Problems with .xtc trajectory visualization

[samira.alsadi@…]

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

[Eric Pettersen]

Hi Samira,

Thanks for reporting this problem. My reading of the third-party XTC/TRR-processing library code that ChimeraX is using to read the trajectory file indicates that error code 12 means that the library can't open the file.
Does the trajectory file name have an unusual (non-ASCII) character in its name, or do any of its parent folders have such characters in their names? If so, using a simpler name might work. One other possibility is that somehow you do not have "read" permission on the file itself -- it which case you would need to change the permissions.
If neither of these possibilities seem to be the culprit, perhaps you could send me the .gro/.xtc files (preferably with the .xtc truncated to just a few frames) and I could investigate further.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab