Cannot find consistent set of bond orders for ring

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-14)
Description
Not sure if this "cannot find consistent set of bond orders for ring system" message is expected.  I get this message for every residue swap done on this structure -- with the swapaa mouse mode this can be a lot of swaps in just one drag, so the messages fill the log.


Log:
UCSF ChimeraX version: 0.9 (2019-05-14)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5c1m format mmCIF fromDatabase pdb

Summary of feedback from opening 5c1m fetched from pdb  
---  
warning | Cannot find consistent set of bond orders for ring system containing
atom CAV in residue 4VO /A:401  
  
5c1m title:  
Crystal structure of active mu-opioid receptor bound to the agonist BU72 [more
info...]  
  
Chain information for 5c1m #1  
---  
Chain | Description  
A | Mu-type opioid receptor  
B | Nanobody 39  
  
Non-standard residues in 5c1m #1  
---  
4VO —
(2S,3S,3aR,5aR,6R,11bR,11cS)-3a-methoxy-3,14-dimethyl-2-phenyl-2,3,3a,6,7,11c-hexahydro-1H-6,11b-(epiminoethano)-3,5a-methanonaphtho[2,1-g]indol-10-ol
(BU72)  
CLR — cholesterol  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PO4 — phosphate ion  
  
  

> swapaa :243 ALA

Cannot find consistent set of bond orders for ring system containing atom CAV
in residue 4VO /A:401  




OpenGL version: 4.1 ATI-2.8.38
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Kind of a nexus of unlikely events: rapidly modifying a structure with a ring system complicated enough (and with poor enough geometry) that the IDATM code can't figure out the bond orders. The (low priority) fix is to see if the code can be improved to successfully determine the bond orders.