Rosetta Application Version Release Log

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Message 41742 - Posted: 2 Jun 2007, 0:59:36 UTC

Rosetta@home has been updated to version 5.68. This version allows us to carry out all-atom refinement for really large symmetric proteins where we simulate only subsystems, fixes a small bug in the RNA mode, and will allow a new sort of RNA simulation with lots of imposed base pairs.
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Message 42675 - Posted: 26 Jun 2007, 19:31:03 UTC
Last modified: 26 Jun 2007, 19:36:24 UTC

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.


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Message 44132 - Posted: 24 Jul 2007, 3:33:11 UTC

Rosetta@home has been updated to 5.72; some older workunits will continue to crunch with 5.68 (see previous post). What\'s new?

This version has a correction to one of the energy terms of the rosetta energy function which could improve discrimination of native structures.

This version fixes a small bug that was slowing down the \'relax\' portion of work units.

The version incorporates several new features to the RNA mode that should greatly reduce file transfer for those workunits.

We will also be testing a new high-resolution energy function for RNA!

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Message 44575 - Posted: 1 Aug 2007, 1:04:23 UTC

Rosetta@home has been updated to 5.73; as with the previous update, some older workunits will continue to crunch with 5.68.

This version fixes a bug in high resolution modeling of RNA, and will let us test a more efficient procedure for closing \"chainbreaks\" introduced in certain workunits.
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Message 44914 - Posted: 12 Aug 2007, 20:55:38 UTC

Rosetta@home has been updated to 5.76; as with the previous update, some older workunits will continue to crunch with 5.68.

This version fixes another bug in high resolution modeling of RNA; due to a rather arcane issue, certain RNA hydrogen bonds were not being scored properly.

We will also be testing a new procedure for closing chainbreaks that should lead to faster recognition that a protein structure is completely wacky, and allow your computer to go on to simulating a new conformation quickly. More efficient, hopefully!

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Message 45713 - Posted: 2 Sep 2007, 23:08:13 UTC

This version adjusts the way that experimental data is used to guide some RNA folding runs; there\'s also a new feature that lets us choose building blocks for RNA folding from different existing source structures.

Also, this version should improve folding efficiency in runs that involve a special type of symmetry (\'\'D2\'\').
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Message 48406 - Posted: 6 Nov 2007, 2:14:08 UTC

Rosetta@home has been updated to 5.81.

This version adds a new feature that allows us to properly model disulfide bonds in proteins.

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Message 48875 - Posted: 20 Nov 2007, 19:05:22 UTC
Last modified: 28 Nov 2007, 19:36:33 UTC

Rosetta@home has been updated to 5.85:

- New features include proper diagnostics for a different kind of symmetry (\'D2\')

- A fix to the modeling of large symmetric complexes, and a lower memory usage by some of those jobs as well.

- A new output format that may be useful for designing new proteins.

- Some major improvements in the energy function used in RNA structure prediction, which we look forward to testing on a large scale!

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Message 49145 - Posted: 28 Nov 2007, 19:39:51 UTC
Last modified: 28 Nov 2007, 19:40:20 UTC

Due to a glitch in our previous application update, the Linux executable didn\'t have the same source code as the Mac and Windows executables. It now matches those executables! For reasons of bookkeeping, the Linux application now has a nominal version of 5.86, but is identical to the 5.85 apps for other platforms.
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Message 49367 - Posted: 4 Dec 2007, 6:34:34 UTC

To fully clarify the current versions:

\"Rosetta beta\" 5.85 (mac/windows) or 5.86 (linux) contain the latest executable.

\"Rosetta\" 5.82 is an old executable -- during lull perids, we are still running a few workunits with this older executable to serve as a very large scale, fully self-consistent test of the structure prediction protocol.
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Message 49688 - Posted: 14 Dec 2007, 15:09:15 UTC

Version 5.89 includes:

  • the ability to model symmetric complexes with new kinds of symmetry (dihedral with several monomers, e.g., D5),
  • a fix for an occasional crash that occured for large symmetric complexes,
  • a new option for regular protein structure prediction that prevents large movements during the full atom refinement,
  • and improvements to the RNA energy function.


Rosetta Informational Moderator: Mod.Zilla
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Message 49835 - Posted: 20 Dec 2007, 20:40:37 UTC

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.
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Message 49916 - Posted: 21 Dec 2007, 21:57:42 UTC

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!
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Message 50334 - Posted: 5 Jan 2008, 1:38:14 UTC
Last modified: 6 Jan 2008, 20:00:58 UTC

Rosetta 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!
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Message 51936 - Posted: 14 Mar 2008, 1:00:43 UTC

Rosetta version 5.95

This version introduces a new \"resampling\" method for diversified sampling of beta topologies. It expands the range of conformation space that Rosetta can search by learning promising regions of search space from previous search results.
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Message 52098 - Posted: 23 Mar 2008, 23:49:50 UTC

Rosetta 5.96 includes a new procedure for modeling large RNAs where experimental information is available. Basically, constraints that bring together parts of the chain that are further apart in sequence are introduced at later stages of the search.
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Message 52673 - Posted: 23 Apr 2008, 22:46:45 UTC - in response to Message 52098.  

Version 1.15 of minirosetta is now released, which includes protocols for doing very fast optimization of multiple starting structures, improved methods for modeling protein structures based on constraints, and faster versions of our all-atom refinement protocol.
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Message 53255 - Posted: 21 May 2008, 23:39:40 UTC

Version 1.24 of minirosetta is now released. This version is similar to 1.15 but contains a fix for a memory leak.
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Message 53632 - Posted: 11 Jun 2008, 18:06:54 UTC

Version 1.28 of minirosetta is now released. This version includes fixes to the graphics screen saver along with scientific updates/additions to the loop modeling, abinitio, and jumping protocols. This version should also clean up old minirosetta database files.

The windows application has not been compressed with UPX in order to enable the BOINC debugging (symstore) utilities. However, later versions will likely be compressed.
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Message 54000 - Posted: 25 Jun 2008, 22:46:30 UTC

Version 5.98 of rosetta is now released. This version includes a fix for the \"t405\" client stalling issue. There are no science related updates in this release.
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Message boards : Number crunching : Rosetta Application Version Release Log



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