Difficult to close cuts

Case number:845833-2010594
Topic:Game: Display
Opened by:Bautho
Status:Open
Type:Suggestion
Opened on:Sunday, October 18, 2020 - 22:15
Last modified:Friday, May 28, 2021 - 04:07

I always have to really zoom in until it actually works.
Also "show outlines" is activated

Is it possible to increase the size of the blue / yellow cut bands ?

(Sun, 10/18/2020 - 22:15  |  7 comments)


agcohn821's picture
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Hi Batz,

Thank you for this suggestion--I have passed it along to the team.

Joined: 09/29/2016
Groups: Gargleblasters

Enlarging the cut bands might be problematic due to the fact that they would then COMPLETELY drown out the Segments that had cuts on both sides, and prevent being able to interact with them at all :(

It's a bit of a kludge, but switching to Line View Mode (in View Options, right-side, second list on the right) will make them very easy to see and interact with.

Hhhmmm... Perhaps if we had a key we could hold down or toggle, that would cause everything to go transparent (like an Alignment ghost protein), EXCEPT for the Cut Bands, where then only THOSE were interactable... What do you think, Batz, would that help? (I know it'd make things easier for me, as someone who uses cuts a LOT)

Bautho's picture
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Joined: 02/16/2012
Groups: Go Science

cut bands

I use cut-bands a lot when it comes to improving bond ideality, which is really helpful.

Then selecting 2 residues and pressing "C" introduces a cut.
If it was possible to close the cut again with the same "C" when selecting the two residues again would be the most convenient.

The main problem for now is the black outlines.
The mouse only turns into a clickable finger when you zoom in enough, and not before... and even then, not in the center of the band but only at its edges.
If I turn off "show outlines" it works very well though.

Alternatively, could the black outlines just not affect the cut-bands?

jeff101's picture
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I was having trouble making and healing cuts on a recent puzzle.
The cuts were located in an interior region of the protein that
was also full of bands. It seems like right now to make cuts 
you have to select 2 adjacent segments and then press cut. It
also seems like to heal cuts you have to click on the very thin
yellow cut bands. With all the obstacles, it was hard to select
the segments or click on the cuts without accidently clicking
on one of the bands and deleting or moving it.

Below are some ideas to make it easier to make and heal cuts:

(1) In the View Menu, have an option to make normal rubber 
bands (not yellow or blue cut bands) invisible or transparent. 
This would help us see certain protein regions more clearly.
If we used bands to force hydrogen or disulfide bonds to form, 
we could also more easily see if the desired bonds have formed
(often such bonds are hidden by the bands used to make them).
If the bands are invisible, please also make them non-selectable. 
Then we won't accidently click on an invisible band and move or 
delete it. 

(2) Have a 2nd way to make cuts. Perhaps call it super-cut. 
If the user selects a large group of segments and then presses 
the super-cut button, Foldit will look for smaller sub-groups 
of adjacent selected segments and for each sub-group it will 
put a cut at each end of the sub-group. Thus, if one selects
segments 1-5, 8, and 12-17 in a 60-segment protein, super-cut
will put cuts between segments 5 & 6, 7 & 8, 8 & 9, 11 & 12,
and 17 & 18. This will free the selected segments from the
rest of the protein. After using super-cut, one could easily
do move, wiggle, or other actions on the very same selected
segments, saving a large # of mouse actions in the process.
If it isn't possible for Foldit to make the super-cut tool,
perhaps someone can make a recipe to do it. This recipe could 
even have a textbox to input which segments to select.
jeff101's picture
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Joined: 04/20/2012
Groups: Go Science

(3) Have a 2nd way to heal cuts. Perhaps call it super-heal.
It would work almost like the super-cut tool. If the user 
selects a large group of segments and then presses the 
super-heal button, Foldit will heal any yellow cuts that 
connect to any selected segment. Thus, if there were yellow 
cuts in a protein between segments 5 & 6, 7 & 8, 8 & 9, 
11 & 12, and 17 & 18, one could heal them all many different 
ways: (a) one could select all segments in the protein and 
then press super-heal, (b) one could select just segments 
5, 8, 12, & 18 and then press super-heal, (c) one could 
select just segments 6-17 and then press super-heal, etc. 
It might be possible to code super-heal as a recipe. If so, 
it would help to have a textbox accept input like "5 8 12 18" 
for example (b) above and "6-17" for example (c) above. 
Nevertheless, to make such a super-heal recipe, we may need 
new LUA commands for cuts: one to determine which pair of 
segments each cut connects and another to determine which 
cuts are yellow (and so healable).

Thanks for reading,
Jeff

Bautho's picture
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This third one would be awesome!

If we had a list similar to the rotamers list, just with cuts and then you can say "heal" for the ones you like to (with e.g. zoom in).

Otherwise writing a LUA script to just heal cuts sounds like an easy task for the ones who can (I can't :D )

jeff101's picture
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Joined: 04/20/2012
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To any who wish to make supercut or superheal
recipes, the wiki page below looks helpful:

https://foldit.fandom.com/wiki/Foldit_Lua_Function_structure.GetCuts

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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