The secondary structure annotations are not working as they previously did.
Both helices and strands have the same graphic (both with arrows). This is also with JABAWS predictions. Also the default colors aren’t what they used to be.
The documentation is not very clear about specifying the secondary structure:
NO_GRAPH
For a row consisting of text labels and/or secondary structure symbols.
{Secondary Structure Symbol},text label,Tooltip text
Currently supported secondary structure structure symbols are H (for helix) and E (for strand)
Any or all value fields may be left empty, as well as the BAR_GRAPH’s text character field, and either or both of the text-label and secondary structure symbol fields of the NO_GRAPH type annotation rows.
Does this mean that each position can contain 3 parameters? If I give a number for the Tooltip text, the number is displayed above the secondary structure graphic and not as a “Tooltip”. Should the digit be in quotes?
Mark
···
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353
Both helices and strands have the same graphic (both with arrows). This is also with JABAWS predictions. Also the default colors aren’t what they used to be.
Yes - this is because the new PDB based protein and RNA secondary structure stuff isn’t quite finished yet. That’s near the top of my hit list for the next 48 hours of hacking…
The documentation is not very clear about specifying the secondary structure:
NO_GRAPH
For a row consisting of text labels and/or secondary structure symbols.
{Secondary Structure Symbol},text label,Tooltip text
Currently supported secondary structure structure symbols are H (for helix) and E (for strand)
Any or all value fields may be left empty, as well as the BAR_GRAPH’s text character field, and either or both of the text-label and secondary structure symbol fields of the NO_GRAPH type annotation rows.
Does this mean that each position can contain 3 parameters? If I give a number for the Tooltip text, the number is displayed above the secondary structure graphic and not as a “Tooltip”. Should the digit be in quotes?
send me an example explaining what you want. In principle Jalview tries to handle what you have given it in a sensible way, but there are some corner cases where it breaks down. The best way of doing this is to model what you want by creating some interactive annotation and then output the annotation file to see what Jalview created.
Jim
ps. thanks for the suggestion re the find command - there is an outstanding feature request about this… perhaps you’d like to locate and vote for it over at issues.jalview.org ?
···
Hi Mark - I’m guessing you are using the ‘nextrel’ build - which is alpha at best.