I have a protein which has a few PTMs in the form of sugars, and I have therefore started experimenting with sugars in PyRosetta. I have found a very nice guide:
which I have used as a starting point together with the documentation e.g.
I start out by initializing PyRosetta with the appropriate options, and import the specific methods I need:
from pyrosetta import * pyrosetta.init('-include_sugars','-write_pdb_link_records') from pyrosetta.rosetta.core.pose.carbohydrates import glycosylate_pose from pyrosetta.rosetta.core.pose import make_pose_from_saccharide_sequence, pose_from_saccharide_sequence
However, whenever I try to use the methods I get runtime errors. If I e.g. enter:
mannose = pose_from_saccharide_sequence('->3)-a-D-Manp')
ERROR: Unrecognized residue ->3)-alpha-D-Manp when building saccharide sequence ->3)-a-D-Manp ERROR:: Exit from: /Volumes/MacintoshHD3/benchmark/W.fujii/rosetta.Fujii/_commits_/main/source/src/core/pose/annotated_sequence.cc line: 478 BACKTRACE: (lot of lines ala 1 ‘rosetta.so 0x000000012135ff78 rosetta.so + 71184248’)
I got the input for ‘pose_from_saccharide_sequence’ from the guide I linked above, so it should be correct. The documentation states that it:
“Return a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name”. I am not an expert on sugars, but as far as I can tell is the input used above ok. I have also tried to input simply ‘galp’, which also does not work.
Can anyone see what I am doing wrong?
My setup is
MacOS 10.14, python 3.6.6, Pyrosetta: PyRosetta4.Release.python36.mac r206