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Recipe: shiftit0
Created by jeff101 25 65
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Name: shiftit0
ID: 101321
Created on: Wed, 08/12/2015 - 09:22
Updated on: Thu, 08/13/2015 - 20:02

8/13/15 238pm *0f.txt code

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jeff101's picture
User offline. Last seen 4 hours 13 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
What does shiftit0 do?

The goal of shiftit0 is to move each alpha-carbon
to another alpha-carbon's position using bands.
It was made in response to the following posts:

Allow Delete and Add on design puzzles

Insert/Delete in Design Puzzles

Tool suggestions
where susume said:

To advance the amino acids one place along the spiral of a helix,
change the helix to sheet and use the tweak tool to advance the
curled sheet one position. Then change it back to helix.

Create hoops (like bands, but the protein can slide through them)

Power Shift 1.0.1 - Brow42

jeff101's picture
User offline. Last seen 4 hours 13 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
How to use shiftit0?

The image on the left below shows the results of a shiftit0 run done on puzzle 1119 after resetting the puzzle, resetting its secondary structure (not auto structures), and using clashing importance=1, low wiggle power, no frozen, and no bands. This run used the default settings for shiftit0. The image on the right was made by resetting the puzzle, and resetting its secondary structure (not auto structures). Both images were colored by rainbow and rendered as cartoon without showing the sidechains.

The Recipe Output (from scriptlog.default.xml) from the above shiftit0 run is listed below:

Running shiftit0 at 08/13/15 14:42:02 on puzzle ID 2000983
   1119: Revisiting Puzzle 84: Giant Anemone
   w/score=3370.234, 49 residues, and 0 user-supplied bands.
sqrt(2)=1.414 sqrt(3)=1.732 pi=3.142.
th4d=109.47 and th8d=70.53 degrees.
Since abands=1-6 means 1 2 3 4 6 8, abands=1 becomes 1.
Got the inputs: nstep=1 aaperstep=10 aaperband=1
   input_dir=1 dir=1 newss=H nwigs=100 wigway=3
   abands=1 rand_orient=0 blen=10 bstr=10 rtiny=0.001
   keep_bands=1 verbose=0 and rand_seed=1439494922.
bxyz=unnormalized band vectors:
   0 0 0 
nbdots=dot products of normalized band vectors:
angmat=angles in degrees from dot products:
Step 1 of 1 starts at 08/13/15 14:43:30 w/score=3370.234:
   Keeping just 0 bands.
   Now have 39 bands on the protein.
   Score=3370.234 at 08/13/15 14:43:37.
   Next global wiggle the backbone 100 times.
   Score=402.093 at 08/13/15 14:49:33.
   Next local wiggle the backbone 100 times.
   Score=402.103 at 08/13/15 14:50:00.
   Step 1 of 1 ends at 08/13/15 14:50:00 w/score=402.103.
End of shiftit0 at 08/13/15 14:50:00 w/score=402.103 and 39 bands.

Click on the image below for a clearer view:

jeff101's picture
User offline. Last seen 4 hours 13 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
shiftit0 has many input options:

shiftit0 is still in the development stage,
so it has many options for input values.
I haven't tested them all extensively,
so please e-mail me to let me know
if you have problems with anything.

One goal is to adapt shiftit0 to
do similar things in mutation puzzles.
It would mutate amino acids and put bands
on their sidechains to shift residues while
preserving their sidechain identities and orientations.

If you have suggestions for future versions of shiftit0,
please let me know. If you code them yourself,
please share the results as Public Recipes.


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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons