Added hydrogen names

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-07-03)
Description
Small and nitpicky, but AddH's number of hydrogen atoms on aliphatic CH2 carbons seems out of step with the standard nomenclature (starting from 2 rather than 1). In 6e2a, for example, the C1 and C3 atoms of GOL (/A:404) get hydrogens named H12,H13 and H32,H33 respectively. In the CCD template, the numbering of these hydrogens is 11,12/31,32. 

In most cases this is meaningless, of course, but PHENIX for example will refuse to go forward if it finds any atom with an unexpected name. Of course, one can just delete the hydrogens and let PHENIX regenerate them to its liking, but I can see users getting annoyed at that.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-07-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6e2a.pdb

6e2a.pdb title:  
Crystal structure of nadh:quinone reductase PA1024 from pseudomonas aeruginosa
PAO1 In complex with nad+ [more info...]  
  
Chain information for 6e2a.pdb #1  
---  
Chain | Description  
A | nitroalkane oxidase  
  
Non-standard residues in 6e2a.pdb #1  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAD — nicotinamide-adenine-dinucleotide  
  

> addh

Summary of feedback from adding hydrogens to 6e2a.pdb #1  
---  
notes | Termini for 6e2a.pdb (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 2  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLY 327  
772 hydrogen bonds  
Adding 'H' to /A GLY 2  
/A GLY 327 is not terminus, removing H atom from 'C'  
2812 hydrogens added  
  

> toolshed show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  
Fetching CCD definition for residue FMN A401  
Fetching CCD definition for residue NAD A402  
Fetching CCD definition for residue GOL A403  
Fetching CCD definition for residue HOH A501  

> select /A:404@C2

1 atom, 1 model selected  

> select up

14 atoms, 13 bonds, 1 model selected  

> select clear

> cofr centerOfView

> cofr centerOfView showPivot true

> select /A:404@C1

1 atom, 1 model selected  

> select /A:404@C2

1 atom, 1 model selected  

> select clear




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

[Eric Pettersen]

That hydrogen naming scheme is certainly inconsistent with the naming in peptide residues, e.g. all of the CH2 hydrogens in an LYS side chain use 2/3, not ½. Not sure why it's one way there and another way in GOL.

[Eric Pettersen]

Seems pretty consistent for ligands to use ½ instead of 2/3 though. Will see what I can shoehorn in there.