<p><a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
<p><em>Process secondary structure from PDB</em> - if selected, then structure information
-read from PDB will be processed to derive secondary structure annotation.
-<p><em>Use RNAView for secondary structure</em> - if selected, the RNAView service will be
-automatically called to derive secondary structure information.
-<p><em>Add secondary structure annotation to alignment</em> - if selected, PDB secondary structure
-annotation will be shown on the alignment when available.
-<p><em>Add Temperature Factor annotation to alignment</em> - 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.
+<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
+called to derive secondary structure information for RNA chains.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
+<p><em>Add Temperature Factor annotation to alignment</em> - 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.
<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
<p><em>Path to Chimera program</em> - 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.
git://source.jalview.org / jalview.git / blobdiff