id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
986	impressions of chimeraX	jir322@…	Conrad Huang	"{{{
Hi Conrad

I've been playing with the 1-8-18 daily build of chimeraX and have the
following observations.

1. nuc side atoms
not supported. Turning off the ribbons is the first thing I do
whenever I load RNA structures.

2. focus #1
not supported
(unknown command focus)

3. viewdockX
Since there is no dialog associated with viewdockX, thus it assumes
I've already loaded the mol2 as #2 say (?), I get an error opening a
DOCK 4 format mol2 file, a file that works perfectly well with
Chimera.

KeyError: 1

File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 181, in _make_structure
substid2residue[atom_data.subst_id].add_atom(atom)

I will send some example files in the following emails.


Thanks

John

If I am just being stupid, can we set up a time to go over this! We
are very keen on using the new ViewDockX features!

Ah, you use 1-origin numbering now.

On side view, the first thing I always do it turn off surface capping
so I can see the molecule I have cut into.  In this version, I tried
autoclip but I still see big colored surfaces not atoms when I clip
the molecule.

rep (resentation)
unknown command
Maybe there is a great reason why this command has changed.



Here is the full trackback for the failure to load a multi-molecule mol2 file
sample molecule file attached

Traceback (most recent call last):
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/gui.py"",
line 465, in _qt_safe
    run(session, ""open "" + quote_if_necessary(paths[0]))
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/run.py"",
line 31, in run
    results = command.run(text, log=log)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"",
line 2569, in run
    result = ci.function(session, **kw_args)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"",
line 42, in open
    from_database=from_database, ignore_cache=ignore_cache, **kw))
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"",
line 111, in open
    models = handle_unknown_kw(session.models.open, paths,
format=format, name=name, **kw)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"",
line 63, in handle_unknown_kw
    return f(*args, **kw)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"",
line 454, in open
    session, filenames, format=format, name=name, **kw)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"",
line 443, in open_multiple_data
    models, status = open_data(session, fspec, format=format, name=name, **kw)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"",
line 403, in open_data
    models, status = open_func(*args, **kw)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/__init__.py"",
line 34, in open_file
    return open_mol2(session, stream, file_name, auto_style, atomic)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 4, in open_mol2
    p = Mol2Parser(session, stream, name, auto_style, atomic)
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 77, in __init__
    while self._read_section():
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 98, in _read_section
    self._section_prelude()
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 221, in _section_prelude
    self._make_structure()
  File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/viewdockx/io.py"",
line 181, in _make_structure
    substid2residue[atom_data.subst_id].add_atom(atom)
KeyError: 1

}}}

[attachment:""firsttry.mol2""]
"	defect	closed	normal		Surface/Binding Analysis		fixed		chimera-programmers Elaine Meng				all	ChimeraX