No spacegroup of name i 4

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
Trying new open command structureFactors option produced this error.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1a0m structureFactors true

Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 249, in
symmetry_from_model_metadata_mmcif  
spgr_descr = Spgr_descr(spgr_str)  
RuntimeError: Spgr_descr: No such SG number  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 43, in open  
db_models = _fetch_from_database(session, db_id, db_name, db_format, name,
ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 434, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 383, in fetch_cb  
return fetch_shim(session, identifier, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 330, in fetch_mmcif  
mmgr = get_map_mgr(models[0], create=True)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 149, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 145, in get_symmetry_handler  
return Symmetry_Manager(structure)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 433, in __init__  
self.cell, self.spacegroup, self.grid, self._has_symmetry = f(*args)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 166, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_mmcif(model)  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 251, in
symmetry_from_model_metadata_mmcif  
raise RuntimeError('No spacegroup of name {}!'.format(spgr_str))  
RuntimeError: No spacegroup of name i 4!  
  
RuntimeError: No spacegroup of name i 4!  
  
File
"/Users/goddard/Desktop/ChimeraX-0.9-rc-2019.06.05.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/symmetry.py", line 251, in
symmetry_from_model_metadata_mmcif  
raise RuntimeError('No spacegroup of name {}!'.format(spgr_str))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

"open 6fk0 structureFactors true" worked. Maybe 1a0m has some problem?

[Tom Goddard]

Also tried 3k2f. It opened without errors but the initial threshold levels were unusably low.

[tic20@…]

1a0m is *very* old - from before the days when deposition of structure 
factors to the PDB were mandatory, in fact. A lot of deposition 
standards have changed. Will investigate this case further in the 
morning.

On 2019-06-05 18:59, ChimeraX wrote:

[tic20@…]

At present, the maps load with a pretty common "default" contour level 
in crystallography (1.5 sigma for normal maps, +/- 3 sigma for 
difference maps). Works out fine in most cases - but I can certainly 
look into some more intelligent model-by-model choice of contour levels. 
Adjusting the contours is mapped to the scroll wheel, and ctrl-scroll 
will let you choose which map you want to contour.

On 2019-06-05 19:04, ChimeraX wrote:

[goddard@…]

Most ChimeraX users will not have a scroll-wheel.  Half of users are likely to be on laptops with a trackpad  Changing scroll wheel behavior from zoom means those that do use that input device will no longer have a mouse binding to zoom, a pretty critical capability.

[tic20@…]

I'm happy to discuss alternatives (including special options for 
pure-touchpad users), but scroll-to-contour is standard in every 
existing crystallography visualisation program I know of. Clipper 
provides a special zoom mouse mode (which brings the camera "inside" the 
model and narrows/widens the gap between clipping planes to provide 
depth cueing) mapped to shift-right-drag. I don't map anything to the 
un-modified right mouse button, so all the standard ChimeraX right mouse 
modes are still available.

On 2019-06-05 19:28, ChimeraX wrote:

[tic20@…]

The problem you ran into with 1a04 is trivial to fix: for some reason in 
that file the space group descriptor has been stored in lowercase (which 
is wrong - first time I've ever seen it). I'll just need to add a line 
to convert to upper. Weirdly, I don't actually get the error - I guess I 
get served the file from a different server, because the one I have also 
has the space group number which takes precedence over the name.

It still runs into trouble later down the track, when trying to work out 
the value of the flag for the free reflections (a surprisingly fraught 
task - essentially no standards here). I suspect it's tripping up 
because this structure is so tiny that the number of free reflections is 
smaller than I anticipated... will investigate tomorrow.

On 2019-06-05 18:54, ChimeraX wrote:

[goddard@…]

Aha.  ChimeraX cached my 1a0m.cif file and it was from 2011.  When I removed that cache file I get the different traceback with error message:

RuntimeError: Cannot determine the correct value for the free reflections in the given FreeR_flag array. Please convert your reflection file to CCP4 or PHENIX format using sftools or phenix.reflection_file_editor. 

[Tom Goddard]

This error was with an old copy of 1a0m.cif from 2011. Probably this does not need fixing if the data was simply bad (lower case space group name) so I am closing this ticket.

Opening the current 1a0m produces another error #2005.