Hello,
I was wondering if Jalview has a solution already built in for this problem
I've been having.
We add columns to all rows in Jalview by highlighting the column to the
immediate left of the position where columns need to be added, holding down
the "Ctrl" key, and using the mouse to right click and drag the column to
the immediate right of where the columns need to be added. If there is
another method to add columns to all rows, please feel free to let me know.
When we add columns using this method, the annotation line for the
secondary structure automatically adds spaces where the new columns were
added. At the moment, it doesn't matter too much. However, when the file is
saved as a stockholm and read back into Jalview, the secondary structure
gives orange coloring which indicates that the secondary structure
information is incorrect.
The current solution to the problem is that when columns are added to all
rows in Jalview, the secondary structure must be manually changed by right
clicking the annotation and clicking "RNA Helix" to replace all of the
spaces with periods ("."). Is it possible for the Jalview program to
automatically add periods instead of spaces when columns are added so that
the secondary structure doesn't stop working correctly when saved?
I'm a teaching assistant in Dr. Gutell's computational biology course at UT
Austin. We are trying to reduce the amount of time spent fixing alignments
due to these specific insertion issues. Is it possible for this issue to be
resolved before classes start at the end of August?
Thanks,
Vaish
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