cxcmd:save saves to documentation directory, not working directory

[Tristan Croll]

Just noticed this when running the ISOLDE tutorial. The commands

cxcmd:save%20isolde_tutorial.pdb%20#1
cxcmd:save%20isolde_tutorial.mtz%20#1

... lead to the files being written to {toolshed directory}/site_packages/chimerax/isolde/docs/isolde/tutorials/intro rather than ChimeraX's current working directory. Will change the tutorial to tell people to just type these commands themselves, for now.

[Tristan Croll]

If I insert a cxcmd:pwd into the documentation file and click it, I get:

Current working directory is: /home/tic20/.local/share/ChimeraX/0.9/site-packages/chimerax/isolde/docs/isolde/tutorials/intro

If just type pwd in the command line, I get:

Current working directory is: /home/tic20/structure_dump/3io0

[goddard@…]

I’ll look into why the ChimeraX help browser is running links with the current working directory changed to the location of the html.

But I think you should use tutorial commands “save ~/Desktop/somefile.pdb #1”.  Most users will not be using Linux, will have started ChimeraX by clicking an icon, and the current working directory is usually some unwritable path like /.

[tic20@…]

I thought about that, but wasn't sure if that would be valid across all 
platforms. I just added some text about the `pwd` command and how to 
change directories using the command line. But if ~/Desktop will work on 
all platforms, then that's an even simpler solution.

On 2019-06-14 17:27, ChimeraX wrote:

[goddard@…]

Yes ~/Desktop works on Linux, Windows, Mac.  Toolbar icons such as the one that saves a snapshot image use ~/Desktop.

[Eric Pettersen]

It's undoubtedly so that tutorials can easily refer to sibling files. While it's questionable whether you'd want 'save' to go to the tutorial directory, 95% of the time your want 'open' to get a file from there.

--Eric

[tic20@…]

Ah! Fair enough - that makes perfect sense.

On 2019-06-14 18:31, ChimeraX wrote:

[Greg Couch]

Yes, this is a feature. Use ~/Desktop/filename for saving.