You are here

rosetta3.4 fragment file problem

5 posts / 0 new
Last post
rosetta3.4 fragment file problem

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/ 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?

Post Situation: 
Wed, 2012-05-16 14:42
David Hoover

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

Thu, 2012-05-17 07:03

I realize now that the 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 I'm guessing fragment_picker is the same, but the script is different.

Thu, 2012-05-17 08:06
David Hoover

David Kim has made changes to 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.

Fri, 2012-05-18 12:16


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 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.

Wed, 2012-05-23 05:33