Error saving mmcif with relModel option

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-20)
Description
Saving model as mmcif using relModel option.


Log:
UCSF ChimeraX version: 0.91 (2019-06-20)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs format session

Summary of feedback from opening
/Users/goddard/ucsf/chimerax/src/bundles/segger/test.cxs  
---  
warning | Unable to restore "SchemesManager" object  
  
opened ChimeraX session  

> ui mousemode rightMode "translate selected models"

> select /A:464@CA

1 atom, 1 model selected  

> fitmap #2 inMap #1

No atoms or maps for #2  

> fitmap #3 inMap #1

Fit molecule 1grl (#3) to map 1080 (#1) using 4182 atoms  
average map value = 1.359, steps = 116  
shifted from previous position = 17.9  
rotated from previous position = 76.5 degrees  
atoms outside contour = 777, contour level = 1.0158  
  
Position of 1grl (#3) relative to 1080 (#1) coordinates:  
Matrix rotation and translation  
0.23473368 -0.97036103 -0.05744179 8.89551209  
0.97199781 0.23364166 0.02513613 40.97958775  
-0.01097033 -0.06173360 0.99803237 0.12626413  
Axis -0.04466641 -0.02389456 0.99871616  
Axis point -21.54839580 26.10360575 0.00000000  
Rotation angle (degrees) 76.51423003  
Shift along axis -1.25041764  
  

> save /Users/goddard/Desktop/test.cif models #3 relModel #1

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.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/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 61, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 124, in write_mmcif  
save_structure(session, f, models, [xforms[m] for m in models],
used_data_names)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 533, in save_structure  
atom_site_residue(r, seq_id, asym_id, entity_id, model_num, xform)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 506, in atom_site_residue  
if xform:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 506, in atom_site_residue  
if xform:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Greg Couch]

Use "if x is not None:" instead of "if x:"