Unsolved

In one of my ROSIE docking2 local_docking jobs (17702), I noticed that its tar archive's output\trigger-00001.dock folder contained several files like proteins_0130.in_progress.bz2 with the unusual size of 42 bytes in addition to many files like proteins_0129.pdb.bz2 and proteins_0131.pdb.bz2 with the more typical size of 82-84 kbytes. Do you know what causes these "in_progress" files to occur and how I can prevent them from occurring? Is the cure as simple as re-opening the job's web page and then reloading its tar archive file?

Thanks!

One of my docking2 docking_local_refine jobs (#17790) output many structures with Fnat=NaN. I am used to seeing Fnat near 1 when the rms value is low and Fnat near 0 when the rms value is high. What would make Fnat give a value of NaN? Should I trust the other scores given for this run? How can I prevent future runs from giving Fnat=NaN?

Thanks!

Hi,

I have a couple questions about fold-trees and how interfaces are calculated in pyrosetta (or rosetta).  I have a structure of an antibody-antigen that I have prepared using rosetta (attached).  A visual inspection shows that residue B:TYR210 is making a number of close contacts with residues in Chain C (the antigen).  However, when I construct an Interface object in pyrosetta, this residue is not identified as being in the interface (using a cutoff of 5.0A):

from rosetta import *

Hi developers,

I wasn't sure where to submit bug reports so I'm posting here instead.

I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.