Old atomic import

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-07-31)
Description
open 6bna
addh hbond false

gives error below


Log:
UCSF ChimeraX version: 0.7 (2018-07-31)  
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102  
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open 6bna format mmCIF fromDatabase pdb

Summary of feedback from opening 6bna fetched from pdb  
---  
notes | Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 6bna #1  
---  
Chain | Description  
A B | DNA (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*(cbr)P*gp*cp*G)-3')  
  

6bna citation:    Kopka, M.L., Yoon, C., Goodsell, D., Pjura, P., Dickerson,
R.E. (1985). Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-
T-BrC-G-C-G. J.Mol.Biol., 183, 553-563. PMID: 2991536. DOI:
10.1016/0022-2836(85)90171-8  
Opened mmCIF data containing 594 atoms and 578 bonds  

addh hbond false

Termini for 6bna (#1) chain B determined from SEQRES records  
Termini for 6bna (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /B DC 13, /A DC 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B DG 24, /A DG 12  
Chain-final residues that are not actual C termini:  
Traceback (most recent call last):  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 55, in cmd_addh  
    add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 130, in simple_add_hydrogens  
    idatm_type, invert, coordinations.get(atom, []))  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/simple.py", line 34, in add_hydrogens  
    _alt_loc_add_hydrogens(atom, alt_loc_atom, *args, **kw)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/simple.py", line 77, in _alt_loc_add_hydrogens  
    idatm_type[atom], atom, (list(atom.neighbors)+coordinations)[0], 3.5)  
  File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 643, in find_rotamer_nearest  
    nb_sc = list(nb._addh_coord)  
AttributeError: 'Atom' object has no attribute '_addh_coord'  
  

AttributeError: 'Atom' object has no attribute '_addh_coord'  
  
File "/Users/goddard/Desktop/ChimeraX July 31
2018.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 643, in find_rotamer_nearest  
nb_sc = list(nb._addh_coord)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[pett]

The Cython code had some 'core.atomic' imports lurking in it, now removed.