problem running SASpy PyMOL plugin on Mac 10.10.5

ATSAS for Linux and Mac, general installation issues, ATSAS online etc.
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tannerjj
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Joined: 2010.09.09 19:35
Location: University of Missouri-Columbia, Columbia, MO, USA

problem running SASpy PyMOL plugin on Mac 10.10.5

#1 Post by tannerjj » 2017.03.12 06:40

I installed the SASpy plugin from /Applications/ATSAS/share/pymolplugin/saspy.py but when I try to use the plugin, PyMOL says

ERROR
ATSAS executables not found in PATH
Please install ATSAS

I'm running PyMOL 1.8.4.2 - Incentive Product with XQuartz 2.7.11 (xorg-server 1.18.4) on Yosemite 10.10.5.

The ATSAS executables are in /Applications/ATSAS/bin/.

The PATH contains ATSAS binaries directory:

Administrators-MacBook-Air-4:SAXS tannerjj$ echo "$PATH"
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Applications/ATSAS/bin
Administrators-MacBook-Air-4:SAXS tannerjj$

Thanks,

Jack Tanner

sasha
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Posts: 46
Joined: 2014.03.05 17:56

Re: problem running SASpy PyMOL plugin on Mac 10.10.5

#2 Post by sasha » 2017.03.14 10:03

Dear Jack,

it this Pymol Incentive version opened from the terminal or by double-clicking an application icon?

I guess you need to edit your pymolrc file (if not there, create it at ~/.pymolrc) by adding the following line:
os.environ["PATH"] += os.pathsep + "/xxx/yyy/bin:"
where /xxx/yyy is the path to the local ATSAS installation.

Restart Pymol and it should work.
If not, please install the open source version of Pymol and run it from the terminal.
You can get it by simply installing homebrew and typing:
brew install homebrew/science/pymol

Please let me know how it goes,

sasha

Liyana
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Posts: 2
Joined: 2018.10.08 11:58

Re: problem running SASpy PyMOL plugin on Mac 10.10.5

#3 Post by Liyana » 2018.10.09 20:42

Dear sasha,

I've installed open-source PyMol and reinstalled the Saspy plugin but can't seem to get the initialisation to work properly. Pymol reported:

'Missing parentheses in call to 'print'. Did you mean print('Warning: pymol library cmd not found.')? (saspy.py, line 28)
Unable to initialize plugin 'saspy' (pmg_tk.startup.saspy).'

Can I have some help with this, please?

Thanks,
Liyana

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