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fragment building

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fragment building

I used the Rosetta web site to generate fragments (3, 9) for the purpose of modeling a protein. The protein(template) I want to model was the template used to generate the fragments. However, when I use those fragments generated by the Rosetta server to model by template protein, I got:

core.fragments.ConstantLengthFragset: line too short skipping line

I then compare the fragment files generated by Rosetta web site to those used in a tutorial...The format is the same. Of course, the contents are different but everything else appears to be identical.

Can some one help me here? I'm at a loss as to what to attempt next...

Thanks, Steve

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Tue, 2015-08-04 09:01

Hey Steve,

All I could find was this:

I know I had a problem using the fragment picker on Robetta for loop fragments where I had to go in and manually change something due to weird format issues, but I completely forget what that entailed.

Tue, 2015-08-04 11:05

That error message occurs when you're trying to read in a fragment file, and a line which is less than 22 characters is encountered.

It's hard to say for certain without seeing the file, but it could be that you have a "blank" like which actually has unprintable characters on it. (One easy way to get that is by having a DOS/Unix line ending mismatch. DOS (Windows) style line endings have an "extra" character when compared to Unix-style ones, so if you read a DOS-style file in Unix-style mode, you can get issues.)

Another reason for the error is comment lines which don't have the '#' as the very first character on the line. (e.g. don't indent the comment with spaces).

Thu, 2015-08-06 08:29

Thanks for your comments…It turns out that when I copied and pasted the fragment texts they were formatted in “dos” instead of “unix” which my linux pyrosetta version requires, and so, once I realized this I just did a dos2unix format change on my fragment filles…This worked fine....

Again, thanks for your comments….helped me realize what was wrong….


Thu, 2015-08-06 11:07