id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1937	Cannot find consistent set of bond orders for ring	goddard@…	Eric Pettersen	"{{{
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.

}}}
"	defect	accepted	minor		Structure Analysis								all	ChimeraX