# Gameplay and Strategies **URL:** https://forum.eternagame.org/c/gameplay-and-strategies/6.md?page=1 [Latest](https://forum.eternagame.org/latest.md) · [Categories](https://forum.eternagame.org/categories.md) · [Tags](https://forum.eternagame.org/tags.md) **Page:** 2 --- ## [Describing direction in secondary structure](https://forum.eternagame.org/t/describing-direction-in-secondary-structure/4421)
**Author:** [@Hearsall](https://forum.eternagame.org/u/Hearsall)\ **Replies:** 8\ **Last updated:** [January 4, 2023, 11:35am UTC](https://forum.eternagame.org/t/describing-direction-in-secondary-structure/4421 "2023-01-04T11:35:46Z")
Is there any established terminology for describing direction in secondary structures? Primary structure has “upstream” and “downstream” but I haven’t seen any equivalent for secondary structure. In relation to boosting… --- ## [Puzzles with incorrect structure at 0 kcal?](https://forum.eternagame.org/t/puzzles-with-incorrect-structure-at-0-kcal/4308)
**Author:** [@Merida](https://forum.eternagame.org/u/Merida)\ **Replies:** 3\ **Last updated:** [September 17, 2022, 12:29pm UTC](https://forum.eternagame.org/t/puzzles-with-incorrect-structure-at-0-kcal/4308 "2022-09-17T12:29:14Z")
Just posting because I’m curious to know what’s happening. (Please forgive me if this topic has been covered already.) In my quest to conquer the Eterna 100, I’ve come across two puzzles in which I’ve found a sequence t… --- ## [Eternacon 2022 presentations and links](https://forum.eternagame.org/t/eternacon-2022-presentations-and-links/4276)
**Author:** [@DigitalEmbrace](https://forum.eternagame.org/u/DigitalEmbrace)\ **Replies:** 21\ **Last updated:** [August 26, 2022, 8:39pm UTC](https://forum.eternagame.org/t/eternacon-2022-presentations-and-links/4276 "2022-08-26T20:39:09Z")
Please share slide decks and links from Eternacon presentations for further reading and learning. --- ## [New Functionality Added to Eterna NUPACK Folding Engine is Live](https://forum.eternagame.org/t/new-functionality-added-to-eterna-nupack-folding-engine-is-live/4246)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 11\ **Last updated:** [August 5, 2022, 2:44am UTC](https://forum.eternagame.org/t/new-functionality-added-to-eterna-nupack-folding-engine-is-live/4246 "2022-08-05T02:44:18Z")
Hello Fellow Eterna Players, Jonathan merged the Eterna source code with the additions I made to the NUPACK calls. These calls exposed the subopt utility found in nupack and allows us now to see the data in-game through… --- ## [First 2 chapters of Draft of new RNA document (book?) Looking for thoughts and wanted to share early](https://forum.eternagame.org/t/first-2-chapters-of-draft-of-new-rna-document-book-looking-for-thoughts-and-wanted-to-share-early/4219)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 12\ **Last updated:** [June 29, 2022, 11:17pm UTC](https://forum.eternagame.org/t/first-2-chapters-of-draft-of-new-rna-document-book-looking-for-thoughts-and-wanted-to-share-early/4219 "2022-06-29T23:17:23Z")
Hi Eterna, I finally got around to writing my new RNA document and it is turning out to be a book… Im dumping everything I have learned and figured out over 10 years? of research on the partition function and the ensemb… --- ## [Developing new psuedoknot logic for Nupack 3.0.4 aka Eterna's version for pknot labs and looking for testers](https://forum.eternagame.org/t/developing-new-psuedoknot-logic-for-nupack-3-0-4-aka-eternas-version-for-pknot-labs-and-looking-for-testers/4253)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [June 26, 2022, 3:48am UTC](https://forum.eternagame.org/t/developing-new-psuedoknot-logic-for-nupack-3-0-4-aka-eternas-version-for-pknot-labs-and-looking-for-testers/4253 "2022-06-26T03:48:34Z")
Hi Eterna, I organically decided to write this post as I could use some help soon and wanted to make sure everyone understands the limitations of pknots in nupack code. So to start, if you read through the papers that … --- ## [First 4 chapters of RNA book on energies and mechanics](https://forum.eternagame.org/t/first-4-chapters-of-rna-book-on-energies-and-mechanics/4228)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 1\ **Last updated:** [June 6, 2022, 10:25pm UTC](https://forum.eternagame.org/t/first-4-chapters-of-rna-book-on-energies-and-mechanics/4228 "2022-06-06T22:25:58Z")
Here is a new draft in which I have connected the RNA energy world and nucleotide bonds to the first 3 laws of physics as part of a connection to statics and then mechanics of materials. It also explains the ensemble and… --- ## [Nucleotide Ensemble Variation shows strong signal for designs with higher fold change](https://forum.eternagame.org/t/nucleotide-ensemble-variation-shows-strong-signal-for-designs-with-higher-fold-change/4226)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [May 23, 2022, 4:51pm UTC](https://forum.eternagame.org/t/nucleotide-ensemble-variation-shows-strong-signal-for-designs-with-higher-fold-change/4226 "2022-05-23T16:51:47Z")
I can all of R101 PNAS paper through the NUPACK script I posted last night and plotted the EV\_classic\_norm deltas for 1,2, and 3 kcal and then compared that to nupacks ensemble defect. I found a clear signal with the EV … --- ## [First version of NUPACK 4.0 jupyterlabs script with MFE and ensemble info](https://forum.eternagame.org/t/first-version-of-nupack-4-0-jupyterlabs-script-with-mfe-and-ensemble-info/4224)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [May 23, 2022, 1:42am UTC](https://forum.eternagame.org/t/first-version-of-nupack-4-0-jupyterlabs-script-with-mfe-and-ensemble-info/4224 "2022-05-23T01:42:06Z")
Hi Eterna, I hope you all enjoy this. This is a jupyterlabs script in python that you can enter the sequence for a single state RNA as well as enter the temp you want to use. You have a choice of energy parameters from … --- ## ["L" mode in design mode](https://forum.eternagame.org/t/l-mode-in-design-mode/4103)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 0\ **Last updated:** [January 26, 2022, 2:55pm UTC](https://forum.eternagame.org/t/l-mode-in-design-mode/4103 "2022-01-26T14:55:44Z")
This isn’t a bug report, etc, just something interesting, a FYI: No fix required. It could also be a “me” thing. “L” mode doesn’t work in design mode for me but I found out how to get there. Here is a way to get “L” mo… --- ## [Randomize](https://forum.eternagame.org/t/randomize/4065)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 2\ **Last updated:** [December 21, 2021, 10:01pm UTC](https://forum.eternagame.org/t/randomize/4065 "2021-12-21T22:01:39Z")
Ok. I can select NT’s to randomize, I see them blinking after selecting the randomize icon. Then what do I do to “scroll” though the random combinations. --- ## [Annotations](https://forum.eternagame.org/t/annotations/4060)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 22\ **Last updated:** [December 21, 2021, 4:23pm UTC](https://forum.eternagame.org/t/annotations/4060 "2021-12-21T16:23:25Z")
I decided to use Annotations by actually reading the directions. Below will be my notes as I climb to the top of my learning curve. The video is a good starting place: https://youtu.be/x4oilwvwnK0 --- ## [Eterna3D Ribosome and beyond](https://forum.eternagame.org/t/eterna3d-ribosome-and-beyond/3978)
**Author:** [@DigitalEmbrace](https://forum.eternagame.org/u/DigitalEmbrace)\ **Replies:** 17\ **Last updated:** [October 2, 2021, 3:41pm UTC](https://forum.eternagame.org/t/eterna3d-ribosome-and-beyond/3978 "2021-10-02T15:41:26Z")
We got our first look today at the new 3D model being developed for in-game visualization. In case you missed the town hall, here are two images the developer Pragya shared with me. I’m wondering if tertiary bonds … --- ## [Database of ribosomal mutations and their effects on experimental viability](https://forum.eternagame.org/t/database-of-ribosomal-mutations-and-their-effects-on-experimental-viability/3931)
**Author:** [@IndoleScroll](https://forum.eternagame.org/u/IndoleScroll)\ **Replies:** 1\ **Last updated:** [July 31, 2021, 2:32am UTC](https://forum.eternagame.org/t/database-of-ribosomal-mutations-and-their-effects-on-experimental-viability/3931 "2021-07-31T02:32:22Z")
Hi. I wanted to share the link to this database with everyone. It is a database of mutations to the 23s and 16s rRNA and their effects on lab viability. The database has not been updated since 2000 and unfortunately i… --- ## [Next-generation sequencer, level 1](https://forum.eternagame.org/t/next-generation-sequencer-level-1/3801)
**Author:** [@jrtuenge](https://forum.eternagame.org/u/jrtuenge)\ **Replies:** 3\ **Last updated:** [February 10, 2021, 12:49am UTC](https://forum.eternagame.org/t/next-generation-sequencer-level-1/3801 "2021-02-10T00:49:59Z")
I’m stuck here… any help would be appreciated! --- ## [A New Trick For Solving Puzzles: Catalyst Points](https://forum.eternagame.org/t/a-new-trick-for-solving-puzzles-catalyst-points/1855)
**Author:** [@starryjess](https://forum.eternagame.org/u/starryjess)\ **Replies:** 17\ **Last updated:** [February 8, 2021, 10:27pm UTC](https://forum.eternagame.org/t/a-new-trick-for-solving-puzzles-catalyst-points/1855 "2021-02-08T22:27:49Z")
lroppy coined the term “boost points” a while ago (a red or green nucleotide put in a loop that lowers the energy of a loop), but since then, thanks to Brourd’s insightful puzzles, we have become aware of another way to … --- ## [Every boost in EternaFold](https://forum.eternagame.org/t/every-boost-in-eternafold/3508)
**Author:** [@ch1ck3n](https://forum.eternagame.org/u/ch1ck3n)\ **Replies:** 3\ **Last updated:** [January 19, 2021, 10:33pm UTC](https://forum.eternagame.org/t/every-boost-in-eternafold/3508 "2021-01-19T22:33:58Z")
Introduction Everything else introduction As we all know, EternaFold is OUT!!!!!! But, everything is wrong. the boosts is wrong. I have made a puzzle that shows how to get the lowest energy possible on hooks and loops… --- ## [Understand between engines](https://forum.eternagame.org/t/understand-between-engines/3758)
**Author:** [@Xnessax](https://forum.eternagame.org/u/Xnessax)\ **Replies:** 2\ **Last updated:** [January 30, 2021, 11:42pm UTC](https://forum.eternagame.org/t/understand-between-engines/3758 "2021-01-30T23:42:27Z")
Hello! i’d liek to invite you guys to ask to me a suggest of edition with my part. maybe can you give some ideas to me to do some more on docs… i’m too slowly sorry when i noticed I woke up earlier it changes my brain he… --- ## [Quad Identity in vienna](https://forum.eternagame.org/t/quad-identity-in-vienna/3740)
**Author:** [@Abinmorth](https://forum.eternagame.org/u/Abinmorth)\ **Replies:** 1\ **Last updated:** [December 13, 2020, 1:25am UTC](https://forum.eternagame.org/t/quad-identity-in-vienna/3740 "2020-12-13T01:25:43Z")
so I was basically noting down all possible quads in excel and comparing the energies. one interesting fact I noticed is, that for all quads the energy stays the same if you rotate the quad by 180 degree. so-GC-----has… --- ## [Game rules explained](https://forum.eternagame.org/t/game-rules-explained/3694)
**Author:** [@gregoriusz](https://forum.eternagame.org/u/gregoriusz)\ **Replies:** 1\ **Last updated:** [October 17, 2020, 7:37pm UTC](https://forum.eternagame.org/t/game-rules-explained/3694 "2020-10-17T19:37:54Z")
Hi all, Maybe im blind but i spent 2 hrs trying to find exact description of rules. I found this tutorial https://www.youtube.com/watch?v=Z-09sAvqXgc&feature=youtu.be which makes think a bit clearer than what is covered… --- ## [IUPAC strategy brainstorm](https://forum.eternagame.org/t/iupac-strategy-brainstorm/3678)
**Author:** [@Abinmorth](https://forum.eternagame.org/u/Abinmorth)\ **Replies:** 1\ **Last updated:** [September 26, 2020, 1:18pm UTC](https://forum.eternagame.org/t/iupac-strategy-brainstorm/3678 "2020-09-26T13:18:11Z")
some thoughts about the lab puzzles with IUPAC constraints, where shape doesn’t matter as much. I think we basically have two types of moves available a) stiffening the loops by putting strong bindings inside b) loose… --- ## [A Gamer's Guide to Eterna](https://forum.eternagame.org/t/a-gamers-guide-to-eterna/3113)
**Author:** [@rna-key](https://forum.eternagame.org/u/rna-key)\ **Replies:** 6\ **Last updated:** [August 12, 2020, 2:29pm UTC](https://forum.eternagame.org/t/a-gamers-guide-to-eterna/3113 "2020-08-12T14:29:47Z")
I’m writing a gamer-oriented guide to solving Eterna puzzles, and am publishing it at https://www.keystone-research-solutions.com/en/item/a-gamers-guide-to-eterna . If you are curious, please check it out. I welcome feed… --- ## [Zigzag tutorial for you](https://forum.eternagame.org/t/zigzag-tutorial-for-you/3550)
**Author:** [@ch1ck3n](https://forum.eternagame.org/u/ch1ck3n)\ **Replies:** 2\ **Last updated:** [August 12, 2020, 6:46am UTC](https://forum.eternagame.org/t/zigzag-tutorial-for-you/3550 "2020-08-12T06:46:28Z")
We all hate zigzags. why are they even a thing? well, it is a thing because it is something that should exist and that is pretty fun. but if people are like “zigzags are too hard” or “cant get stable” WELL THEIR NOT i… --- ## [I just want to know if these are bugs in eterna](https://forum.eternagame.org/t/i-just-want-to-know-if-these-are-bugs-in-eterna/3534)
**Author:** [@ch1ck3n](https://forum.eternagame.org/u/ch1ck3n)\ **Replies:** 3\ **Last updated:** [July 18, 2020, 1:15am UTC](https://forum.eternagame.org/t/i-just-want-to-know-if-these-are-bugs-in-eterna/3534 "2020-07-18T01:15:12Z")
so uh energy is so weird on these puzzles is it supposed to be like this? --- ## [ContraFold boosts & basics](https://forum.eternagame.org/t/contrafold-boosts-basics/3510)
**Author:** [@ch1ck3n](https://forum.eternagame.org/u/ch1ck3n)\ **Replies:** 2\ **Last updated:** [July 6, 2020, 1:37am UTC](https://forum.eternagame.org/t/contrafold-boosts-basics/3510 "2020-07-06T01:37:15Z")
hmm. 3 more folding engines. I’ve covered one: etrenafold. I heard it’s pretty weird. I know it’s pretty weird. but no one ever talks about contrafold. I think it’s pretty much the same as eternafold, but who knows? let’… --- ## [C boost hooks in EFOLD](https://forum.eternagame.org/t/c-boost-hooks-in-efold/3505)
**Author:** [@ch1ck3n](https://forum.eternagame.org/u/ch1ck3n)\ **Replies:** 3\ **Last updated:** [July 3, 2020, 4:00pm UTC](https://forum.eternagame.org/t/c-boost-hooks-in-efold/3505 "2020-07-03T16:00:23Z")
As we all know, we just got the new folding engine, EFOLD! And I think you can boost the HOOK, putting a C next to the closing pair. This shape is stable and this shape is not stable The energy dropped from 3.0… --- ## [Next-Genaration Sequencer 4 out of 11](https://forum.eternagame.org/t/next-genaration-sequencer-4-out-of-11/3146)
**Author:** [@SonicHH](https://forum.eternagame.org/u/SonicHH)\ **Replies:** 13\ **Last updated:** [May 20, 2020, 12:46am UTC](https://forum.eternagame.org/t/next-genaration-sequencer-4-out-of-11/3146 "2020-05-20T00:46:00Z")
I’m trying to figure out the fourth puzzle in the Next Generation Sequencer level 4 out of 11. The hint said that the 1-12 pair should be GU and the 3-10 pair should be GC but it didn’t work. ANd nothing I tried in ord… --- ## [LinearDesign is out! (from the authors of LinearFold and LinearPartition)](https://forum.eternagame.org/t/lineardesign-is-out-from-the-authors-of-linearfold-and-linearpartition/3125)
**Author:** [@lhuang3](https://forum.eternagame.org/u/lhuang3)\ **Replies:** 3\ **Last updated:** [May 13, 2020, 1:16am UTC](https://forum.eternagame.org/t/lineardesign-is-out-from-the-authors-of-linearfold-and-linearpartition/3125 "2020-05-13T01:16:00Z")
It turns out we can computationally design the most stable mRNA sequence for any given protein. For the spike protein of SARS-CoV-2 (which Moderna uses for its mRNA-1273 vaccine), LinearDesign exact mode takes ~1.6 hours… --- ## [How Eterna players can generate 100,000 promising OpenCRISPR designs in just eight weeks](https://forum.eternagame.org/t/how-eterna-players-can-generate-100-000-promising-opencrispr-designs-in-just-eight-weeks/3117)
**Author:** [@Omei](https://forum.eternagame.org/u/Omei)\ **Replies:** 116\ **Last updated:** [April 30, 2020, 6:25pm UTC](https://forum.eternagame.org/t/how-eterna-players-can-generate-100-000-promising-opencrispr-designs-in-just-eight-weeks/3117 "2020-04-30T18:25:00Z")
Well, here we are, with a new challenge and an experimental capacity for analyzing 10 times as many designs as ever before. Wow! I can imagine that many experienced players rolled their eyes a bit when then saw the goa… --- ## [The XOR Collective Challenge](https://forum.eternagame.org/t/the-xor-collective-challenge/3102)
**Author:** [@Gerry\_Smith](https://forum.eternagame.org/u/Gerry_Smith)\ **Replies:** 17\ **Last updated:** [March 15, 2020, 5:47pm UTC](https://forum.eternagame.org/t/the-xor-collective-challenge/3102 "2020-03-15T17:47:00Z")
XOR Collective Clarity Challenge The Question: Can we collectively see with sharper clarity and create design solutions more efficiently than by ourselves? This challenge is open to ALL eterna members who have not al… [Previous page](https://forum.eternagame.org/c/gameplay-and-strategies/6.md) [Next page](https://forum.eternagame.org/c/gameplay-and-strategies/6.md?page=2)