Here you asked the question "While we're here... what's the difference between "nstructs" and "decoys" and "attempts" and "models"?? Why are all four terms used?" Did you/we ever get a definition of these terms?

Nope, I didn't. I'm still wondering.

Perhaps you could change the thread title and use this thread to more explicitly pose the question.

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

I don't see an option to change the title of this thread.

Hmmm, there used to be a small little box that showed the subject line and if the thread was started by you, you could actually change it. But I can't recall what to do to make it appear. Thought you just replied to the same thread. But maybe you had to edit your original post. Seems the new BOINC server release doesn't work the way it used to.

[edit] oh! that's it! Make a post, then EDIT your post and then look up above the box for the text of your message and you'll see a little text box with the thread's subject, and then you can change it, since you created this thread.

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

I and others are looking for definitions of the terms used in the task output; terms like nstruct, model, decoy, attempt.
What does it mean to have "1 starting structure built 30(nstruct) times?"
Or "This process generated 20 decoys from 20 attempts."?
Is a decoy the same as a model? Decoy sounds clandestine!

Could someone from the project help us out here? Or could a moderator expedite this? Seems like it would be nice to have these in the Q&A that is being built.

Moving to Science forum to define terms used in graphic as compared to result files.

---

Rosetta Moderator: Mod.Sense

I and others are looking for definitions of the terms used in the task output; terms like nstruct, model, decoy, attempt.
What does it mean to have "1 starting structure built 30(nstruct) times?"
Or "This process generated 20 decoys from 20 attempts."?
Is a decoy the same as a model? Decoy sounds clandestine!

Could someone from the project help us out here? Or could a moderator expedite this? Seems like it would be nice to have these in the Q&A that is being built.

Here are some quick definitions for you folks:

nstruct - an abbreviation for "number of structures," which is the number of structures that will be created within a Rosetta run.
model - a predicted model for a given protein (or RNA, thanks to Rhiju's work!)
decoy - a decoy is also a model for a given protein (or RNA). This term came about during the early days of energy function design, when people first started writing energy functions to discriminate between "native" structures, which are correct structures solved by experimental methods, and "decoy" structures, which are computationally created structures that are incorrect to some degree. I found the term to be odd when I first encountered it as well, but I've since grown accustomed to it. In most contexts, model and decoy can be used interchangeably.
attempt - an attempt to create a structure. Some structures created by Rosetta are obviously incorrect, and these are thrown away by some filters measure various characteristics of the energy function, and thus is not saved. This is usually done during the ab-initio phase of our runs, which is extremely fast compared to the full-atom manipulation and scoring of the decoy.

Cheers,

James

---

People become acclimated to seeing a somewhat consistent set of stats in their task outputs. On occasion if someone sees something other than the "norm" they might conclude that a task is deficient in someway, or their machine is experiencing problems (I have seen comments posted based on this).

So, for example, if we are used to seeing:

DONE :: 1 starting structures built 18 (nstruct) times
This process generated 18 decoys from 18 attempts

can we in fact infer anything pos or neg about the task if instead we see:

DONE :: 1 starting structures built 20 (nstruct) times
This process generated 15 decoys from 18 attempts