id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15080 Better handling of multi-character chain IDs for Modeller Elaine Meng Eric Pettersen "There is something seriously weird about this structure, and I can reproduce that Modeller gives a failure message, but I don't know which part of the data that it hates. Even if I delete the ligand before modeling missing segments, it still fails, so maybe it's something with the sequence. open 7b6w format mmcif fromDatabase pdb delete ligand seq chain /AAA ui tool show ""Model Loops"" modeller refine 1/AAA:1:internal-missing numModels 2 fast false adjacentFlexible 1 protocol standard -> fails with Modeller error output Traceback (most recent call last): File ""ModellerModelling.py"", line 95, in a.make() File ""/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py"", line 42, in make AutoModel.make(self, exit_stage) File ""/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py"", line 141, in make self.homcsr(exit_stage) File ""/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py"", line 624, in homcsr self.check_alignment(aln) File ""/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py"", line 577, in check_alignment aln.check() File ""/usr/lib64/python3.8/site-packages/modeller/alignment.py"", line 213, in check self.check_structure_structure(io=io) File ""/usr/lib64/python3.8/site-packages/modeller/alignment.py"", line 222, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number "" FIRST"", chain "" AAA""; atom file name: ./7b6w_1.pdb" defect assigned moderate Structure Prediction all ChimeraX