# Please review the proposed puzzles for the initial OpenCRISPR round **URL:** https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861 **Category:** Uncategorized **Created:** [August 14, 2017, 11:25pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861 "2017-08-14T23:25:00Z") **Posts on this page:** 20 **Page:** 3
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 16, 2017, 7:10pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/60 "2017-08-16T19:10:00Z")
**FMN 1a - ON** In NuPACK with FMN bound in state 2 the guide sequence from nt 14-20 mispairs with nts 135-148 ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 16, 2017, 7:16pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/62 "2017-08-16T19:16:00Z")
Yes, that’s seems to be the the typical symptom.  By strengthening the desired folding, I can satisfy state 2 (complete with DNA binding) in NUPACK, but haven’t been able to satisfy both states at the same time. ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 16, 2017, 7:30pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/63 "2017-08-16T19:30:00Z")
**NuPACK** **FMN 1a - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGGAGGAUAUACAAAGAGUAUGAUGAUGAGAUGUAUUCAUCUCAUCAUCGUACUCAAACAUGAGGAUCACCCAUGUAGAAGGCCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 16, 2017, 7:42pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/64 "2017-08-16T19:42:00Z")
**NuPACK** **FMN 1b - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACAAGAAGGUACAAAACAUGAGGAUCACCCAUGUAAGGCUAGAGUUAUGAAUUCAUAGCUCUAGCCAAUACAUAGUGAGGAUAUUGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 16, 2017, 7:59pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/65 "2017-08-16T19:59:00Z")
**NuPACK** **FMN 1b - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGCAGAAGGUAUAUAUUAAUUCUUAAGAUGUAGACUGUCUAUUGAUAGUCUACAUCAACAUGAGGAUCACCCAUGUAAGGAUAUGCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 16, 2017, 9:35pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/66 "2017-08-16T21:35:00Z")
**NuPACK** **FMN 2 - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUGUCAAACAUGAGGAUCACCCAUGUAAUGAAGGAUAUGAGUAUUCUCAGAAGGUCAUCAUGUUAUAAAUAAAUGAGAUAUAGACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU An admittedly ugly design, still with all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 **NuPACK** **FMN 2 - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCGCAUUUAUAACAUGAGGAUCACCCAUGUAGGAUAUGCGUAUUCGCAGAAGGACGUGGAAGUAGACUGAUUCAGUCUACAGCGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 **NuPACK** **FMN 3 - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACAACAUGAGGAUAUGUGUAUUCACAGAAGGCAUAAGAUGAUGUAUUCAUCAUCAAUACAUGAGGAUCACCCAUGUUUUAUGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 **NuPACK** **FMN 3 - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACGCAAAUGUAGGAUAUCUGGAUUCAGAGAAGGACAUGAGGAUCACCCAUGUAAGACUAGAGAUGAUUCAUCUCUAGUCAAAUGCGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 **NuPACK** **FMN 4 - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGGAGAGGUUGCUCAACAUGAGGAUCACCCAUGUAGGAAAGCCUUAGGCAUCAAGGAUAUCGUUUCUACGAGAAGGUGAGUACCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 **NuPACK** **FMN 4 - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACAAGAUGAUCGAGACUAUUGUCUCGAUCAUCAACAUGAGGAUCACCCAUGUAGGAUAUCAGGAUUCUGAGAAGGGCAUGAGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU With all other constraints met, in state 2 the guide sequence from nt 11-20 mispairs with nts 135-148 ---
### Author: ![yulan](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/y/df705f/32.png) [@yulan](https://forum.eternagame.org/u/yulan) #### Post date: [August 17, 2017, 2:01pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/67 "2017-08-17T14:01:00Z")
For **NuPACK**** TEP 3 & 4** : having a hard time solving both On and OFF (with Vienna solving came quite easily)… I’ll keep trying ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 17, 2017, 5:17pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/69 "2017-08-17T17:17:00Z")
Thank you Andrew, for continuing to post these.  Nando and I have discussed the issue, and he is going to experiment with tweaking the NUPACK parameters to see if it brings the predictions more in line with Vienna’s.  But then, it may be NUPACK that better predicts what will actually happen in the lab. In either case, your solutions will be an important part of making that judgement call. ---
### Author: ![josegp](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/j/e47774/32.png) [@josegp](https://forum.eternagame.org/u/josegp) #### Post date: [August 17, 2017, 10:00pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/70 "2017-08-17T22:00:00Z")
Thanks Nando ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 17, 2017, 11:09pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/71 "2017-08-17T23:09:00Z")
Status on the NUPACK issue:  Nando has confirmed that NUPACK is doing something wonky on the CRISPR puzzles.  He has experimented with the NUPACK-specific puzzle definitions (which account for why you may find that sequences you posted yesterday are folding differently in NUPACK today), and that doesn’t seem to fix things.  But he hasn’t given up yet. ---
### Author: ![yulan](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/y/df705f/32.png) [@yulan](https://forum.eternagame.org/u/yulan) #### Post date: [August 18, 2017, 4:23pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/72 "2017-08-18T16:23:00Z")
**NuPACK**** TEP 3 & 4** still not able to solve either On or OFF… offcourse I’m not that experienced nor systematic (yet)… Also, behavior of folding seems erratic with small mutations, not sure how to describe what I’m seeing: folding jumps all over the place, smaller molecule often falls off in state 2 when other restraints are being met… Fun to see differences between engines though and great to be able to look at these lab candidates already (much needed good practice) ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 18, 2017, 5:26pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/73 "2017-08-18T17:26:00Z")
Great news!  Nando found and fixed a bug in the NUPACK-specific code.  Here’s a slight mod to Andrew’s solution for FMN 4 - ON that works for all three folding engines: GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGGAGAGGUUGCUCAACAUGAGGAUCACCCAUGUAGGAAAGCCUUAGGCAUCAGAAGGCGCGUUUCUGCGAGGAUAUGAGUACCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU ![](https://d2he8ud106d9gn.cloudfront.net/original/2X/e/ed3780f947802a2487ad60f9acb5be28cbb10dc1.png "Image https//d2r1vs3d9006apcloudfrontnet/s3\_images/1637835/RackMultipart20170818-127915-1pk7e54-Screen\_Shot\_2017-08-18\_at\_101520\_AM\_inlinepng1503076746") You will probably need to flush your browser cache to get everything up to date. I suspect and hope that it won’t be difficult to get NUPACK solutions now.  But for a thorough test, it would be a relief if we could get confirmation that every puzzle has a NUPACK solution now.  Even better would be a solution for each puzzle that satisfies all three folding engines, but that’s not necessary.  So if you keep testing and posting, Eli and I will continue to keep the spreadsheet up to date. ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 18, 2017, 5:31pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/74 "2017-08-18T17:31:00Z")
Ah!  There’s been another change in some of the FMN puzzles.  Eli brought our attention to the fact that past experimental results have strongly indicated that rotating the FMN aptamer in FMN puzzles 2-4 would be beneficial.  So that change is also made, and explains why past solutions to those puzzles will now fail. ---
### Author: ![Omei](https://forum.eternagame.org/user_avatar/forum.eternagame.org/omei/32/4420_2.png) [@Omei](https://forum.eternagame.org/u/Omei) #### Post date: [August 18, 2017, 5:46pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/76 "2017-08-18T17:46:00Z")
One more thing – If you’ve already worked on an FMN puzzle that has been changed, you’ll also need to reset the puzzle, in addition to clearing the browser cache. ---
### Author: ![Astromon](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/a/b77776/32.png) [@Astromon](https://forum.eternagame.org/u/Astromon) #### Post date: [August 18, 2017, 11:48pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/78 "2017-08-18T23:48:00Z")
ok. ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 19, 2017, 7:37am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/79 "2017-08-19T07:37:00Z")
**FMN 1a - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACGCAGGAUAUGAGUUCACAUGAGGAUCACCCAUGUAAAACCUUUAGUUGGAGAUUCUCCGACUAAGGUUGAUCUUCAGAAGGGCGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU Solution works in all 3 models. ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 19, 2017, 4:16pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/80 "2017-08-19T16:16:00Z")
**FMN 1a - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGAAGGAUAUGCAAGGAGUAUGAUGAUGAGAUGUAUUCAUCUCAUCAUCGUACUCAAACAUGAGGAUCACCCAUGUAGAAGGUCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU Solution works in all 3 models. ---
### Author: ![Astromon](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/a/b77776/32.png) [@Astromon](https://forum.eternagame.org/u/Astromon) #### Post date: [August 19, 2017, 6:32pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/81 "2017-08-19T18:32:00Z")
Is there a new link to the updated Fmn CRISPR puzzles or does deleting eterna flash take care of it? ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 19, 2017, 6:45pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/83 "2017-08-19T18:45:00Z")
I had to delete my browser cookies Astro, I’m using chrome. ---
### Author: ![AndrewKae](https://forum.eternagame.org/user_avatar/forum.eternagame.org/andrewkae/32/4570_2.png) [@AndrewKae](https://forum.eternagame.org/u/AndrewKae) #### Post date: [August 19, 2017, 7:01pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/84 "2017-08-19T19:01:00Z")
**FMN 1b - ON** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACAAGAAGGUACAAAACAUGAGGAUCACCCAUGUGAAGAAUAGAGUUAUGAAUUCAUAGCUCUAUGGUUACAUAGUGAGGAUAUUGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU Solution works in all 3 models. **FMN 1b - OFF** GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGCAGAAGGUAUAUAUUAAUUCUUAAGAUGUAGACUGUCUAUUGAUAGUCUACAUCAACAUGAGGAUCACCCAUGUAAGGAUAUGCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU Solution works in all 3 models. [Previous page](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861.md?page=2) [Next page](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861.md?page=4)