Write PDB: 'polymeric_res_names' arg is not a sequence

[doonam@…]

The following bug report has been submitted:
Platform:        Darwin-17.3.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-10-06)
Description
I tried to save pdb file

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-10-06)  
How to cite UCSF ChimeraX  

open /Users/doonam/Dropbox/ScottB_Coot_session/MIA.pdb ↵

Summary of feedback from opening
/Users/doonam/Dropbox/ScottB_Coot_session/MIA.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
23 messages similar to the above omitted  
  

addh hbond false ↵

Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
Unknown hybridization for atom (P) of residue type MIAA  
24 hydrogens added  

save h_.pdb ↵

Traceback (most recent call last):  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.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
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/__init__.py", line 50, in save_file  
    rel_model=rel_model, serial_numbering=serial_numbering)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/pdb.py", line 108, in save_pdb  
    (serial_numbering == "h36"), polymeric_res_names)  
TypeError: 'polymeric_res_names' arg is not a sequence  
  
TypeError: 'polymeric_res_names' arg is not a sequence  
  
File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/pdb.py", line 108, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  

save h.pdb ↵

Traceback (most recent call last):  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.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
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/__init__.py", line 50, in save_file  
    rel_model=rel_model, serial_numbering=serial_numbering)  
  File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/pdb.py", line 108, in save_pdb  
    (serial_numbering == "h36"), polymeric_res_names)  
TypeError: 'polymeric_res_names' arg is not a sequence  
  
TypeError: 'polymeric_res_names' arg is not a sequence  
  
File
"/private/var/folders/6q/0gtmbyf129g94z9fkcnq9k_40000gn/T/AppTranslocation/88A39E66-4D3E-44B5-8ED4-BA4C31A1847A/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/pdb/pdb.py", line 108, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.30.12
OpenGL renderer: Intel(R) Iris(TM) Graphics 650
OpenGL vendor: Intel Inc.

[Eric Pettersen]

Thanks for reporting this. It will be fixed in tonight's build. For just adding hydrogens and wrting a PDB file, you could use regular Chimera instead ChimeraX if you need to get it done today.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Now fixed. In next daily build.