I saw the latest great video from Susume. But you need quite chance to find the sheets and other macro-structures with this method.
What would be great is the following tool:
-Like for medical scanner navigation: a slice navigation tool. You have a 2D slice (of even a tick slice or ships) that crosses the density and you can move it forward or backward. You don't see anything else than this slice. You don't need any segment inside of the cloud if you ant to explore the cloud (nice if you build your SS outside the cloud and you want to explore the cloud on mid game).
It would be more quick than Shift-Q then hide backward and front. Then try again with another shift-Q (where you need always some segment to focus on).
-Option completely hiding the puzzle (not the cloud), like we can hide the cloud not the puzzle.
and this would also be great:
http://fold.it/portal/node/2001413
and/or a tool that could help "putting the sheet into its cloud":
Shif-Q on a segment (of the sheet for example). Then you can anker the slice on this segment. When you move the segment, the focus follows the segment - or better the number of selected segments (as if you move and shift-Q in parallel).
I wish it were easier to navigate the Z direction.
This inspired me to play around with the controls. Place a small piece of protein in the cloud. Mouse over it and hit Shift-Q to give it the focus. Bring up the Move tool on that piece. Use Shift-drag on the purple tool to move the piece in the Z dimension - the camera focus will follow it into and out of the screen, letting you move forward and back through the cloud. Not great, but maybe it's better than having to roll 90 degrees and back to move through that dimension.
Indeed it does…I have used this method for some time (think I referred to it last night when discussing yr excellent vid Subsume)
In the most recent Developer Chat
(http://fold.it/portal/node/2002210)
from 15:10-15:21, bkoep and jflat06 discussed
letting players "trim unwanted residues" in
electron density puzzles so that their electron
densities would match the experimental electron
density better.
If the trimmed residues are at the end of the
protein chain, this seems fine to me, but if
the trimmed residues are in the middle of the
protein chain, things get more complicated. If
you remove the trimmed sidechains, maybe you
lose some hydrogen bonds or create more voids
in the protein. If you remove the trimmed backbones
too, you might need to apply some constraints so
that the remaining parts of the protein chain stay
a reasonable distance apart.
Perhaps a better way is to make like an
invisibility cloak around the residues you want to
trim. The trimmed residues are not really removed
from the protein chain. Instead, the trimmed residues
behave like they normally do and give normal
Rosettta/Foldit scores, but the invisibility cloak
sets all of their calculated electron densities to zero.
In the "Electron Density" menu above, would it be possible to have several options as below:
One option (the default) shows both the protein and the experimental electron density the normal way, based on settings in the "View" menu for the protein and based on settings in the "Electron Density" menu for the electron density (ED).
Another option makes the experimental electron density disappear and calculates what ED the present protein conformation would give. It then renders the calculated ED the way it would normally render the experimental ED.
Perhaps a 3rd option would make the present protein conformation disappear and would render both the experimental and calculated ED's the normal way, based on the settings in the "Electron Density" menu. If the experimental and calculated ED's could be shown with different shades or colors, I think that would help.
With options like these, players could force the protein into all beta-sheet and then see what the ED would look like for all beta-sheet. Similarly, players could try all alpha-helix and then see what the ED for all alpha-helix looks like. Players could force disulfide or hydrogen bonds to form and then calculate what the ED would look like. I think this would open new ways for players to do ED puzzles.
Ideally, the closer the present protein conformation is to the desired one, the more similar the calculated ED will be to the experimental ED.
Thanks for reading!
