[PyMOL] Re: invoking pymol the unix way on os x

[William S. <wg...@ch...>]

You can call the executable inside an application and it will work in the 
normal unix way, eg

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

You might want to make an alias or a function or a symbolic link like

alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL

or

pymol() { /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL "$@" ; }

or

ln -s  /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL 
/usr/local/bin/pymol


more here, on the wiki:

http://www.pymolwiki.org/index.php/Launching_PyMOL#MacOS_X:


HTH,

Bill



> From: "Andrew Wollacott" <sen...@gm...>
> To: pym...@li...
> Subject: [PyMOL] running macpymol in the background from the terminal
>
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>
> hello,
>
> I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
> terminal.app) using the "open" command.
>
>> open test.pdb
>
> I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
> open when I do this.  The problem I have when doing this is that when
> entering the "pwd" command into pymol, I get the following:
>
> PyMOL> pwd
> /
>
> so pymol thinks it's running from the root directory.  This makes it tough
> for me to load more pdbfiles into pymol using the "load" command as I must
> first "cd" into the directory with pymol.  Just a note, that in version 0.9=
> 8,
> using the "open" command, pymol would recognize what directory it was opene=
> d
> from.
>
> Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
> gets the output from pymol.  I've tried to run pymol in the background so
> that I can continue to use this terminal window while stilll having pymol
> open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
> I
> could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
> verbose compared to "open test.pdb"
>
> I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
> t
> since version 0.98 worked fine, I was wondering if anyone has a workaround
> for this inconvenience.
>
> Thanks.
>
> - Andrew Wollacott