I am in need of some major help.
I am running the SEWING application because I am copying the secondary structures that fit onto a particular primer, and some key binding residues are located on the loop between two beta strsnds - so I need to generate a new segment file with a few beta strands.
The problem is that when I start running the segment file generator code on the linux terminal, it ends with just "parsing motif file" and I have no output. The motif file is in DSSP in just the same format the example page shows. I attatched the command lines in a text file below (have tried with and without "-output:file:all" and got the same result.
Can anybody help?
Some things to note:
- I am running ubuntu linux off of a bootable USB, and use storage by mounting my computer's hard drive
- I am way more fluent in PyRosetta, so if anybody knows if pyrosetta has a segment file generation, please tell... I haven't seen anything on the pyrosetta directories.