Posts by Yifan Song

21) Message boards : Number crunching : minirosetta 2.15 (Message 67780) Posted 21 Sep 2010 by Yifan Song Post: minirosetta is updated to add new protocols for symmetrical oligomers and membrane proteins.
22) Message boards : Number crunching : minirosetta 2.11 (Message 66052) Posted 10 May 2010 by Yifan Song Post: It could be an error with server timed out. It's been busy with the app/database update as well as casp prep. All tasks erroed out when downloading. <core_client_version>6.10.43</core_client_version> <![CDATA[ <message> WU download error: couldn't get input files: <file_xfer_error> <file_name>relax_options_lrm_ghoo_sc12_run01_A_yfsong</file_name> <error_code>-224</error_code> <error_message>file not found</error_message> </file_xfer_error> <file_xfer_error> <file_name>S_rb1_1unr_native_0000.pdb</file_name> <error_code>-224</error_code> <error_message>file not found</error_message> </file_xfer_error> <file_xfer_error> <file_name>yfsong_lrm_ghoo_sc12_run01_A.zip</file_name> <error_code>-224</error_code> <error_message>file not found</error_message> </file_xfer_error> <file_xfer_error> <file_name>boinc_rb1_1unr.pdb</file_name> <error_code>-224</error_code> <error_message>file not found</error_message> </file_xfer_error> </message> ]]> I have reset and reattached the project with no result, stll the same error. Any idea what to do more? 7 different machines (Intel C2D, Xeon, WinXP x86, WinXP x64).
23) Message boards : Number crunching : minirosetta 2.14 (Message 66050) Posted 10 May 2010 by Yifan Song Post: More CASP related updates.
24) Message boards : Number crunching : Rosetta Application Version Release Log (Message 66049) Posted 10 May 2010 by Yifan Song Post: minirosetta 2.14 is out
25) Message boards : Number crunching : Minirosetta 2.00 (Message 64414) Posted 9 Dec 2009 by Yifan Song Post: Validate errors in workunits with the name: mix_score13_hb_rlbd_1ttz__IGNORE_THE_RESTlr13_DECOY_16324_* ... AdeB Thanks! There was a bug when we combine lr5, 8, 10 and 13 to make a large test. As a result, a few lr13 ones end up with too small input file and running too fast for the validation server. This should be fixed soon.
26) Message boards : Number crunching : Rosetta Application Version Release Log (Message 64413) Posted 9 Dec 2009 by Yifan Song Post: minirosetta 2.02 is up: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=5176
27) Message boards : Number crunching : minirosetta 2.02 (Message 64412) Posted 9 Dec 2009 by Yifan Song Post: minirosetta 2.02 is now up with bugs fixes for using earlier versions of input files.
28) Message boards : Number crunching : lr8_combine_smooth_torsion_it00 - All Errors? (Message 64230) Posted 26 Nov 2009 by Yifan Song Post: Yes, it should be safe now. The new 'redo' jobs should be good. :p
29) Message boards : Number crunching : lr8_combine_smooth_torsion_it00 - All Errors? (Message 64217) Posted 25 Nov 2009 by Yifan Song Post: Sorry about this error. It was a mistake from my side. It was a rather old submission, which I increased the running size and forgot that with the new version, those running flags are obsolete.
30) Message boards : Number crunching : Minirosetta 2.00 (Message 64012) Posted 11 Nov 2009 by Yifan Song Post: The large increase to the executable size could be due to the inclusion of a number of protocols that has been developed over the last 2 years. Those protocols were not able to compile with the boinc build until now. There shouldn't be any difference in running the tasks though, the only difference is the time it takes to update.
31) Message boards : Rosetta@home Science : mega score 12 rldb work units (Message 64010) Posted 11 Nov 2009 by Yifan Song Post: By looking at my results page, I see tasks with names of the form: mega_lrx_seq_score12_rlbd_xxxx_ ...and I note that those tend to have 500,000 or more models run, and they also tend to have RSMDs over 1.5. In other words, we ran 5 or 10 times more models and still did not come up with an answer as close to the true structure as we would like to be, or as close as we get for other proteins. I was curious what is behind these work units? What is being studied with the larger sample size? There are a few reasons to run these large tasks. 1. As Mike said, one of the main aim of these studies is not just finding the structure closest to the native one, but also to explore as much conformational space as possible, so that we can learn whether we can discriminate between the true structure and the wrong ones. 2. To get enough sampling so that we can improve energy functions to better reproduce structural features observed in native structures. 3. To get enough "wrong" high energy structures, analyze them, and explore new protocols to increase sampling efficiency. As for the sampling amount vs. rmsd, I think it should be noted that for crystal structures, the resolution also becomes poorer with the size of the protein. A 1.5Å resolution structure is still extremely useful for many types of studies. Second, the amount of phase space grows exponentially with the degrees of freedom, which is the length of the sequence. So, doing 5-10 times more sampling may not be that powerful if the protein is even just a few more residues bigger.
32) Message boards : Number crunching : Minirosetta 2.00 (Message 63966) Posted 6 Nov 2009 by Yifan Song Post: minirosetta 2.00 is now up. The energy function optimization we've been working on for the last few month are now in. This version also fixes some stability issues brought in by 1.98.
33) Message boards : Number crunching : Rosetta Application Version Release Log (Message 63965) Posted 6 Nov 2009 by Yifan Song Post: Minirosetta 2.00 is now up.
34) Message boards : Number crunching : Minirosetta 1.98 (Message 63886) Posted 30 Oct 2009 by Yifan Song Post: Mike has figured out where the bugs are and is currently working on them. there seems to be a conflict between the symmetry code and disulphide, which is why a lot of symm runs are failing. also, there is an api bug for zip, which causes some of the i/o problems. hopefully we'll be able to update at the beginning of next week.
35) Message boards : Number crunching : Minirosetta 1.98 (Message 63718) Posted 16 Oct 2009 by Yifan Song Post: Hmm, I can't figure out right away where these errors could be from. They are rather old work units which has been running ok. The same type of jobs also passed the alpha test on ralph for v1.98. I'll do some more tests over the weekend.
36) Message boards : Number crunching : Rosetta Application Version Release Log (Message 63717) Posted 16 Oct 2009 by Yifan Song Post: Sorry for the late post. Minirosetta v1.98 is up.
37) Message boards : Number crunching : Minirosetta 1.98 (Message 63695) Posted 15 Oct 2009 by Yifan Song Post: As David described in his journal (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#63383), we are working on improving energy functions. Currently, a lot of parameters are either defined in the code or in minirosetta_database. The new options allow us to test different energy functions from command line. One example of what we plan to test in the coming weeks is a hydrogen bond potential with sharper distance and angular dependence. As many of you know, hydrogen bond plays an important role in drug design, as well as in protein/DNA interface design for gene therapy. However the exact form and magnitude of hydrogen bond is still underdetermined. Now from command line we can change the shape of hydrogen bond potential, and test whether they agree with the experimental data we've collected. What do these "options" mean exactly?
38) Message boards : Number crunching : Minirosetta 1.98 (Message 63690) Posted 15 Oct 2009 by Yifan Song Post: A few more command line level options are added. Report bugs here.
39) Message boards : Number crunching : Granted Credit taking forever.... (Message 63371) Posted 15 Sep 2009 by Yifan Song Post: Thanks for all of your patience. The validator is indeed catching up. TFLOPS is steadily climbing as well. It sums up the last 24 hrs of credit, so it might take another day to get the TFLOPS value back to before.
40) Message boards : Number crunching : Granted Credit taking forever.... (Message 63342) Posted 14 Sep 2009 by Yifan Song Post: Thanks Yifan. Let's hope so. Though I note the bk1 and bk2 servers aren't running right now. Part of the problem or part of the solution? It's part of the solution. DEK rearranged the validator servers a bit. They are just temporarily not showing properly on the webpage.

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