On Nov 6, 2024, at 8:16 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX users!

Dealing with the session contained loaded md trajectory of 10000 snapshots for a quite big system I got the following error trying to save this session

  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save
    Command(session, registry=registry).run(provider_cmd_text, log=log)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save
    saver_info.save(session, path, **provider_kw)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save
    return cxs_save(session, path, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922, in save
    session.save(output, version=version, include_maps=include_maps)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 651, in save
    fserialize(stream, data)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
    stream.write(packer.pack(obj))
                 ^^^^^^^^^^^^^^^^
  File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
  File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
  File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
  File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap
  File "src/_serialize.pyx", line 253, in chimerax.core._serialize._encode_ext
  File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
  File "msgpack/_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack
  File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
  File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap
  File "src/_serialize.pyx", line 226, in chimerax.core._serialize._encode_ext
  File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
  File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
  File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large

ValueError: bytes object is too large

File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.

Would it be possible to reduce the number of frames loaded as coordset e.g. closing the last 6000 frames ?

Many thanks in advance!

Enrico

_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/