(6.1) At 8:39 in Susume's Rama Map #2 - Copying a Loop
video (https://www.youtube.com/watch?v=o4ZOY8MBG9g),
the 3D view of the protein is colored using the
ABEGO color scheme. I see red, blue, green, and
yellow regions there, as if each residue has its
dihedral angles in its amino acid's preferred
region of the Rama Map. What color is used in the
ABEGO color scheme for a residue with dihedral
angles outside its amino acid's preferred region,
where the Rama Map will be white? I think there
should be a 5th color (not red, blue, green, or
yellow) on these residues in the 3D view of the
protein.
Also at 8:39, the Rama Map shown has 2 points along
the x axis and 1 point along the y axis. One of the
points along the x axis should be one end of the
protein, and the point along the y axis should be the
other end of the protein. The 3D view of the protein
has a yellow triangle at one end (the top of the
left-most strand) and a red triangle at the other end
(the top of the 2nd strand from the right). Do these
colors make sense compared to where these residues
appear on the Rama Map?
These questions are related to (6) above because if a
5th color is used in the ABEGO color scheme, one can
quickly tell which residues of the protein have dihedral
angles outside their amino acids' preferred regions
(just look for the residues with this 5th color in the
3D view of the protein).
The image below is from Susume's Rama Map #2 - Copying a Loop
video at 8:39 (https://www.youtube.com/watch?v=o4ZOY8MBG9g)
There are also some suggestions in the comments to the rama map blog post: http://fold.it/portal/node/2002173
It would also help the developers and scientists if we could (in future feature updates) give a try and keep the suggestions in the same thread*, so that they are less likely to get lost and easier to track for the team. :)
(8.1) In lieu of commands like GetPhiPsi and SetPhiPsi that read or set the dihedral angles to particular values, it would be useful to have a way to reset the dihedral angles for a large group of residues to the same values. Then players could easily make any of the 3 linear groups (p.21 fig.8) or 5-10 main regions of the Rama Map (p.10) discussed on pp.6-8,10-11,21 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398/ and cited by Susume at http://fold.it/portal/node/2002349
Manually, one could select a large group of points (residues) on the Rama Map and then drag them all simultaneously to a single point on the Rama Map. In LUA, there could be a command like CopyPhiPsi(goal_res,selected_res) that would copy the dihedral angles from residue number goal_res to all the residue numbers in the array selected_res.
These copy functions would make life easier for players without giving us access to the numerical values of the dihedral angles.
bump,
Actually, it would be great to see all 1-10 suggestions implemented.
The most I would personally use are 6 and 10 but all would be great.
Bump. Suggestion (8.1) above would come in handy in the poly-proline puzzles.
Earlier today I tried to make a bunch of extra proline residues have dots
in the Rama Map where the poly-proline helix's dots lie. In the end, I
dragged these dots one by one into the desired spot on the Rama Map. It
would have been nice if I could have selected all these proline residues
using the Selection Interface and then dragged all of their Rama Map dots
into the desired spot simultaneously.
(11) Would it be possible to have a View Option that
lets us switch between the normal black & white dots
on the Rama Map and a set of Rama Map dots colored
the same way the backbone residues are colored on
the main rendering of the protein? This way, we could
have the Rama Map dots colored by Rainbow to show the
order of the residues, by Hydro to show hydrophobic
& hydrophilic residues, by Score to show which
residues are scoring well, by AAColor to show which
amino acid types have which phi,psi angles, etc.
(11.1) If we switch the Rama Map dots from
black and white to color, let Foldit also
change the background colors in the Rama Map
from red, yellow, green, and blue to different
shades of gray. This should help us more
easily see the colored Rama Map dots.
