rosetta3.4 fragment file problem

[Anonymous]

In Rosetta 3.4, the fragment picker puts out a new format. AbinitioRelax does not recognize it. I get this error:

ERROR: no fragment to compute secondary structure
ERROR:: Exit from: src/core/fragment/SecondaryStructure.cc line: 68

If I run exactly the same command but with the old style fragment files, it works fine. Is there something I’m missing?

[Anonymous]

I’m not aware of anything changing in fragment picking or AbinitioRelax for 3.4. I’ll ask around.

[Anonymous]

I realize now that the make_fragments.pl script option -old_name_format does more than keep the filename format the same. It actually changes the format of the fragment files. I’ve turned that option on by default in make_fragments.pl. I’m guessing fragment_picker is the same, but the make_fragments.pl script is different.

[Anonymous]

David Kim has made changes to make_fragments.pl that would have been released with 3.4, but he tells me none of the changes are to the format and that he wonders if it’s a platform issue.

[Anonymous]

Hi

Yes, in general fragment_picker is the same, although from time to time someone adds extra columns on the right side of the file. I presume make_fragments.pl removes them when asked to do so. I don’t think the fact that now the file format is different causes any trouble; it has been extensively tested in ab-initio.

[Author]

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