AddH: acc_phi_psi() takes 8 positional arguments but 9 were given

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-15)
Description
Structure protonation

Log:
UCSF ChimeraX version: 0.9 (2019-01-15)  
How to cite UCSF ChimeraX  

> open 1k5k fromDatabase pdbe_updated

Summary of feedback from opening 1k5k fetched from pdbe_updated  
---  
warnings | Atom H1 is not in the residue template for MET #1 in chain A  
Mismatched number of atoms (1379 vs. 1374)  
  
1k5k title:  
Homonuclear 1H Nuclear Magnetic Resonance Assignment and Structural
Characterization of HIV-1 Tat Mal Protein [more info...]  
  
Chain information for 1k5k  
---  
Chain | Description  
1.1/A 1.2/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | TAT protein  
1.3/A | TAT protein  
  
  

> addh hbond true

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 1k5k #1.3/A PRO 14 N because it is missing
heavy-atom bond partners  
Not adding hydrogens to 1k5k #1.3/A PRO 14 CA because it is missing heavy-atom
bond partners  
Not adding hydrogens to 1k5k #1.3/A PRO 14 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 1k5k #1.3/A PRO 14 CD because it is missing heavy-atom
bond partners  
Not adding hydrogens to 1k5k #1.3/A PRO 14 HD3 because it is missing heavy-
atom bond partners  
449 messages similar to the above omitted  
Unknown hybridization for atom (O) of residue type PRO; not adding hydrogens
to it  
Unknown hybridization for atom (O) of residue type GLY; not adding hydrogens
to it  
Unknown hybridization for atoms (OG, O) of residue type SER; not adding
hydrogens to them  
notes | Termini for 1k5k (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1k5k #1.1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 1k5k #1.1/A GLU 87  
Chain-final residues that are not actual C termini:  
55 hydrogen bonds  
Termini for 1k5k (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1k5k #1.2/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 1k5k #1.2/A GLU 87  
Chain-final residues that are not actual C termini:  
57 hydrogen bonds  
No usable SEQRES records for 1k5k (#1.3) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 1k5k #1.3/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 1k5k #1.3/A SER 16  
Chain-final residues that are not actual C termini:  
donor: 1k5k #1.3/A SER 16 N acceptor: 1k5k #1.3/A PRO 21 O  
  
Traceback (most recent call last):  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2612, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 58, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 158, in hbond_add_hydrogens  
in_isolation=in_isolation, **prot_schemes)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 166, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 243, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 594, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/F6EC338C-8C32-40FE-825D-A7B8BC4C6DA7/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 594, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.9
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

This is because of the mmCIF reader messing up the connectivity of some members of NMR ensembles, and therefore a duplicate of #1195. I have added lpravda@… to the cc list for that ticket. The PDB version of 1k5k works fine. Also, it would seem unnecessary to add hydrogens to NMR ensembles!