Re: [scipion-users] EMAN2 e2display and the Scipion menu

[Jose M. de la R. T. <del...@gm...>]

Dear Patrick,

Thanks for showing Scipion to your users and providing us with feedback.
See answer below.

On Thu, Apr 26, 2018 at 12:30 AM, Patrick Goetz <pg...@ma...>
wrote:

> So, I got my users to take a look at Scipion, and we immediately had a few
> more questions.
>
> The very first was "my favorite way to view images is e2display [.py, an
> EMAN2 program] -- can we run this through Scipion?"
>
Nope, e2display.py is not currently accessed through the menu. The default
viewer (although some other can be used in some
cases) is the Xmipp viewer. Back in time we modified it to allow easy
manipulation of subset creation and other features, but
we can not do this with other viewers.


>
> e2display.py does not appear in the Scipion menu, but oddly appears to be
> called through eman boxer?  If I try just running it as
>
>    /opt/scipion/software/em/eman-2.12/bin/e2display.py
>
You can launch it using the following command:
scipion e2display.py [extra args]


>
> there are missing python modules (e.g. EMAN2_meta).
>
I don't know what EMAN2_meta is, I haven't heard about it before. Have you
checked the version?

>
> So, first question is there any way to get e2display.py through the menu,
> or is there already a superior image display utility there?
>
We could integrate the e2display.py, but as I said, one of the main
utilities is the ability to create subset. e2display.py is a great viewer,
but it has a great disadvantage when it comes to particle sets and
subset...it only manage its own format and in many cases there is
a need to convert the particles to hdf, which is not desired with now a
days huge datasets.

>
> Second, the menu seems to be fixed and not generated by what applications
> are installed?  I haven't installed relion yet, but it appears in the
> Scipion menu.
>
EM programs that are not install should appear in gray and with (not
installed) label in the menu.


>
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