P.S. one question- if I apply the smooth md script on the trajectory and then cut it using your python script, do I need to apply the smooth md script again on the truncated coordset ? Il giorno mer 6 nov 2024 alle ore 20:29 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Thank you very much Eric !
Cheers
Enrico
Il giorno mer 6 nov 2024 alle ore 17:36 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, You would have to use Python. I've attached a script that will lop off the last half of a trajectory's frames. You could run it multiple times to keep lopping off half.
--Eric
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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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 <http://chimerax-1.8.app/Contents/Library/Frameworks/Python.framework/Version...>", 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/