Rosetta application updated

[Desti]

October 20, 2005
The rosetta application has been updated on all platforms. The updated versions should have a smaller memory footprint and the OSX version should also run on 10.3.9+.

[Desti]

November 11, 2005
The rosetta application versions have been updated and we are currently beta testing the screen saver version developed by Jack Schonbrun. The updated versions include new methods for increasing diversity in our search strategy and a few minor bug fixes.

[Desti]

Linux/x86 4.80 20 Dec 2005 0:56:06 UTC
Mac OS X 4.79 20 Dec 2005 6:02:35 UTC

The new applications have modifications in the scientific code. The modifications were, again, made to allow increased diversity in the search. The app can now read in larger protein fragment libraries, and the number of score specific cycles can be increased. The screen saver was slightly modified to allow rotation of the native structure. Bin in our group was able to find a bug that may have caused an infinite loop in certain very infrequent circumstances, but we do not know if this is the bug people are seeing. There is no difference between the *topology_sample_nnnnn and the *topology_sample_nnn_nnnnn work units. The additional number (nnn), specifies a batch number used in our new work generator.

I do not know what is causing these errors but I will look into it. I would try restarting boinc and seeing what happens. I'll be posting something up on the web site soon about these recent changes.

[Desti]

March 28, 2006
With Rom Walton's help, we've made good progress debugging rosetta. For starters, Rom has fixed the annoying "leave in memory" bug by updating the BOINC API to use TerminateProcess instead of exit to shut down the application. TerminateProcess halts any executing threads and then cleans up after the application instead of relying on the application to clean up after itself. Additional information for debugging has also been added to help track down remaining bugs like the "1% bug." For example, there are now fractional percent complete values (.01,.02, etc.) that will help us determine where jobs are getting stuck. Windows users can also help us track down bugs further by downloading the program database file (http://boinc.bakerlab.org/rosetta/downl ... telx86.pdb where X.XX is the latest version number) and placing it in the "BOINC/projects/boinc.bakerlab.org_rosetta" directory (the same directory where the rosetta executable resides). Currently, this file is not automatically packaged with the executable to reduce bandwidth usage. The program database file provides additional debug information that gets written to stderr. We are optimistic that with Rom's help and feedback from participants, we will soon be able to track down and fix the remaining issues with rosetta and continue to reduce the error rate for the project.

[Desti]

April 7, 2006
The rosetta application was updated to include some new scientific code. The application version numbers have been changed to be consistent with Ralph@home. Since error rates have decreased significantly, we decided to increase the default cpu run time to 4 hours. The previous default was 2 hours.

[Desti]

April 20, 2006
Application upgraded to 5.01. New version includes fixes that will allow more aggressive searching, and a mechanism to abort big jobs that get restarted more than 5 times on a client.

[Desti]

May 9, 2006
Application upgraded to 5.12. New version includes the ability to send out workunit descriptions and rescaled graphics for big proteins. For more information see this thread.


(1) We're on a mission to cut down memory requirements for Rosetta@home. You'll hopefully see a smaller memory footprint with 5.12 compared to 5.07, and it may even get smaller on the next application update!

(2) Some users are noticing a slowdown in other applications, such as Windows Media Player, when using the latest Rosetta@home. If you are seeing something similar, please post the workunit and your type of computer here, so that we can track it down.

[Desti]

May 11, 2006
Rosetta@home updated to 5.13. New version fixes some debugging code that was causing slowdowns in a small fraction of clients.

[Desti]

Version 5.24 is up:

1. The symbol store that we put in 5.22 was not properly activated, so we're giving it another shot.

2. We can now use prior predictions for which parts of the chain are buried or exposed to guide the Rosetta search.

3. We can efficiently assemble predefined domains of the protein chain into a whole structure.

[Desti]

Rosetta@home has been updated to version 5.70. This version has some bug fixes for the RNA ab initio folding and symmetric folding and docking mode. We've also tried to fix some of the jumping around of the rmsd trajectory (the right hand rectangle), though the scaling still isn't perfect. Finally, we are also able now to model protein complexes with a different kind of symmetry than before.

Another interesting change: we are now able to send out workunits with the older application (5.68) and the newer one (5.70). This is advantageous because the older one is "stable" and lets us carry out long-term experiments such as looking for very rare low energy conformations with hundreds of thousands of workunits over several months. The new one has bug fixes for some modes as well as new features. The new one will be called "rosetta_beta_5.70" -- you can check out this link to see what's crunching.

[Desti]

Rosetta@home has been updated to version 5.90. New stuff:

1. Better conformational space exploration of proteins with "dihedral" symmetry.

2. Reduced virtual memory requirements ... 5.89 which was causing problems on some machines.

3. Compiled with the newest BOINC API, which should allow new users that download upcoming versions of the BOINC client to run Rosetta properly.

The linux executable has been updated to 5.91. Scientifically, this is exactly the same code as 5.90, but this version should include a fix in the cpu-run-time counter that was causing errors!

[Desti]

The linux executable has been updated to 5.93. This version includes an improved treatment of dihedral
symmetry of proteins. This is a common, biologically important symmetry found among protein
homooligomers (a collection of proteins with the same sequence and often structure). Thanks for
supporting rosetta@home!