Hi Mark - I'm guessing you are using the 'nextrel' build - which is
alpha at best.
On 08/07/2014 18:55, Mark A Saper wrote:
1. 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..
2. The documentation is not very clear about specifying the secondary
structure:
o NO_GRAPH
o For a row consisting of text labels and/or secondary structure
symbols.
o /{Secondary Structure Symbol}/,/text label/,/Tooltip text/
o 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 ?
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