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Recipe: Quickfix 3.5.5
Your rating: None Average: 4.6 (114 votes)


Name: Quickfix 3.5.5
ID: 100698
Created on: Mon, 02/16/2015 - 20:56
Updated on: Tue, 06/04/2019 - 18:02

Option to keep freezes and bands, manage slow filters

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Joined: 09/24/2012
Groups: Go Science

More idealize functions in case of small idealize score
Idealize starts only after first normal loop (starts with original Quickfix)
Disjunct list in order not to repeat always same thinks (but regular disjunct reset in order to find new worst).
2 filer management options (filter only for scoring or always but wiggling)
Quick shake action on low clashing score.
Each loop, the threshold is changed: can be used overnight, still gaining micropoints (only ok if you absolutely want to keep this structure - ok for design or de novo on a beautiful structure)
Record of big steps (when stopping, undo 2-5 times in order to select what you prefer)
Result recorded in note for a free segment

Used to: see original (fixing after manual changes). I use it on start design puzzle, freezing helixes ans sheets, for fragment score enhancement. Then unfreezed, overnight.
I use it on all puzzle, start, middle and end game to try to eliminate red segments on relative scores.

Joined: 09/24/2012
Groups: Go Science

ShBug fixed for puzzle with ligand

Joined: 09/24/2012
Groups: Go Science

Fixed quadruplet out of range

Added new Cut Worst function
The idea is to select the worst quadruplets (bellow a certain threshold), to cut inside or before or after it, wiggle all, uncut, wiggle all.

This function is activated only after several loops (when the protein is stable enough), or after 3 loops when points are above 9000. The default is no activation ("never run wiggle all"), because this function could explode the protein. The default option is thus like original QF3.2

When button "never wiggle all" is unchecked and score is above 9000, loop 4 cuts inside the worst zones, loop 5 cuts inside and then before, further loops cut inside, before then after the worst zone.

I tested this new "CutWorst" function on end puzzle and it gained some unexpected micro points. It seems that all strategies (inside, outside) are able to gain points, so that I did not make it an explicit option.

Joined: 09/24/2012
Groups: Go Science

unnoticed sym bug fixed

Joined: 09/24/2012
Groups: Go Science

Better filter management (case option filter enabled)

Joined: 09/24/2012
Groups: Go Science

More options to better protect parts of protein (see dialog)
New functions:
-rebuild worst ideality
-shake or mutate worst hiding & worst clashing
Mutate worst only (instead of mutate all including freezed in original version)

Joined: 09/24/2012
Groups: Go Science

Recognizes contact puzzles as filtered puzzles (which allows filter management options)

Joined: 09/24/2012
Groups: Go Science

Fixed bug keep freezed backbones

Joined: 09/24/2012
Groups: Go Science

Sorry, fixed bug keep freezed

Joined: 09/24/2012
Groups: Go Science

Disable undo graph in order to save time
Fixed unideal loop bug

Joined: 09/24/2012
Groups: Go Science

3.3.5: reduce the number of movements in sketchbook puzzles
3.3.6: more big steps saves and more undos left (can be useful for filtered puzzles, in order to retrieve a result with correct filter bonus)

Joined: 09/24/2012
Groups: Go Science

Check for no high filter cost on filtered puzzles

Joined: 09/24/2012
Groups: Go Science

Tip max filter cost / case (only available for filtered puzzles):

10-20 pts filter loss is ok (it's less than losing an ideal loop, but enough for accepting some residue scoring too low);

Set it to 999 in order to deactivate this function and save some time (it's the default for puzzles > 8-9000 pts, when filters alone are enough to select the best score)

Joined: 09/24/2012
Groups: Go Science

Trying some deep idealizing on regular basis.

Joined: 09/24/2012
Groups: Go Science

Fixed a score bug

Joined: 09/24/2012
Groups: Go Science

v3.5.2 SKETCHBOOK hard decision if score not met (to be tested): load old best
v3.5.3 small corrections
v3.5.4 fixed uncutted segments bug after several loops
v3.5.5 filter management for design puzzles

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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, RosettaCommons