id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
1310	"Help link in Log wrong URL for ""bumps"" command"	Elaine Meng	Greg Couch	"{{{
The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-09-15)
Description
Help link in Log wrong URL for ""bumps"" command

I have a bumps.html manpage in the same place as for other commands, but the helplink in the Log looks somwhere else.

E.g. just try using “bumps” without arguments to get the Log link, then click that link, to get traceback:


 No help found for 'help:/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bumps/bumps.html'



Log:
UCSF ChimeraX version: 0.8 (2018-09-15)  
How to cite UCSF ChimeraX  

open 1zik format mmCIF fromDatabase pdb ↵

1zik title:  
GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...]  
  
Chain information for 1zik #1  
---  
Chain | Description  
A B | general control protein GCN4  
  
  

show :tyr ↵

label :tyr ↵

set bgColor white ↵

set bgColor white ↵

label background none ↵

set bgColor black ↵

hbonds reveal true ↵

98 hydrogen bonds found  

~hbonds ↵

label delete ↵

molmap protein 5 ↵

close ↵

open 2gbp ↵

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

molmap protein 5 ↵

bumps #2 center ligand ↵

Found 0 bumps, minimum height 1, base area 10  

close ↵

open 1zik ↵

1zik title:  
GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...]  
  
Chain information for 1zik #1  
---  
Chain | Description  
A B | general control protein GCN4  
  
  

molmap protein 5 ↵

bumps #2 center :tyr ↵

Found 0 bumps, minimum height 1, base area 10  

bumps #2 center @ca ↵

Found 0 bumps, minimum height 1, base area 10  

bumps #2 center @ca min .2

Expected a keyword  

bumps #2 center @ca minimumHeight .2

Expected a keyword  

No help found for
'help:/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/bumps/bumps.html'  

close ↵

bumps

Missing or invalid ""volume"" argument: empty atom specifier  

No help found for
'help:/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/bumps/bumps.html'  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	minor		Help System		fixed		Tom Goddard				all	ChimeraX