id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5365	errors in tutorials for developers + fixes	rgizinski@…	Eric Pettersen	"{{{
Dear ChimeraX developers,

I'd like to report few problems I came across when I was doing tutorials 
on developing tools extending ChimeraX functionality.
I refrain from sending them in .txt file cause it may be seen as 
security threat even without any ill intentions at my side.
Below, I list you issues I've found with workarounds and/or fixes I 
implemented in order to adress them.

Thank you for your time and development of ChimeraX.

With love,

Radosław Giziński


====== BUG / ERROR / SUGGESTION ======

#1 ERROR
     in tutorial 02 ""Add a Command"" :
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_command.html
     file: 'cmd.py', line: 141, TypeError: _mean() got multiple values 
for argument 'axis'
     was:
     cofm = coords.mean(coords, axis=0)
     working solution:
     cofm = coords.mean(axis=0)

#2 ERROR
     in tutorial 02 ""Add a Command"" :
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_command.html
     ChimeraX formces user to use SEQCROW bundle when command ""tutorial 
highlight"" is used cause ChimeraX recognises SEQCROW bundle as default 
utility the provides ""highlight"" functionality.
     working solution:
     define other, unique name for ""tutorial highlight"" command like: 
""tutorial highlight_01""

#3 ERROR  :
     in tutorial 04 ""Add file format"":
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_read_format.html
     ""Install the SEQCROW bundle to open ""XYZ file"" format files. Opener 
for format 'XYZ file' is not installed; see log for more info""
     working solution:
     define custom .abc (or any other) suffix that is not part of 
'standard' formats used by ChimeraX in bundle_info.xml
     line 38: <Provider name=""XYZ"" suffixes="".xyz""
     to <Provider name=""ABC"" suffixes="".abc""
     line 44: <Provider name=""XYZ"" />
     to <Provider name=""ABC"" />
     also, change benzene.xyz file extension to benzene.abc for 
compatibility

#4 Suggestion for Tutorial 07 ""Define a Chemical Subgroup Selector"":
     Add example use of newly added selector: ""sel endres"" in command line

==========================================



}}}
"	defect	closed	normal		Documentation		fixed						all	ChimeraX