Hi Paul,
check out
https://pymolwiki.org/index.php/Cartoon#Breaking_Up_a_Visualization_with_Cartoon_Skip
You'll want to skip the residues you want to make transparent in the
original (opaque) object, and include some more residues on both ends in
the copy you want to make transparent. Skip the additional residues and
make the copy transparent.
HTH,
Christian
Am 23.07.2018 um 17:00 schrieb Paul Miller:
>
> Hi Jarrett
>
>
> Thanks for this, however, the trajectories of the cartoon change when
> only part of it is shown so that the transparent and non-transparent
> segments to not connect seamlessly.
>
>
> Cheers, Paul
>
>
> Paul Steven Miller (PhD)
> Postdoctoral Researcher
> University of Oxford
> Wellcome Trust Centre for Human Genetics
> Division of Structural Biology
> Roosevelt Drive
> Oxford
> OX3 7BN
>
>
> ------------------------------------------------------------------------
> -----Original Message-----
> From: "Jarrett Johnson" <jarrett.john...@schrodinger.com
> <mailto:jarrett.john...@schrodinger.com>>
> To: "Paul Miller" <p...@strubi.ox.ac.uk <mailto:p...@strubi.ox.ac.uk>>
> Cc: "Pymol User list" <pymol-users@lists.sourceforge.net
> <mailto:pymol-users@lists.sourceforge.net>>
> Date: 07/23/18 15:47
> Subject: Re: [PyMOL] cartoon range transparency help
>
> Hello,
>
> That seems to be the case for that command. One workaround for
> this is to use the 'create' command to create a new object
> identical to your source object and make that one transparent.
> I've attached a quick example.
>
> Jarrett J.
>
> On Mon, Jul 23, 2018 at 9:36 AM, Paul Miller <p...@strubi.ox.ac.uk
> <mailto:p...@strubi.ox.ac.uk>> wrote:
>
> Hi
>
>
> I have Pymol version 2
>
>
> When I try to make a range of a cartoon transparent
>
>
> e.g. I type: set cartoon_transparency, 0.5, /4COF//A/1:20
>
>
> it comes up with following error:
>
>
> Setting-Warning: 'cartoon_transparency' is a
> object-state-level setting
>
>
> Does this mean one cannot make part of a cartoon transparent?
>
>
> Cheers, Paul
>
>
> Paul Steven Miller (PhD)
> Postdoctoral Researcher
> University of Oxford
> Wellcome Trust Centre for Human Genetics
> Division of Structural Biology
> Roosevelt Drive
> Oxford
> OX3 7BN
>
>
> ------------------------------------------------------------------------------
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>
>
> --
> Jarrett Johnson,
> Schrödinger
>
>
>
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