Saving marker sets: Slices are not implemented

[karim.rafie@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-66-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-10-10)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/home/karim/Desktop/Ad41_Phenix/Ad41_ASUmap_correctHandedness_postprocessed_masked.mrc

Opened Ad41_ASUmap_correctHandedness_postprocessed_masked.mrc, grid size
270,270,250, pixel 1.09,1.09,1.09, shown at level 0.01, step 2, values float32  

> close #1

> open
/home/karim/Desktop/Ad41_Phenix/Ad41_map_correctHandedness_postprocessed_masked.mrc

Opened Ad41_map_correctHandedness_postprocessed_masked.mrc, grid size
1190,1190,1190, pixel 1.09, shown at step 1, values float32  

> ui mousemode rightMode "mark plane"

> ui mousemode rightMode "mark maximum"

> ui mousemode rightMode "delete markers"

> ui mousemode rightMode "delete markers"

> ui mousemode rightMode "delete markers"

> ui mousemode rightMode "delete markers"

> ui mousemode rightMode "delete markers"

> close #2

> ui mousemode rightMode "mark surface"

> ui mousemode rightMode "resize markers"

> ui mousemode rightMode "move markers"

> transparency 50

Invalid "format" argument: Should be one of 'aln', 'bmp', 'cmap', 'dcd',
'dsn6', 'fasta', 'gif', 'gltf', 'jpeg', 'markers', 'mmcif', 'mol2', 'mrc',
'mtz', 'obj', 'pdb', 'pir', 'png', 'ppm', 'pseudobonds', 'session', 'stl',
'tiff', or 'x3d'  

> save marker format markers models #2

Traceback (most recent call last):  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export  
result = self.export_func(session, path, **kw)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 42, in save_file  
return cmmfiles.write_cmm(session, path, models)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 21, in write_cmm  
f.write(markersets_as_xml(mlist))  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 87, in markersets_as_xml  
lines.append(markerset_as_xml(ms))  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 39, in markerset_as_xml  
rgb = tuple(r/255 for r in m.color[:3])  
NotImplementedError: Slices are not implemented.  
  
NotImplementedError: Slices are not implemented.  
  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 39, in markerset_as_xml  
rgb = tuple(r/255 for r in m.color[:3])  
  
See log for complete Python traceback.  
  

Invalid "format" argument: Should be one of 'aln', 'bmp', 'cmap', 'dcd',
'dsn6', 'fasta', 'gif', 'gltf', 'jpeg', 'markers', 'mmcif', 'mol2', 'mrc',
'mtz', 'obj', 'pdb', 'pir', 'png', 'ppm', 'pseudobonds', 'session', 'stl',
'tiff', or 'x3d'  

> save marker format markers models #2

Traceback (most recent call last):  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export  
result = self.export_func(session, path, **kw)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 42, in save_file  
return cmmfiles.write_cmm(session, path, models)  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 21, in write_cmm  
f.write(markersets_as_xml(mlist))  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 87, in markersets_as_xml  
lines.append(markerset_as_xml(ms))  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 39, in markerset_as_xml  
rgb = tuple(r/255 for r in m.color[:3])  
NotImplementedError: Slices are not implemented.  
  
NotImplementedError: Slices are not implemented.  
  
File "/usr/bin/chimerax-2019.10.10/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 39, in markerset_as_xml  
rgb = tuple(r/255 for r in m.color[:3])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.145
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Fixed.

Atom.color is returning a tinyarray which does not allow slicing. This should probably be changed since it is common to slice rgba[:3].