Posts by srettie

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 108109) Posted 20 Feb 2023 by srettie Post: And the word is "Decoys" for some strange reason only known to rosetta staff . I can hopefully clear that up a little. When predicting protein structures we generate possible structures for a given sequence of amino acids and score them using the Rosetta energy function. These structures can be any chemically reasonable structure and can vary wildly from the correct one. If we have enough sampling and diversity in these decoys of the real structure we can obtain a complete (or at least close to complete) energy landscape for a given sequence, with an energy minimum at the correct structure.
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 108059) Posted 17 Feb 2023 by srettie Post: fix_test job failures should be unrelated to any boinc issues. Those errors are a bug on my part, that I found and I'm pretty sure I fixed. Doing another test to confirm. Edit: I should also clarify that I cancelled all remaining fix_test jobs as soon as I noticed. Sorry about that.
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 108056) Posted 17 Feb 2023 by srettie Post: Yes, our apologies for the delay. We thank you all for your patience and continued support.
4) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 108054) Posted 17 Feb 2023 by srettie Post: Hi everyone, thank you all for your feedback on the issues we've been having. Thanks to these comments we were able to track down the issue, and a preliminary job has been working great. However, I jumped the gun and looks like I made a mistake on the large batch submission. I will remove those jobs. I apologize for the error. Fingers crossed we should have lots of (good) jobs to send out soon. Thank you again.
5) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 107942) Posted 10 Jan 2023 by srettie Post: Hello, I have passed this on to the people in charge. Thank you everyone for posting the issue here.
6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 107232) Posted 11 Oct 2022 by srettie Post: I'll see about talking our Rosetta@Home team tomorrow. Sorry for the delay on this.
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 107096) Posted 6 Oct 2022 by srettie Post: Ooh, new batch of tasks again? No idea how big yet We could get used to this I certainly hope so! Looks like things are running okay so far. This is batch 2. ~5mil total for this experiment on the way.
8) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 107022) Posted 2 Oct 2022 by srettie Post: Hello, these are from me. I thought I'd double check how things looked on the forums after submitting such a massive run. This is part of a massive sampling of small cyclic peptides generated using some pretty cool tweaks to Alphafold 2. The term hallucinated refers to protein structures generated using this method: https://www.nature.com/articles/s41586-021-04184-w These jobs are generating energy landscapes for structurally diverse cluster centers. I'm super excited about these results and really appreciate the incredible amount of computation available from Rosetta@home. The info we get from this will help us put together a massive set of peptide backbones for binder design projects in the future. I hope to be submitting more... Assuming I'm not breaking any rules by monopolizing this resource. Thank you all! -Stephen
9) Message boards : Number crunching : Minirosetta android 3.83 (Message 87041) Posted 11 Aug 2017 by srettie Post: Hello Usuario1_S, I am so sorry, this is mine. I'm not sure why this job is failing as it was set up in the same way as other jobs that did not fail and is an incredibly similar scaffold. It is 100% my fault for not noticing sooner and ending it. I apologize for the wasted computational time. I will be much more vigilant in future. Won't happen again.