errors in tutorials for developers + fixes

[rgizinski@…]

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

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

[pett]

Dear Radosław,

Thanks for taking the time to alert us about these problems. I will work to remedy them as soon as I can.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[pett]

Again, thanks for the feedback.

Fixed #1 as per your suggestion.

I don't think #2 is actually a problem. I only get the message about SEQCROW if I type "highlight" rather than "tutorial highlight". I think you just mistakenly typed "highlight" instead of "tutorial highlight".

I view #3 as a bug in ChimeraX. It should prefer an installed bundle over one that isn't installed when trying to open a file. I have committed a fix for this behavior and it will be in the next daily build.

For #4 I added an example command to the section where it discusses what the selector does. Thanks for the idea!

--Eric