Re: [PyMOL] Session scene compatibility with MacPymol?

[Pete Meyer]

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 
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 .  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
>  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  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 
> 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
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Re: [PyMOL] Session scene compatibility with MacPymol?

[Paul Paukstelis]

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 .  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  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 
 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 > 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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Re: [PyMOL] how to hide dashed artificial cartoon?

[Thomas Holder]

Hi Albert,

The dashed loop should only appear if you have changed the "cartoon_gap_cutoff" 
setting:
http://pymolwiki.org/index.php/cartoon_gap_cutoff

Cheers,
  Thomas

On 09 Sep 2016, at 04:26, Albert  wrote:

> Hello:
> 
> I noticed that if I show my structure as cartoon, there would be a 
> "dashed loop" cartoon filling in the missing part of my structure. I am 
> just wondering how can we disable PyMol show the missing part automatically?
> 
> Thank you very much
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] how to hide dashed artificial cartoon?

[Albert]

Hello:

I noticed that if I show my structure as cartoon, there would be a 
"dashed loop" cartoon filling in the missing part of my structure. I am 
just wondering how can we disable PyMol show the missing part automatically?

Thank you very much

Albert

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