Message boards : Number crunching : Discussions about release log entries
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Cureseekers~Kristof Send message Joined: 5 Nov 05 Posts: 80 Credit: 689,603 RAC: 0 |
Version 5.24 is up: Rhiju gave this info in the Rosetta Application Version Release Log, but it doesn't sound very clear to me. Can someone give a little more info about the changes? Maybe David in a journal? Member of Dutch Power Cows |
Rhiju Volunteer moderator Send message Joined: 8 Jan 06 Posts: 223 Credit: 3,546 RAC: 0 |
Sorry, time has been a little short for us lately because of CASP -- we're still monitoring feedback. Really quickly: The "symbol store" (a.k.a. the PDB file) is a file that translates the gobbledygook we get from the occasional Rosetta@home crash into plain English, so that we can track down where and why in the code an error occurs. Its super useful, but has been a little tricky to set up. The "prior predictions" of burial or exposure come from other neural networks that are trained to look at protein sequences and guess which parts are on the inside and outside of the fold. This was just a quick first implementation; you can expect more progress in September. As for domains... if a protein is more than ~150 residues long its just too difficult to sample every possible conformation extensively. Luckily most real proteins of large sizes (>200 residues) subdivide into domains of 70-150 residues that appear to fold into independent pieces that are not too intertwined with each other. So before we submit jobs to Rosetta@home, we often cut up a sequence into putative domains(based on algorithms like Ginzu and RosettaDom, developed by members of the Baker lab). Then we try to fold those pieces of the protein individually, and we can now use Rosetta@home (5.24 onwards) to take those individual sub-folds and pack them together into the final structure for the whole protein chain. Thanks for asking the question -- I'll post this clarification in the version log, too. Version 5.24 is up: |
Rhiju Volunteer moderator Send message Joined: 8 Jan 06 Posts: 223 Credit: 3,546 RAC: 0 |
There was a question in another thread about these mysterious comments on 5.24, so here's some clarification (I hope): The "symbol store" (a.k.a. the PDB file) is a file that translates the gobbledygook we get from the occasional Rosetta@home crash into plain English, so that we can track down where and why in the code an error occurs. It is super useful, but has been a little tricky to set up. The "prior predictions" of burial or exposure come from other neural networks that are trained to look at protein sequences and guess which parts are on the inside and outside of the fold. This was just a quick first implementation; you can expect more progress in September. As for "domains"... if a protein is more than ~150 residues long its just too difficult to sample every possible conformation extensively. Luckily most real proteins of large sizes (>200 residues) subdivide into domains of 70-150 residues that appear to fold into independent pieces that are not too intertwined with each other. So before we submit jobs to Rosetta@home, we often cut up a sequence into putative domains(based on algorithms like Ginzu and RosettaDom, developed by members of the Baker lab). Then we try to fold those pieces of the protein individually, and we can now use Rosetta@home (5.24 onwards) to take those individual sub-folds and pack them together into the final structure for the whole protein chain. Version 5.24 is up: |
Moderator9 Volunteer moderator Send message Joined: 22 Jan 06 Posts: 1014 Credit: 0 RAC: 0 |
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Bob_Pombrio Send message Joined: 5 Jun 06 Posts: 1 Credit: 20,574 RAC: 0 |
Rosetta 5.25 is up! How about some update instructions! I've also noted that if I stop running the graphics I do not get system lockups any longer on Win Xp. |
anders n Send message Joined: 19 Sep 05 Posts: 403 Credit: 537,991 RAC: 0 |
How about some update instructions! I've also noted that if I stop running the graphics I do not get system lockups any longer on Win Xp. Hi Bob The 5.25 app. uploads automatic, no need to do anything. About the grafics problem some grafic cards do have problems it´s not Win Xp. Check your Boinc client so you have the latest release. Happy cruching :) Anders n |
Astro Send message Joined: 2 Oct 05 Posts: 987 Credit: 500,253 RAC: 0 |
How about some update instructions! I've also noted that if I stop running the graphics I do not get system lockups any longer on Win Xp. I too used to get the fatal windows errors with Rosetta, but since 5.24 they've been gone. you might be able to use the screensaver again. tony |
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