Re: [PyMOL] visualizing a transparent surface within a transparent surface

[Thomas Holder]

Hi Nasir,

Incentive PyMOL 1.7.6 introduced a cross-object order independent transparency 
mode (transparency_mode=3). The method is a heuristic and not as pretty as ray 
tracing, but useful since it guarantees that nothing gets accidentally hidden 
due to rendering method limitations. Not sure if it satisfies your needs for 
rendering a pretty movie, but worth a try.

PyMOL> set transparency_mode, 3

Cheers,
  Thomas

On 16 Feb 2016, at 20:50, Nasir Bashiruddin  wrote:

> Thanks for the tip Adam! 
> 
> However, it would be nice to make movies in the way I requested.
> 
> Nasir
> 
> On Wed, Feb 17, 2016 at 12:41 AM, H. Adam Steinberg 
>  wrote:
> I get around this by rendering both items separately and then combining the 
> two images in photoshop.
> 
> Is there a way to do what Nasir is asking directly in PyMOL?
> 
> 
> 
> > On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin  wrote:
> >
> > Hello!
> >
> > So, I've had this problem for a while now.
> >
> > I have a ligand that goes deep into a protein.
> >
> > I have the ligand with stick representation.
> >
> > I have the protein in cartoon representation.
> >
> > I have both ligand and protein surfaced with 0.5 transparencies.
> >
> > The ligand surface is yellow and the protein surface is gray80.
> >
> > The protein cartoon is set to transparency, 0.5 as well.
> >
> > I want to show how the ligand goes deep into the binding site of the 
> > protein.
> >
> > I can see the ligand surface going into the protein surface but when I Ray, 
> > the yellow ligand surfaces that go into the protein disappear.
> >
> > How do I get the Ray quality and keep the ligand surface that is within the 
> > protein from disappearing?
> >
> > Hope I explained this well.
> > BTW, surface mode is set to 1 to include all atoms
> >
> > Nasir

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] visualizing a transparent surface within a transparent surface

[Nasir Bashiruddin]

Thanks for the tip Adam!

However, it would be nice to make movies in the way I requested.

Nasir

On Wed, Feb 17, 2016 at 12:41 AM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:

> I get around this by rendering both items separately and then combining
> the two images in photoshop.
>
> Is there a way to do what Nasir is asking directly in PyMOL?
>
>
>
> > On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin 
> wrote:
> >
> > Hello!
> >
> > So, I've had this problem for a while now.
> >
> > I have a ligand that goes deep into a protein.
> >
> > I have the ligand with stick representation.
> >
> > I have the protein in cartoon representation.
> >
> > I have both ligand and protein surfaced with 0.5 transparencies.
> >
> > The ligand surface is yellow and the protein surface is gray80.
> >
> > The protein cartoon is set to transparency, 0.5 as well.
> >
> > I want to show how the ligand goes deep into the binding site of the
> protein.
> >
> > I can see the ligand surface going into the protein surface but when I
> Ray, the yellow ligand surfaces that go into the protein disappear.
> >
> > How do I get the Ray quality and keep the ligand surface that is within
> the protein from disappearing?
> >
> > Hope I explained this well.
> > BTW, surface mode is set to 1 to include all atoms
> >
> > Nasir
> >
> --
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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> >
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
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Re: [PyMOL] visualizing a transparent surface within a transparent surface

[H. Adam Steinberg]

I get around this by rendering both items separately and then combining the two 
images in photoshop.

Is there a way to do what Nasir is asking directly in PyMOL?



> On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin  wrote:
> 
> Hello! 
> 
> So, I've had this problem for a while now.
> 
> I have a ligand that goes deep into a protein.
> 
> I have the ligand with stick representation.
> 
> I have the protein in cartoon representation.
> 
> I have both ligand and protein surfaced with 0.5 transparencies.
> 
> The ligand surface is yellow and the protein surface is gray80.
> 
> The protein cartoon is set to transparency, 0.5 as well.
> 
> I want to show how the ligand goes deep into the binding site of the protein.
> 
> I can see the ligand surface going into the protein surface but when I Ray, 
> the yellow ligand surfaces that go into the protein disappear. 
> 
> How do I get the Ray quality and keep the ligand surface that is within the 
> protein from disappearing? 
> 
> Hope I explained this well.
> BTW, surface mode is set to 1 to include all atoms
> 
> Nasir
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


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[PyMOL] visualizing a transparent surface within a transparent surface

[Nasir Bashiruddin]

Hello!

So, I've had this problem for a while now.

I have a ligand that goes deep into a protein.

I have the ligand with stick representation.

I have the protein in cartoon representation.

I have both ligand and protein surfaced with 0.5 transparencies.

The ligand surface is yellow and the protein surface is gray80.

The protein cartoon is set to transparency, 0.5 as well.

I want to show how the ligand goes deep into the binding site of the
protein.

I can see the ligand surface going into the protein surface but when I Ray,
the yellow ligand surfaces that go into the protein disappear.

How do I get the Ray quality and keep the ligand surface that is within the
protein from disappearing?

Hope I explained this well.
BTW, surface mode is set to 1 to include all atoms

Nasir
--
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