Include Blueprint Tool and Rama Map in all puzzles

Case number:845813-2007751
Topic:Game: Tools
Opened by:jeff101
Status:Open
Type:Suggestion
Opened on:Thursday, May 9, 2019 - 22:51
Last modified:Tuesday, May 21, 2019 - 00:32

I think someone else requested this recently, but I haven't found a Feedback for it,
so here goes.

Please include the Blueprint Tool and Rama Map in all puzzles, not just Design Puzzles.
Many puzzles start with extended chains that are all sheet or loop, and the Blueprint
Tool lets us quickly convert such structures into whatever folded structures we want.
The Blueprint Tool also helps with partially-folded structures because it gives an
up-to-date and easy-to-read display of the present sequence, secondary structure
settings, and abego structure classifications for each residue, and this display
changes as the structure changes, even while recipes run.

(Thu, 05/09/2019 - 22:51  |  4 comments)


jeff101's picture
User offline. Last seen 13 hours 22 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

One qualm I have about the present Blueprint Tool is that for long
sequences, you cannot show the entire sequence on the screen at once.
Perhaps there could be an option to let the sequence wrap around onto
several lines so the entire sequence could be on the screen at once.
There could also be an option that wraps around but lets one change
which residue is at the center of the display. It would also help if the
Blueprint Tool's bounding box's height & width could both be expanded
or contracted to give a variety of box sizes.

jeff101's picture
User offline. Last seen 13 hours 22 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Being able to vary the height & width of the Blueprint Tool's bounding box 
could help monitor patterns that repeat every 20 amino acids, for example.
One could set the width so that only 20 amino acids show in each row of
the Blueprint Tool, center the bounding box on an appropriate residue,
and the next and previous rows would wrap around to show above and below 
the residue at the center of the Blueprint Tool's display.

Below is adapted from my Forum post about Designing Square Barrels
(https://fold.it/portal/node/2005553):

In Puzzle 1546, I used 2 different starting sequences & secondary structure 
settings, each with 107 residues. One of them I called Je1a:

     000000000111111111122222222223333333333444444444455555555556 
     123456789012345678901234567890123456789012345678901234567890 
     eeHeeHeeHeeHeeHeeHeeHeeHeeeeHeeeeHeeeeHeeeeHeeeeHeeeeHeeeeHe = 2nd str
Je1a=vtLvtLvtLvtLvtLvtLvtLvtLtvtvLtvtvLtvtvLtvtvLtvtvLtvtvLtvtvLt = AA seq

     00000000000000000000000000000000000000011111111
     66666666677777777778888888888999999999900000000
     12345678901234567890123456789012345678901234567
     eeeHeeeeHeeeeHeeeeHeeeeHeeHeeHeeHeeHeeHeeHeeHee = 2nd structure
Je1a=vtvLtvtvLtvtvLtvtvLtvtvLvtLvtLvtLvtLvtLvtLvtLvt = AA sequence

Je1a with rows of length 20 instead of 60 aligns the HeeeeH/LtvtvL repeats 
for residues 24-84, letting one more easily monitor them as their secondary 
structure, abego color, and even primary sequence change:

...

eeeeHeeeeHeeeeHeeeeH
tvtvLtvtvLtvtvLtvtvL 25-44

eeeeHeeeeHeeeeHeeeeH
tvtvLtvtvLtvtvLtvtvL 45-64

eeeeHeeeeHeeeeHeeeeH
tvtvLtvtvLtvtvLtvtvL 65-84

...

Je1a with rows of length 12 instead of 60 aligns the HeeH/LvtL repeats 
for residues 1-24 & 84-107, letting one more easily monitor them as their 
secondary structure, abego color, and even primary sequence change:

eeHeeHeeHeeH
vtLvtLvtLvtL 1-12

eeHeeHeeHeeH
vtLvtLvtLvtL 13-24

...

eeHeeHeeHeeH
vtLvtLvtLvtL 85-96

eeHeeHeeHee
vtLvtLvtLvt  97-107
jeff101's picture
User offline. Last seen 13 hours 22 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Sometimes when watching the Blueprint Tool during a Design Puzzle,
I've seen the secondary structure setting for a residue change.
Maybe I made this happen accidentally by clicking on the residue
at the wrong time, for example. In any event, having the Blueprint
Tool helped me notice the structure change and fix it right away.
I might not have noticed the change until much later otherwise.

Joined: 05/19/2017
Groups: None

Moreover: Building blocks being inserted into junctions between secondary structures for trial and error is really intuitive! I always wondered why I couldn't try doing that in Prediction puzzles.

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