Posts by olange

1) Message boards : RALPH@home bug list : minirosetta v1.43 bug thread (Message 4379)
Posted 3 Dec 2008 by olange
Post:
Hi Path7, thanks for the report.

the application should make checkpoints pretty regularly. also the runtime looks really long. I will run this WU locally and check things out.

what CPU was this WU running on ?

-Oliver
2) Message boards : RALPH@home bug list : Ralph v1.42 (Message 4366)
Posted 27 Nov 2008 by olange
Post:
Hi Conan,

the loop-errors are indeed an error in the input data. It shows why the ralph-project is so useful to us. Without ralph I would'nt have been able to spot these errors before running the jobs in a bigger scale on boinc.

For the current project - development of a general and automatable comparative modelling machinery - we have ca. 40 target proteins each coming with 200 alignments to homologues proteins. These homologues proteins are somewhat similar to the target, and hence provide valuable structural clues, however, some parts are wrong and other parts are missing. A typical strategy is to rebuild everything which is missing and a couple of residues around that region.
We are curious, however, if we can improve on that by also rebuilding other parts of the aligned regions, since these can be quite far from the target structure.
Right now we try to find out where exactly we should struck the balance between rebuilding and copying homologues structure. This requires to scan a range of cutoffs. this is done by a script that creates loop-files, which encode exactly what has to be rebuild and what shall be kept rigid.
The script generated 40*200*10 = 80.000 files. A lot of files. Due to a bug in the script, however, some contained subtle errors. I checked a handful of input conditions on our local machines and they were fine. So I went ahead and checked a larger number of input conditions on ralph. This revealed errors in some cases and thus valuable information to revise the script.

Thank you for your interest and your help crunching for our science,
Oliver






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