I have run into difficulties when trying to model loops in ChimeraX. I have successfully aligned the structure with the FASTA sequence, but no matter which switch I use in the command
i.e., all-missing, internal-missing, or only a selected region, I get identical error:
Opened 1 sequence from 7tdg.fasta
Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps
modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard
Exception in thread Thread-18 (_run_function):
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 1038, in _bootstrap_inner
self.run()
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)