I guess it would depend on the format of the original trajectory file, but for a DCD trajectory file I tested the resulting ChimeraX session was very similar in size.  However I would expect a session to be considerably smaller than a PDB-format trajectory since: 1) PDB is ASCII, and 2) there is a ton of duplicated information in a PDB trajectory (atom names, residue names, etc.).

--Eric

On Mar 12, 2024, at 1:30 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Okay I gotcha thank you very much Eric !

BTW I noticed that the chimera-X session containing a loaded md trajectory typically occupy less space compared to a single file (pdb or netcdf) of the same trajectory without any visualisation ..

Enrico

Il giorno lun 11 mar 2024 alle ore 21:39 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico,
ChimeraX relies on MessagePack for its session saving, and MessagePack has a limit of 4.3GB for a single object, and your loaded trajectory model must be larger than that.  Saving a session with all your trajectory data would use a bunch of disk space and be slow to load.  I’d recommend instead just working with your original non-trajectory structure, saving that as a session once it’s the way you want, and then after restoring that session then load in the full trajectory coordinates.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Mar 10, 2024, at 1:04 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera-X users!

I got the following error on my  iMAC equipped with Intel CPU after an attempt to save a Chimera-x (ver 1.71) session containing a loaded netcdf trajectory with 7500 frames (with the same system containing only 5000 frames, ain't no problems !!).

Yours with thanks

Enrico

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127, in <lambda>
    lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file",
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
    _dlg.display(session, **kw)
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62, in display
    run(session, cmd)
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912, in save
    session.save(output, version=version, include_maps=include_maps)
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641, in save
    fserialize(stream, data)
  File "/Applications/ChimeraX-1.7.1.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 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.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 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.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.
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