AddH fails after residue deletion

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.5.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-02-19)
Description
AddH fails after deleting a residue within a chain. If I look at `chain.residues` for the offending chain, `None` is inserted in place of the deleted residue.

Log:
> select /D:6

14 atoms, 14 bonds, 1 model selected  

> delete sel

> addh hbond true

Summary of feedback from adding hydrogens to 6g2j_h.pdb #1.3  
---  
notes | No usable SEQRES records for 6g2j_h.pdb (#1.3) chain A; guessing
termini instead  
No usable SEQRES records for 6g2j_h.pdb (#1.3) chain B; guessing termini
instead  
No usable SEQRES records for 6g2j_h.pdb (#1.3) chain C; guessing termini
instead  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2617, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 58, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 163, in hbond_add_hydrogens  
_prep_add(session, structures, unknowns_info, **prot_schemes)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 407, in _prep_add  
real_N, real_C, fake_N, fake_C = determine_termini(session, structures)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/util.py", line 47, in determine_termini  
rn, rc, fn, fc = guess_termini(chain)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/util.py", line 132, in guess_termini  
if res.number + 1 < next_res.number:  
AttributeError: 'NoneType' object has no attribute 'number'  
  
AttributeError: 'NoneType' object has no attribute 'number'  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/util.py", line 132, in guess_termini  
if res.number + 1 < next_res.number:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Problem only occurs if SEQRES records (or mmCIF equivalent) are missing. Fixed.