<pre>While playing puzzle 2137, I tried using the Pick Sidechains
tool (https://fold.it/portal/node/2006271) to move some
sidechains into places more occupied by the Electron Density.
This led to some questions/suggestions about this tool:
(1) Are the Rotamers in the Sidechain Picker menu listed with
the most prevalent/common/preferred ones at the top and the
least prevalent/common/preferred ones at the bottom? Do the
ones at the top generally score higher than the ones at the
bottom?
(2) In the Sidechain Picker menu, some of the rotamers listed
have the same names. This can be confusing if I am taking notes
and then later want to redo certain things. It would be helpful
if for each rotamer listed, there was a number indicating how
far down in the list it is. Then a list like:
mtt, tpp, tmm, tmt, mtt, tpp
could instead be labelled as:
1 mtt, 2 tpp, 3 tmm, 4 tmt, 5 mtt, 6 tpp
and it would be easy to record that I picked rotamer 1 mtt
instead of 5 mtt, or rotamer 2 tpp instead of 6 tpp.
Thanks for reading!</pre></code>
(1) Yes, the Pick Sidechains rotamers are listed in order of prevalence, with the most common rotamer at the top of the list. That means the rotamers at the top tend to have a better Sidechain subscore (use the TAB key to see the subscore breakdown for a residue). But it is still possible for a more common residue will score worse overall due to the other subscores, like clashing or H-bonding.
(2) Yes, this is a serious problem with the Pick Sidechains panel. The rotamer IDs are not very good identifiers, because they are neither memorable nor unique. We actually have a fix for this in the works, but it has been delayed by other high-priority projects. Hopefully we can finish that update soon!
If the rotamers in the Pick Sidechains menu were numbered 1, 2, 3, etc.
from top to bottom, would these numbers match the "position" numbers
used in the Foldit LUA command rotamer.SetRotamer ?
Function
void rotamer.SetRotamer(integer segmentIndex, integer position)
Description
Snap the sidechain at the given segment to a rotamer.
(Range 1 to rotamer.GetCount()).
https://foldit.fandom.com/wiki/Foldit_Lua_Functions#rotamer.SetRotamer
