I am trying to read a silent file with the function poses_from_silent(), but I get an error about an unrecognized residue:
for pose in poses_from_silent(silentFile): pose
core.io.silent.SilentFileData: Reading all structures from silent.out core.io.silent.SilentFileData: Finished reading X structures from silent.out
$HOME/miniconda2/lib/python2.7/site-packages/pyrosetta-2018.31+release.231d1f3-py2.7-linux-x86_64.egg/pyrosetta/io/__init__.pyc in poses_from_silent(silent_filename) 66 ss = sfd.get_structure(tag) 67 pose = Pose() ---> 68 ss.fill_pose(pose) 69 yield pose
File: /home/benchmark/T/rosetta.Glass/_commits_/main/source/src/core/pose/annotated_sequence.cc:191 [ ERROR ] UtilityExitException ERROR: can't find residue type for XX at pos XXX in sequence M[MET:NtermProteinFull]...
However, when I am working with a single pdb file there is no problem to do this; I am currently loading the params file, for a single pdb, with the function pose_from_file() as follows:
pose = Pose() generate_nonstandard_residue_set(pose,paramsFile) pose_from_file(pose, pdbFile)
which loads correctly the params file into a new pose object and then it is passed to the pose_from_file() function.
Is there an analog way for loading the params file as to be read by the poses_from_silent() function?