Re: [PyMOL] Session scene compatibility with MacPymol?

[Pete M. <me...@hk...>]

For what it's worth, for teaching/training (and general research use), I've
always recommended using pml scripts instead of pse sessions.  Turning on
logging can help with tracking what should end up going into the pml.

It's a little more work, and requires a little more forethought - but it's
also something that essentially never has issues with different PyMOL
versions.  If anyone's curious, the only one I ran into was when PyMOL
changed how density maps were interpreted ("just load this block of density
over this region" to "treat this density as a seed for symmetry
expansions") around the 1.4 -> 1.5 transition.

Best,
Pete


On Fri, Sep 9, 2016 at 8:53 AM, Paul Paukstelis <sho...@gm...>
wrote:

> Jared,
>
> Thanks for the input. I'll suggest it to my students. Unfortunately, many
> don't have Macs, and some are dependent on using our departmental computer
> labs (Windows) and are therefore stuck with the educational build.
>
> I wonder if there are plans to update the educational version to allow
> backward scene compatibility? Not having that is a real pain for incentive
> users wanting to use mol. vis. for instruction purposes (having to recreate
> all the scenes!)
>
> Also, it seems strange to have an option to export a pse to an older
> version, but not have it actually be compatible with that older version!
>
> --paul
>
> On 09/08/2016 03:10 PM, Sampson, Jared M. wrote:
>
> Hi Paul -
>
> I'm a little late on this thread, but thought I'd add my 2¢.  Probably the
> easiest way get around this issue (as you realize) is probably to save a
> 1.7.4.5-compatible PSE file.  But, for the adventurous, there is another
> way:
>
> With a small effort (and the willingness to use the command line), your
> students with Macs can replace the older Educational build of MacPyMOL with
> a current version of Open Source PyMOL for free using the command line
> package manager, Homebrew <http://brew.sh/>.  They just need to open up
> Terminal.app and type the following 3 commands:
>
>
> # Install Homebrew (run the command below, which downloads the installer,
> and follow the prompts)
> /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.
> com/Homebrew/install/master/install)"
>
> # Install XQuartz
> brew install Caskroom/cask/xquartz
>
> # Install PyMOL
> brew install pymol
>
>
> Pretty much everything homebrew installs goes into `/usr/local/Cellar` and
> gets symlinked to `/usr/local/bin`, and shouldn't interfere with any other
> standard software.  One notable exception is that Homebrew Cask
> <https://caskroom.github.io/> items like Xquartz.app typically go into
> /Applications, because Cask handles the downloading of apps and installers
> and runs installers automatically.  Of course, you can just as easily
> download XQuartz from the project website <https://www.xquartz.org/> and
> install it manually if you prefer.
>
> It may take a few minutes to build PyMOL and its few dependencies. But
> that's it!  Now to open PyMOL they can open a Terminal window, `cd` to
> whatever directory they want to work in, and launch PyMOL by typing
> `pymol`.  This would not only get them a more up-to-date PyMOL version, but
> as an added bonus, a little exposure to a Unix command line environment.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
>
> On Sep 2, 2016, at 4:24 PM, Paul Paukstelis <sho...@gm...>
> wrote:
>
> Are there known session issues with MacPymol? I've saved a session for
> my students to look at using my linux incentive linux build and tried
> various session compatibility settings (1.6, 1.74, 1.76) but in all
> cases the preset scenes I've saved in the session are not loaded when
> the session is opened in MacPymol (educational version 1.7.6 I believe).
>
> Thanks,
>
> --paul
>
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-- 
Peter A Meyer, PhD

Structural Biology Data Grid - data.sbgrid.org