PDB secondary structure -annotation will be shown on the alignment when available. -
Add Temperature Factor annotation to alignment - if selected, PDB Temperature Factor -annotation will be shown on the alignment when available. +read from PDB will be processed and annotation added to associated sequences. +
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 chains in the structure. +
Add Temperature Factor annotation to alignment - if selected, values extracted from the Temperature Factor +column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
Default structure viewer - choose JMOL or CHIMERA for viewing 3D structures.
Path to Chimera program - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS. If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program.