id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1931	Atom spec parsing consumes torsion command angle argument	goddard@…	Conrad Huang	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-09)
Description
open 5c1m
torsion /A:84@CD1,CG,CB,CA -109
Must specify exactly 4 atoms for 'torsion' command; you specified 3 
torsion /A:84@CD1,CG,CB,CA -109.0

Atom spec parsing gobbles the angle argument in the torsion command if the angle is a negative integer and results in an error where only 3 atoms of the 4 specified in the torsion command are recognized.  Works correctly if the angle has a decimal point.

Atom spec parsing should not consume the extra argument.




Log:
UCSF ChimeraX version: 0.9 (2019-05-09)  
© 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  
  
  

> torsion /A:84@CD1,CG,CB,CA -109

Must specify exactly 4 atoms for 'torsion' command; you specified 3  

> torsion /A:84@CD1,CG,CB,CA -109.0




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

}}}
"	defect	closed	normal	1.0	Command Line		fixed		Eric Pettersen Elaine Meng				all	ChimeraX