Rosetta-News

[cappy]

wieder was aus dem journal

The last day of the CASP8 meeting is tomorrow--while I was not able to attend James and rob have reported back that the meeting has been very exciting.

there are now summary statistics on the performance of all groups in CASP8 available at

http://prodata.swmed.edu/CASP8/evaluati ... e.html#top

hmm wenn ich das richtig lese hat rosetta platz 1

[cappy]

eine news

Due to a limitation on command line length set by BOINC, the jobs with name *_ZN_ABRELAX_* have their command lines automatically truncated when sent out on Rosetta@Home.This caused all the WUs to fail right away. We have canceled all these WUs and are currently investigating why they were not caught on our testing server in the first place. Sorry about any incovenience and this is a new lesson for us to learn.

[Obi]

Eine Neuigkeit vom 10. Dez:

We are now recommending systems with at least 512MB of memory. The majority of tasks will run fine with 256MB but some tasks will involve larger proteins that will use more memory.

In Deutsch:

Wir empfehlen nun Systeme mit wenigstens 512MB Speicher. Die Mehrheit der Aufgaben wird zufriedenstellend mit 256MB laufen aber einige werden größere Proteine umfassen, die mehr Speicher brauchen werden.

Und ein neues Posting im Journal

Mike Tyka's results from your calculations over the past two weeks on rosetta@home are truly exciting! Many of you have found, starting from an extended chain, structures that are close to the crystal structure but much lower in energy. When Mike inspects your very low energy structures, in many cases it seems possible that they may be better models than the experimentally determined structure. We never expected to be in this situation so soon! Our next step is to see whether these low energy structures may actually be as or more consistent with the experimental data than the deposited crystal structure. If true, this would be a new step forward for computational structural biology!

Zu Deutsch:

Mike Tyka's Ergebnisse aus Ihreren rosetta@home Berechnungen über die letzten zwei Wochen sind wirklich aufregend! Viele von Ihnen haben, ausgehend von einer gestreckten Kette, Struckturen gefunden, die nahe an der Kristallstrucktur, aber energetisch viel günstiger liegen. Als Mike Ihre sehr niedrigen Energiestruckturen inspizierte, schien es in vielen Fällen möglich das diese bessere Modelle abgeben würden, als die experimentell festgelegte Strucktur. Wir haben nie erwartet so früh in dieser Situation zu sein! Unser nächster Schritt ist zu prüfen ob diese Niedrig-Energie-Struckturen tatsächlich besser mit den experimentellen Daten übereinstimmen als die hinterlegte Kristallstrucktur. Falls ja, würde dies ein neuer Schritt in Richtung rechenbetonte struckturelle Biologie sein!

[DO3PSN]

Na das hört sich dochmal extrem gut an! Bleibt abzuwarten, was sich daraus entwickelt.

Gruß

Philipp

[yoyo]

Das müßte dann mal in die Aktuelle_Ereignisse, oder?
yoyo

[hias]

is drin

[cappy]

gibt mal wieder eine news ausm journal vom david baker

The presentations made by the CASP8 assessors are now available at http://predictioncenter.org/casp8/docs. ... sentations.

We apologize for the outages over the past several weeks. The very good news is that Mike Tyka, Andrew Leaver-Fay and David Kim in an all out effort the past two weeks have identified the causes of many of the remaining errors some of you have been getting with the new rosetta code, and we hope that the error rate will now be much lower. I am very excited to see the results of the next weeks of calculations on rosetta@home--we are investigating some very fundamental issues. I'll give you a full report when your results are back in and we have had a

hier noch die google übersetzung

Die Präsentationen, die von den Prüfern CASP8 sind ab sofort in http://predictioncenter.org/casp8/docs. ... sentations.

Wir entschuldigen uns für die Ausfälle in den vergangenen Wochen. Die gute Nachricht ist, dass Mike Tyka, Andrew Leaver-Fay und David Kim in einem Anstrengungen der letzten zwei Wochen haben die Ursachen für viele der verbleibenden Fehler einige von Ihnen haben sich mit dem neuen rosetta-Code, und wir hoffen, dass die Fehlerquote wird jetzt deutlich geringer. Ich bin sehr gespannt auf die Ergebnisse der nächsten Wochen von Berechnungen auf Rosetta @ Home - Wir untersuchen einige sehr grundlegende Fragen. Ich gebe Ihnen einen vollständigen Bericht, wenn Sie Ihre Ergebnisse sind wieder in, und wir haben eine Chance, über ihre Auswirkungen.

desweiteren gibs ein beitrag im thread protein-protein docking at rosetta@home

Hello,

At this point, the coordinates for the previous target in CAPRI have not been released so I can't yet report on whether our predictions thanks to ROSETTA@HOME have been successful. I'll let you know as soon as I hear from the organizers.

In the meantime, another round of CAPRI (round 17) was announced today. The modeling task this time involves homology modeling and docking at the same time. So, we would be able to test both aspects of ROSETTA as well as the ability to dovetail the two tasks. Such modeling challenges are quite common in real-world scenarios, where we know the structure of one of the partners but only have a template for the other. So, this round of CAPRI offers us a chance to see how well we do at such a task.

Over the next few days, I'll send out a very small number of simulations on ROSETTA @ HOME to test the protocols that I intend to use this time. These will involve both rigid-body docking of the partners and backbone motions (and you'll be able to see how those combine using the graphics application). Later in the week I will submit a large batch of trajectories to carry out the actual prediction task.

I'm excited to see how well we do at this and will keep you posted on the results from previous round of CAPRI.

[cappy]

mal wieder was aus dem journal von david baker

We are very excited--the new improved mini Rosetta code should now be running on your computers, hopefully very smoothly, and we have really exciting fundamental science questions that you will be helping us tackle this week. HIgh on the list are the comparison of Rosetta low energy structures to native structures I mentioned recently (might the Rosetta models in some cases be more accurate??), and a comprehensive test of new comparative modeling methodologies we have developed after CASP8 last summer based on what we learned from your CASP8 results. We have developed several different approaches which use the information from already solved related structures to different extents, and we are excited to learn how the new methods compare to our CASP8 approach and which of the new methods is the best.

[cappy]

so es gibt eine neue minirosetta version 1.54 hier das englische changelog *falls wer es übersetzen möchte kann das gerne tun und wird hier gerne gesehen

Hello All!

We're ready for a new update. I want to say thank all of you who have helped over the last months to find and fix errors in minirosetta. A particular thank you goes to those who have donated their time over on RALPH and helped with their active feedback - we managed to find a number of difficult and rare bugs and put some new features into minirosetta that should help conserve computer time. Read about it here: http://ralph.bakerlab.org/forum_thread.php?id=431
and here http://ralph.bakerlab.org/forum_thread.php?id=432
I should add that work over there will continue,but now supplemented with information from Rosetta@HOME.

This update is highly focused on bugfixing and stability issues - we have virtually no new science in it, but: We will hopefully now be able to run the science projects that have been in the pipeline waiting for BOINC - we're expecting quite a bit of work to go out very soon indeed. See Dr. Baker's journal for more details.


Features/Fixes:
1.54 Release CHANGELOG


* Faster loop closing in FoldCST/Abinitio (affects cc_* cc2_* cs_* WUs), should help with overrunning WUs.

* Bug fix concerning intermittent crashes in relax benchmark jobs (_rlbd_) jobs - caused by buggy input file reader.

* Bug fix for a potential instability in handling text files (affects all types of WUs).

* Bug fix in checkpointing machinery, states were not being correctly restored, probably contributing to long runtimes. (affects cc_* cc2_* cs_* WUs)

* Increased the density of checkpoints to lose less time on restarts and address the weired "backjumping" of the time reported in this thread. This will still happen, but the jumps should be much smaller (basically maximally as long as the time between checkpoints.)

* Added checkpointing to Loopclosing part of FoldCST. (affects cc_* cc2_* cs_* WUs)

* Added checkpointing to Looprelax.

* The Watchdog has been checked and improved, now returning information on the aborted jobs to help us figure out how the remaining long running models come about. The watchdog will now abort if the runtime exceeds your preferred runtime + 4 hours. In other words the WUs should not overrun for more than around 4 hours. If they do please let us know !!

* Added a limit ont he number of decoys per WU: 99. The WU will end gracefully after that and give full credit. This should address issues with excessive upload problems.

* Fixed a bug in the BOINC API concerned with unzipping the input data. (I will let the BOINC guys know about this)

* Fixed a strange problem in the options system leading to early crashes on some systems.

* Two nasty instabilities fixed deep in the FoldConstraints/abinitio protocol (cc_* tasks and other homology modelling tasks)

* Generally implemented much better error reporting - many many potential problems will now show up a meaningful error messages and not random segmentation faults.



NOTE: This new version contains a lot of debug output still. YOu will see that the stderr fills up with stuff - that is ok . It does not slow down the program nor cause much extra upload - but it tells us a lot about where things can go wrong still.


Despite all these fixes there are, i'm sure, many problems left. Most of them occur extremely rarely now though or are highly specific to particular machines. Thus we have decided to move the current version over from RALPH to Rosetta@HOME and give it a go on a much larger scale. Our effords to keep the failure rate down will continue and your time donations over on RALPH as well as error reports are still highly appreciated.

Please let us know how things work out there. Particularily i'd like to know about


* Stuck workunits
* Overrunning workunits (WUs should now, due to the new watchdog, never run more than 4 hours longer than the preferred user time)
* Problems with checkpointing.
* Any other strange behaviour.




Happy crunching - I'm very excited to see how this new version will pan out.

Mike

[cappy]

mal wieder eine post im protein-protein docking at Rosetta@Home thread von sarel, die google übersetzung ist leider nicht so der hit also falls wer so nett wäre das ganze zu übersetzen

Hello,

The second stage of this round of CAPRI has started. This targets the same two partners as the previous stage, but we have been given the coordinates of the structure which previously we had to predict based on homology modeling. From a preliminary analysis James (who had produced this homology model) and I found that the homology model that we used in the previous stage was largely correct except for one long loop which we modeled incorrectly. Nevertheless, it seems like the main binding modes that we predicted previously would be unaffected by the modeling of that loop. Now that we have the coordinates of that structure we should be much better placed to make high-accuracy predictions.

One word of caution is that as in the previous stage the system that we're modeling is quite large (450 residues across both protein partners). We've run such simulations before using ROSETTA @ HOME with no memory issues but I expect result files to be quite large. Please let me know if you run into any trouble.

[cappy]

noch ein kleiner nachtrag von sarel

Yes, sorry for not mentioning. As posted by Saharak, the jobs have _CAPRI prominently in the name. They would also be visually recognizable because you will see a small protein 'orbiting' around a very large protein (that's the docking step). Then, side chains will come up (packing) and finally you will see some backbone motions. I'm running two prediction strategies here, one where only one of the partners undergoes backbone motions (named _br_one_docking) and the other with both partners (_br_both_docking). This is because in this stage of the experiment we were given the exact coordinates of one of the partners and I would like to see whether backbone motions are any help in such cases (my hypothesis is that backbone motions shouldn't help and this is a great way to find out!).

Thanks for participating!

[cappy]

hier ein neuer beitrag aus dem rosetta forum aus dem thread science update for R@H, falls wer den text übersetzen möchte nur zu

Hi All,

wow - it's been a long time since i posted here. So - what's been going on ?
Those of you following the forums will have seen us labouring away to make minirosetta more stable. The latest result of these effords is minirosetta_1.54
which we have been running hard on BOINC over the last 3 weeks and that has proven to be quite a bit more reliable then the prvious version. There will be a few more minor updates, but all in all its time to focus on science again !

Yeah! So we currently have a lot of stuff going on. We currently have about 2.5 Million WUs (!) queued up here - that's gonna generate quite a large amount of data over the next few weeks!

For homology modelling we are finally crunching to find out some vital answers about all the different methods we use to establish which ones work best in which situations as well as to optimize their parameters.
We're about to launch some more investigations into those algorithms that align unknown with know sequences to establish how to best make use of the huge amount of protein structural data that scientist have already collected - there'll be another 1.5M or so workunits going out soon!

We are also optimizing the energy function and are finding some curious things about the area of conformational space directly surrounding the native structure. We're currently crunching a massive amount of sampling to get very finegrained. In some cases Rosetta's lowest energy structure deviates a little from the true structure and we're investigating if this is due to xtal packing. If so then maybe rosetta is actually giving a more representative answer of what the protein looks like in solution then suggested by the crystal. Very curious.

Further there is more docking going on, as well as a number of investigations into how to improve sampling for abinitio structure prediction by varying the energycomponents.

All in all this a super-exciting time for us & we'll be posting interesting developments here !

Thanks for crunching !

Mike