UNDER CONSTRUCTION
What are the various secondary structural assignment codes used by SST?
C =
COIL
E =
Strand of SHEET
G =
RIGHT-handed 3_10 helix
H =
RIGHT-handed ALPHA helix
I =
RIGHT-handed PI helix
g =
LEFT-handed 3_10 helix
h =
LEFT-handed ALPHA helix
i =
LEFT-handed PI helix
3 =
3_10-like TURN (right/left-handed)
4 =
ALPHA-like TURN (right/left-handed)
5 =
PI-like TURN (right/left-handed)
T =
Uncharacterized TURN
- =
UNASSIGNED residue
| =
SSE start/end boundary -- Note: end point of one SSE is the start point of the next
: =
Point were a (usually right-handed alpha) helix begins to tighten or loosen -- indicative of a 3_10 or pi helical cap/end
How do I download the results generated by SST?
The assignment output shown in the scrollable text area on results page can be downloaded via the link directly above that area.
How do I download a pymol script for my run with secondary structural assignments loaded as selections?
Above the scrollable text area on the results page where the assignment results are displayed is a link 'Click to download pymol script with assignments'. Clicking this link will download a tarball containing (1) the structure you submitted (renamed as 'struct.pdb') along with (2) the pymol script (called struct.pdb_Seg.pml) containing SST assignments. Running pymol on the script on your local machine will generate a cartoon with each assigned region/segment shown as a selector.
When I rerun a structure, the colors of various assignments in the pymol script change, why ?
Colours are assigned to various secondary structural regions randomly. Also, since SST is still evolving, it is important to keep track of the version number of SST (latest is version 1.6) if you are rerunning after a while has passed. This information can be gathered from the header part of the text output displayed on the results page. This may cause the assignments to (slightly) differ between versions.
Can I download a standalone version of SST?
Not yet, but this will soon be made available. In the meantime contact Arun Konagurthu to request a command line access to SST.
Who do I contact to report a bug, or request a feature?
How do I cite SST?
A. S. Konagurthu, A. M. Lesk, L. Allison, Minimum Message Length inference of secondary structure from protein coordinate data. Bioinformatics 28(12):i97-i105 (2012)