This thread is for the project to post version release information as new versions of the Rosetta application are deployed.
Discussions and other posts will be moved to other threads to keep this thread focused on release information.
For information related to the current Work Units being processed please see this thread.
Version 5.22 is up:
1. We have put in a symbol store to give us more debugging
information. We'll only get this information back, though, if you
have the latest BOINC release, available here. If you have the time, please download it!
This will be our number one debugging tool.
2. Apps that can't find the appropriate libraries to display graphics
(for whatever reason) will now not display graphics. Hopefully, this
will help with some of the rare cases where graphics is triggering
3. We removed the excessive print statements to stdout.txt that were
filling up some users's disks for a particular kind of workunit.
4. We we made some fixes to the graphics, like removing the ghost
"Accepted Energy" and making sure all protein pictures are properly
5. There have been some fixes to clean up how different threads (e.g.
rosetta itself, graphics, the watchdog) shut down at the end of the
run. We expect this to reduce errors.
6. A version for Mac Intel machines has been released!
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.
Rosetta 5.25 is up!
In 5.24 (and previously) there were occasional runs that were
producing funny behavior for some
clients that had stopped Rosetta and
restarted from a checkpoint. These clients would repeatedly
start from the same checkpoint repeatedly, even after
finishing each prediction. Keep us posted on bugs!
Quick note: some of the posts to this thread have been moved here
to keep the version log clean. Thanks!
Rosetta@home has been updated to version 5.32 -- our first update after CASP7. The new update has two major new features:
1. protein sidechains are shown in the graphics during Rosetta full-atom simulation stage details;
2. A new type of structure prediciton task -- protein-protein docking is running on Rosetta@Home details;
Report any problems you encounter with the new version here.
Rosetta Moderator: Mod.Sense
Rosetta 5.34 has a few new features to allow us to test more accurate energy functions and more interesting variations in the protein's bond geometry.
In Rosetta 5.3.6:
The workunits with varying bond geometry were slow in the previous release, and led to some very uneven crediting. We've put in features that significantly accelerate those workunits. There are also fixes that will allow us to test more accurate energy functions.
There are some fixes for graphics to make the native fold always show up. Finally, we're trying out a new output format that will enable us to send back results for designed proteins (e.g., for HIV vaccines) in compressed format.
In Rosetta 5.3.6:
? 5.36 I think
Rosetta@home has been updated to version 5.40. The update introduces a new type of simulation -- predicting the structure of amyloid fibrils ( details here). It is believed that understanding fibrils such as these will be instrumental in treating Alzheimer's disease.
A new application feature allows output of structures with non-ideal backbone and sidehchain geometries. This opens the door for large-scale tests on the experimentally solved structures to better understand their features, which may help to make the Rosetta model more like those native structures.
And several fixes have been implemented to address some of the screen saver problems people have been seeing.
The Rosetta@Home user experience keeps getting better with your feedback. Keep those reports coming. Post here with v5.40 issues.
Rosetta Moderator: Mod.Sense
1. fix the bug of do checkpointing even after Rosetta is finished.
2. fix the bug of "error" deleting some intermediate files after they are gzipped.
3. when the watchdog catches a stuck run and there is no models completed, stop the WU and report back instead of throwing a cilent error. Server will handle this case and assign credit accordingly.
4. fix some other bugs related to Rosetta Science, especially some docking bug-fixes important for proceeding CAPRI 11 jobs.
A new feature of reading Rosetta commands from an input file.
Report problems with this version here
Rosetta version 5.43
We are mainly trying to increase stability in this release... we have turned off mouse rotation and sidechains temporarily, after reports that they caused crashes for a small percentage of users. [In the next update, we will reintroduce these features after testing some ideas to make the graphics more robust!]
Some other (small) modifications include: testing a slight modification of the energy function for secondary structure in all-alpha proteins; and allowing the "broken-chain" protocol to be guided by low-resolution data from cryo-electron microscopy.
Rosetta version 5.45
In this release, we've made some bug fixes in the graphics and have turned the display of sidechains and mouse rotation of the protein back on. We are hoping the graphics in this release are significantly more stable.
There are also some minor modifications in the science code.
I almost forgot to mention that we've also started using UPX (http://upx.sourceforge.net/ to compress the windows and linux executables. The result is a 3 fold reduction in the size of the windows app and 2 fold for linux. We'd like to thank Rytis Slatkevicius for suggesting UPX.
Rosetta version 5.46
In this release, we've fixed the bug observed in V5.45 which has caused a high rate of "watchdog termination" for workunits, especially docking ones "DOC..." Please note that even with the fix, watchdog errors can still be seen sometimes and that is because Rosetta simulations get stuck during searching large, complicatined energy landscape, but this should happen randomly at a very low rate.
There are also some minor modifications in the science code.
Boinc is updated to 5.48. We are including a special symmetric docking protocol and a fix to the problem of frequent watchdog terminations of docking workunits. Keep us posted on bugs here!
Rosetta@home is at version 5.51 with some new features!
1. The style of graphics has been updated to use a "cartoon" representation of the backbone.
This format has ribbons for alpha helices and arrows from beta strands, and was popularized
by Jane Richardson and others in the 1980s. Its the style that we actually use to visualize and
assess structures in the lab, and the style most commonly used for scientific publication.
2. There are some "easter eggs" -- you can change the color of sidechains from the keyboard if
you view Rosetta@home from the BOINC Manager (show graphics) rather than as a screen saver.
3. A new mode of Rosetta has been implemented that carries out structure prediction for ribonucleic acid (RNA), which is thought to be dominant biopolymer at early stages of life, back before there
was DNA and proteins.
Rosetta@home is now updated to version 5.54. The main features are:
1. RNA modes should now correctly crunch though as many workunits as your CPU run time preference allows (typically 4 hours), instead of always trying to do 30 structures.
2. A few glitches in the graphics have been fixed. In particular, a small fraction of users reported problems with crashes. In this update, we've tried to make the code more robust, so please let us know here if you cannot see graphics consistently.
Rosetta@home is at version 5.59. There are several new features:
1. There were issues for Rosetta@home on a small fraction of Macs for the last couple updates. This appears to be fixed. Thanks to all the Mac users who posted here, attached their computers to Ralph, and helped us resolve this issue!
2. The "percentage complete" steadily increases every five seconds during the workunit. It should be reasonably accurate except in the occasional workunit that goes a little over your preferred CPU run time; this happens when your workunit has an exceptionally promising score, and Rosetta decides to continue crunching. In those cases, the percentage complete is slowly updated so that the estimated time to completion stays around 10 minutes.
3. The "estimated time to completion" is occasionally a little off at the beginning of the workunit; no need to worry about it!
4. We have implemented a more accurate energy function for RNA, thanks to your efforts with the previous apps.
5. We have implemented a new mode of Rosetta that simultaneously simulates folding and docking of two symmetric chains. This was inspired by a protein whose crystallographic data we are trying to "phase" as well as the many proteins in Nature that form symmetric dimers.
Rosetta@home has been updated to version 5.62.
This version has the following features and updates:
1. there is now checkpointing for pose and jumping jobs
2. the percent complete has been fixed so that it will no longer go to zero after a restart if a checkpoint or model was made.
3. there are a few science related updates
Rosetta@home has been updated to version 5.64
There are a few new things:
1. This version has checkpointing for the fold_and_dock mode!
2. In the previous app (5.62), a change in the BOINC libraries caused a problem with older PowerPC Macs. This update should fix that problem.
3. We have added a new option to allow bigger moves during symmetric refinement of protein complexes.
4. We have also enhanced our ability to guide runs with information from previous runs by perturbing the energy function with a "barcode" (look for the word BARCODE to show up in some of your workunit names).
Rosetta@home has been updated to version 5.67.
1. This version allows us to specify extra information (from experiments) for which parts of an RNA should be buried and which parts should be exposed.
2. This version also allows the simulation of very large symmetric systems (like viruses) by actually modeling only a subsystem and inferring the energy and fold of the whole system.
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.
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.
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!
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.
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!
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'').
Rosetta@home has been updated to 5.81.
This version adds a new feature that allows us to properly model disulfide bonds in proteins.
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!
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.
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.
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
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!
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
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.
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.
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.
Version 1.24 of minirosetta is now released. This version is similar to 1.15 but contains a fix for a memory leak.
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.
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.
Version 1.32 of minirosetta is now released. This version includes various updates to the graphics application. Minirosetta graphics now look like rosetta++ graphics. Additionally, a linux graphics application is now available.
The minirosetta database is now being packaged and distributed with the application to deal with backwards compatibility.
Please keep in mind that the graphics frame rate may be reduced due to the extra overhead of shared data between the worker application and the graphics application. To increase the frame rate at the cost of cpu cycles, you can set the "Percentage of CPU time used for graphics" R@h project preference to a higher value than the default.
Also keep in mind that there may still be issues with the linux graphics application.
The minirosetta application has been updated to version 1.39. In this version, we added two important applications to minirosetta, docking and protein folding with explicit zinc metal ion. New features have been added to the graphic to show chain colors for a multi-chain protein complex and display metal ions by sphere.
The minirosetta application has been updated to version 1.40. This version contains improved protein-protein docking along with small-molecule ligands and the capabilities to do design, where the surface amino-acid residues are allowed to mutate during the simulation. Messages on the Scientific aspects will be posted on the message board.
The minirosetta application has been updated to version 1.45. This version contains various bug fixes related to long run times and finer checkpointing for relax jobs and a possible fix to the preemption problem. It also includes a fix for the h-bonding nan problem.
THe application has been updated to 1.47. This contains bugfixes to address the sporadic errors occuring in cs_vanilla workunits.
Further it fixes a problem with constraints which allows us to now run homology modellling jobs with constraints, which should improve prediction results.
THe application has been updated to 1.54. For details go here:
THe application has been updated to 1.65. This contains a small number of bugfixes, but mainly new science, particularily folding with sparse experimental data (In particular residual dipolar couplings http://en.wikipedia.org/wiki/Residual_dipolar_coupling )
1.67 is up !
1.71 is up !
Rosetta 1.75 is out - update your firewalls.
Rosetta 1.76 is up. Fixing a bug that causes 'Validation Fails'
Rosetta 1.80 is up.
1.86 is out.
1.90 is up
Version 1.91 is up. It is identical to 1.90, but uses a new database to avoid the recent signature verification problems that have been encountered.
No changes are required on the home user's BOINC setup. The new version will be downloaded automatically. You may need to review your firewall or anti-virus software if they need to be aware of the new application.
We will be using the same "Problems with..." thread as the 1.90 version:
Rosetta Moderator: Mod.Sense
1.95 is up :)
1.95 is repackaged to 1.96.
I'll be working this weekend to make sure it runs fine.
Sorry for the late post. Minirosetta v1.98 is up.
Minirosetta 2.00 is now up.
minirosetta 2.02 is up:
Minirosetta 2.03 is out!
Minirosetta has been updated to 2.05.
This version includes a fix to checkpointing for a specific type of job, and other minor updates.
There were very interesting questions on the boards regarding this new protein-interface design run, particularly with respect to checkpointing, so below is an explanation that is somewhat more technical.
The aim of this project is to redesign a protein that would inhibit a pathogen (see http://boinc.bakerlab.org/forum_thread.php?id=4477). The computational strategy that we've implemented looks for an exquisite and very rare geometric relationship between amino acid residues on the surface of the redesigned protein and the target pathogenic protein. The method can very quickly go through multiple starting points and triage most of them. Those that pass this triaging step are then subjected to rounds of design.
Often people explain the problem of protein folding as an energy landscape in which you're trying to identify minima corresponding to stable structures. Due to the rarity of the combination of amino acid conformations that we're looking for the energy landscape might be best described as a golf course: a few good conformations are scattered across a vast and bland space. The rarity of these points and the vastness of the space make the huge processing power of ROSETTA @ HOME an ideal place to identify these putative binders.
Since each simulation -even fruitful ones- are quite short, in-trajectory checkpointing does not seem necessary at this point (and would probably increase the disk-writing load unnecessarily). With release 2.05 the between-trajectory checkpointing issue should be resolved.
Minirosetta 2.10 is out !
Minirosetta 2.11 is out !
minirosetta 2.14 is out
minirosetta 2.15 is out. see here for the update
minirosetta is reverted to 2.14 (now 2.16)
minirosetta is updated to 2.17 to fix the memory and invalidation errors.
minirosetta is updated to 3.46 with new development and bug fixes.