impressions of chimeraX

[jir322@…]

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

firsttry.mol2​

[jir322@…]

Added by email2trac

[Elaine Meng]

Hi John,
I think all your problems are solved!  :-D


Currently, ChimeraX does not automatically show nucleotide representations like Chimera does. The nucleotides command only affects special nucleotide sidechain representations, not ribbons (and this was also true in Chimera). You can turn off ribbons in ChimeraX with “~cartoon” (or “~ribbon” or “hide cartoon” or “hide ribbon” or “cartoon hide” or “ribbon hide”).

http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html
http://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html

If you did have nucleotide sidechain representations like slabs and/or tubes, the command to turn them off and show atoms instead in ChimeraX is “~nuc” (same as in Chimera) or “nuc atoms” (different from Chimera).  However, neither of these turn off ribbons, nor did they in Chimera.

http://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.html


Command in ChimeraX is “view” or “view #1”

http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html


Just open the file first, e.g. command  “open ~/Desktop/myfile.mol2” and then use command “viewdockx” 

http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html

I hope this helps,
Elaine

[Elaine Meng]

Oops, missed a couple.  


Autoclip means don’t clip anything (keep planes outside structures). 
http://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html

Sorry, I guess there isn’t a solution to this one yet (no way to turn off a surface cap in ChimeraX), other than to hide the surface or make it transparent.


The ChimeraX command is “style."  We made changes that we thought were improvements in usability/mnemonics.  (atomspecs have also changed in various ways, e.g. chain symbol is / now)

http://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html
http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html

[jir322@…]

Hi Elaine

Thanks for all this.  All great, except my multi-mol2 files don't
read. May I drop by to chat?

John

John Irwin
UCSF Pharmaceutical Chemistry
http://irwinlab.compbio.ucsf.edu


On Mon, Jan 8, 2018 at 1:42 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

[Conrad Huang]

The mol2 files should work in tomorrow's build. ChimeraX expected a "substructure" section for each model. It now just makes something up, like Chimera 1.

[jir322@…]

thank you thank you!

We can obviously change our code, but if you can accommodate this
Chimera-compatible format it would be ideal for legacy files.

On Mon, Jan 8, 2018 at 4:56 PM, ChimeraX
<ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

[Tom Goddard]

I added the ability to turn off the surface cap over the hole created by clipping. The command is "surface cap false". There is also a preference setting, menu ChimeraX/Preferences... on Mac under the Clipping tab, Surface caps. You can turn that off and press the Save button so clipping will leave holes for all future sessions.

[Conrad Huang]

Nucleotides code has been updated to provide many more display options, all accessible from the tabbed toolbar.