Rosetta Application Version Release Log

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Message 14237 - Posted: 21 Apr 2006, 7:20:00 UTC
Last modified: 21 Apr 2006, 22:20:08 UTC

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.

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Message 18183 - Posted: 8 Jun 2006, 21:16:42 UTC - in response to Message 16410.  
Last modified: 8 Jun 2006, 22:29:55 UTC

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
errors.

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
centered.

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!

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Message 19021 - Posted: 20 Jun 2006, 23:28:11 UTC - in response to Message 18183.  

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.


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Message 19528 - Posted: 30 Jun 2006, 4:27:59 UTC
Last modified: 30 Jun 2006, 4:31:12 UTC

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!

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Message 29214 - Posted: 12 Oct 2006, 1:47:14 UTC

version 5.32:

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.
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Message 29979 - Posted: 25 Oct 2006, 0:41:37 UTC

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.
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Message 30397 - Posted: 31 Oct 2006, 22:50:39 UTC - in response to Message 29979.  

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.
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Message 30439 - Posted: 1 Nov 2006, 14:07:50 UTC - in response to Message 30397.  

In Rosetta 5.3.6:
...


? 5.36 I think
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Message 31161 - Posted: 15 Nov 2006, 2:11:00 UTC

Rosetta v5.40:

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.
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Message 31880 - Posted: 1 Dec 2006, 1:27:52 UTC
Last modified: 1 Dec 2006, 1:45:47 UTC

Rosetta 5.41

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
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Message 32624 - Posted: 14 Dec 2006, 5:41:20 UTC

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.


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Message 35738 - Posted: 30 Jan 2007, 2:45:35 UTC
Last modified: 30 Jan 2007, 3:25:47 UTC

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.

edit:

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.
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Message 36636 - Posted: 13 Feb 2007, 2:28:26 UTC

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.
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Message 37316 - Posted: 1 Mar 2007, 23:48:29 UTC
Last modified: 1 Mar 2007, 23:57:50 UTC

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!
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Message 37724 - Posted: 12 Mar 2007, 20:08:42 UTC

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.


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Message 38067 - Posted: 21 Mar 2007, 0:27:42 UTC
Last modified: 21 Mar 2007, 0:32:51 UTC

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.
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Message 38869 - Posted: 2 Apr 2007, 20:07:11 UTC

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.




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Message 40232 - Posted: 2 May 2007, 19:40:09 UTC

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
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Message 40460 - Posted: 7 May 2007, 1:24:03 UTC
Last modified: 7 May 2007, 1:25:42 UTC

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).




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Message 41404 - Posted: 24 May 2007, 23:28:16 UTC

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.




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