Two H-bond pseudobonds between same atom pair

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2019-12-24)
Description
The hbond command makes two hydrogen bonds between the same pair of atoms (one being a water).  For example in 4n6h atom :EJ4@OAA and water :1324@O have two pseudobonds between them when hbond :EJ4 is used.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2019-12-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4n6h format mmCIF fromDatabase pdb

4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  
  

> hbonds :EJ4

10 hydrogen bonds found  

> delete pbonds sel

> select #1.2

9 pseudobonds, 1 model selected  

> delete pbonds sel

> select #1.2

8 pseudobonds, 1 model selected  

> select :1324

1 atom, 1 model selected  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

This is deliberate. There is one pseudobond for every donor→acceptor H-bond. For the two atoms in question, either one could be the donor/acceptor, hence two pseudobonds. The total number of pseudobonds equals the total number of D→A H-bonds found.