1) How come native structure and RSDM was removed from graphic screen in a current Rosetta version -5.25?
If answer that no native structure is know for protein - how could it be? The whole point of the project is improving Rosetta method so we are basically supposed to run "benchmarks" with different parameters/methods and compare outcomes against each other and against known structure.
2) Is there version history exist, so anyone can see what improvements was done, what changes was made...

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1) How come native structure and RSDM was removed from graphic screen in a current Rosetta version -5.25?
If answer that no native structure is know for protein - how could it be? The whole point of the project is improving Rosetta method so we are basically supposed to run "benchmarks" with different parameters/methods and compare outcomes against each other and against known structure.
2) Is there version history exist, so anyone can see what improvements was done, what changes was made...

1) was for the CASP challenge - the native structures were known but not released until the end of the competition.
2)I think this was requested recently but hasn't been implemented yet. Of course the more time they spend telling us what they're improving, the less time they spend improving it ;)

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dcdc has it for number 1.

Here's what you were looking for on the second:
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

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1) Ok, CASP was a nice reason, but it is over for 3 weeks now!
2) Cmon, it would take less then a minute to add few short sentences to change log file. Just what is new and what was improved in current version compare to previous one. The only reason I see they don't do that - is no progress have been made...

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oh - ok thanx.

dcdc has it for number 1.

Here's what you were looking for on the second:
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

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1) How come native structure and RSDM was removed from graphic screen in a current Rosetta version -5.25?
If answer that no native structure is know for protein - how could it be? The whole point of the project is improving Rosetta method so we are basically supposed to run "benchmarks" with different parameters/methods and compare outcomes against each other and against known structure.

Rosetta is used both on unknown proteins, as with the "CASPR" work units, and on proteins of known structure. When the structure is known, then the RMSD is shown in the graphic. In the end, the goal is to run against a protein of unknown structure, and make an accurate prediction. This is put to the test every two years with CASP where proteins that are undergoing the process of determining their structure via X-ray are presented as a challenge to research groups around the world. The structures are not know, but are under study, and so will be known in a matter of weeks. So, this forces a blind prediction to be made, and then later, when the structure is known, the predictions can be compared to the actual structure that is found.

2) Is there version history exist, so anyone can see what improvements was done, what changes was made...

The project index has lots of useful information. I believe you'll find some of what you want on the link entitled "Rosetta Application Version Release Log"

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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/

1) Ok, CASP was a nice reason, but it is over for 3 weeks now!

...actually... there is still a challenge for teams working on "refinement" that is going on. You can learn more about CASP7 refinement here.

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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/

1) Ok, CASP was a nice reason, but it is over for 3 weeks now!

This is true, but the utility of CASP is still not over for our lab. We're still submitting workunits on some proteins to investigate how increased sampling and different approaches can influence our results. Also while CASP is over, not all of the structures are released (less than half of the proteins that I've worked on have been released, and I'm very interested in them). This means that the CASP workunits are still a blind test for us! Also, as Feet1st points out, CASPR is still ongoing and the lion's share of our workunits are directed towards that.

2) Cmon, it would take less then a minute to add few short sentences to change log file. Just what is new and what was improved in current version compare to previous one. The only reason I see they don't do that - is no progress have been made...[/quote]

If people are interested in what's being added to the Rosetta application, I'll add some more detail on changes when I update the application this week. There are at least two scientifically interesting updates that will be added in the next version, including changes that allow Rosetta@Home to be efficiently and effectively used for our vaccine design trials, and a new term that will be used to measure how tightly a given structure is packed together. I'll go into more detail when I update the application later this week.

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Oh, thanx dcdc, Ethan and Feet1st - you guys perfectly answered my questions! :)
And James Thompson:)

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