id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9812	Problems with .xtc trajectory visualization	samira.alsadi@…	Eric Pettersen	"{{{
Upon loading a .gro file and then opening an .xtc file to view a Gromacs trajectory, while the .gro file is shown correctly, it won't let me open the trajectory, showing the error message:


Traceback (most recent call last):
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\open_command\dialog.py"", line 162, in _qt_safe
    run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + (""""
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py"", line 38, in run
    results = command.run(text, log=log, return_json=return_json)
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2897, in run
    result = ci.function(session, **kw_args)
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 119, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2897, in run
    result = ci.function(session, **kw_args)
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 194, in provider_open
    models, status = collated_open(session, None, [data], data_format, _add_models,
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 464, in collated_open
    return remember_data_format()
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py"", line 435, in remember_data_format
    models, status = func(*func_args, **func_kw)
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\md_crds\__init__.py"", line 100, in open
    num_coords = read_coords(session, data, structure_model, md_type,
  File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\md_crds\read_coords.py"", line 21, in read_coords
    num_atoms, coords_list = read_xtc_file(file_name)
ValueError: read_xtc_natoms failure; return code 12

ValueError: read_xtc_natoms failure; return code 12

File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\md_crds\read_coords.py"", line 21, in read_coords
num_atoms, coords_list = read_xtc_file(file_name)


What could it be? I have a 121000 atom-system. It showed the same error with a .trr file, so I thought I would convert my trajectory into a lighter .xtc format, but apparently that isn't the issue. Is the system too big? I might try removing water molecules.



Thank you in advance,

Samira Al Sadi


}}}
"	defect	closed	normal		MD/Ensemble Analysis		can't reproduce						all	ChimeraX